bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020‒05‒24
forty-two papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit
  1. TET1 and 5-Hydroxymethylation Preserve the Stem Cell State of Mouse Trophoblast.
  2. Discovery of genes required for body axis and limb formation by global identification of retinoic acid-regulated epigenetic marks.
  3. A central role for canonical PRC1 in shaping the 3D nuclear landscape.
  4. MEDEA: analysis of transcription factor binding motifs in accessible chromatin.
  5. Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance.
  6. Metabolic remodeling during somatic cell reprogramming to induced pluripotent stem cells: involvement of hypoxia-inducible factor 1.
  7. De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas.
  8. Chemotherapy-induced S100A10 recruits KDM6A to facilitate OCT4-mediated breast cancer stemness.
  9. A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning.
  10. H3K4me1 Distribution Predicts Transcription State and Poising at Promoters.
  11. Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage.
  12. The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells.
  13. Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors.
  14. HOX13-dependent chromatin accessibility underlies the transition towards the digit development program.
  15. Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms.
  16. Determinants of transcription factor regulatory range.
  17. SETD5-Coordinated Chromatin Reprogramming Regulates Adaptive Resistance to Targeted Pancreatic Cancer Therapy.
  18. TFEB regulates murine liver cell fate during development and regeneration.
  19. KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain.
  20. Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics.
  21. ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines.
  22. Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks.
  23. Pitx2-Sox2-Lef-1 interactions specify progenitor oral/dental epithelial cell signaling centers.
  24. Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance.
  25. RORγt-driven TH17 Cell Differentiation Requires Epigenetic Control by the Swi/Snf Chromatin Remodeling Complex.
  26. 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.
  27. Cdk8 is required for establishment of H3K27me3 and gene repression by Xist and mouse development.
  28. Methylation of a CGATA element inhibits binding and regulation by GATA-1.
  29. Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium.
  30. RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function.
  31. Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing.
  32. N6-methyladenosine regulates glycolysis of cancer cells through PDK4.
  33. Pioneer transcription factors in chromatin remodeling: The kinetic proofreading view.
  34. Transcriptome-wide organization of subcellular microenvironments revealed by ATLAS-Seq.
  35. Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs.
  36. MLL4 is required after implantation whereas MLL3 becomes essential during late gestation.
  37. scVAE: Variational auto-encoders for single-cell gene expression data.
  38. Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains.
  39. scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures.
  40. Quantifying genetic effects on disease mediated by assayed gene expression levels.
  41. Chromatin as a key consumer in the metabolite economy.
  42. HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer's disease.
  1. Stem Cell Reports. 2020 May 13. pii: S2213-6711(20)30149-1. [Epub ahead of print]
    TET1 and 5-Hydroxymethylation Preserve the Stem Cell State of Mouse Trophoblast.
    Claire E Senner, Stephanie Chrysanthou, Sarah Burge, Hai-Yan Lin, Miguel R Branco, Myriam Hemberger.
      The ten-eleven translocation factor TET1 and its conferred epigenetic modification 5-hydroxymethylcytosine (5hmC) have important roles in maintaining the pluripotent state of embryonic stem cells (ESCs). We previously showed that TET1 is also essential to maintain the stem cell state of trophoblast stem cells (TSCs). Here, we establish an integrated panel of absolute 5hmC levels, genome-wide DNA methylation and hydroxymethylation patterns, transcriptomes, and TET1 chromatin occupancy in TSCs and differentiated trophoblast cells. We show that the combined presence of 5-methylcytosine (5mC) and 5hmC correlates with transcriptional activity of associated genes. Hypoxia can slow down the global loss of 5hmC that occurs upon differentiation of TSCs. Notably, unlike in ESCs and epiblast cells, most TET1-bound regions overlap with active chromatin marks and TFAP2C binding sites and demarcate putative trophoblast enhancer regions. These chromatin modification and occupancy patterns are highly informative to identify novel candidate regulators of the TSC state.
    Keywords:  DNA hydroxymethylation; DNA methylation; TET1; chromatin interactions; embryonic stem cells; enhancers; epigenetics; gene regulation; trophoblast stem cells
    DOI:  https://doi.org/10.1016/j.stemcr.2020.04.009
  2. PLoS Biol. 2020 May 18. 18(5): e3000719
    Discovery of genes required for body axis and limb formation by global identification of retinoic acid-regulated epigenetic marks.
    Marie Berenguer, Karolin F Meyer, Jun Yin, Gregg Duester.
      Identification of target genes that mediate required functions downstream of transcription factors is hampered by the large number of genes whose expression changes when the factor is removed from a specific tissue and the numerous binding sites for the factor in the genome. Retinoic acid (RA) regulates transcription via RA receptors bound to RA response elements (RAREs) of which there are thousands in vertebrate genomes. Here, we combined chromatin immunoprecipitation sequencing (ChIP-seq) for epigenetic marks and RNA-seq on trunk tissue from wild-type and Aldh1a2-/- embryos lacking RA synthesis that exhibit body axis and forelimb defects. We identified a relatively small number of genes with altered expression when RA is missing that also have nearby RA-regulated deposition of histone H3 K27 acetylation (H3K27ac) (gene activation mark) or histone H3 K27 trimethylation (H3K27me3) (gene repression mark) associated with conserved RAREs, suggesting these genes function downstream of RA. RA-regulated epigenetic marks were identified near RA target genes already known to be required for body axis and limb formation, thus validating our approach; plus, many other candidate RA target genes were found. Nuclear receptor 2f1 (Nr2f1) and nuclear receptor 2f2 (Nr2f2) in addition to Meis homeobox 1 (Meis1) and Meis homeobox 2 (Meis2) gene family members were identified by our approach, and double knockouts of each family demonstrated previously unknown requirements for body axis and/or limb formation. A similar epigenetic approach can be used to determine the target genes for any transcriptional regulator for which a knockout is available.
    DOI:  https://doi.org/10.1371/journal.pbio.3000719
  3. Genes Dev. 2020 May 21.
    A central role for canonical PRC1 in shaping the 3D nuclear landscape.
    Shelagh Boyle, Ilya M Flyamer, Iain Williamson, Dipta Sengupta, Wendy A Bickmore, Robert S Illingworth.
      Polycomb group (PcG) proteins silence gene expression by chemically and physically modifying chromatin. A subset of PcG target loci are compacted and cluster in the nucleus; a conformation that is thought to contribute to gene silencing. However, how these interactions influence gross nuclear organization and their relationship with transcription remains poorly understood. Here we examine the role of Polycomb-repressive complex 1 (PRC1) in shaping 3D genome organization in mouse embryonic stem cells (mESCs). Using a combination of imaging and Hi-C analyses, we show that PRC1-mediated long-range interactions are independent of CTCF and can bridge sites at a megabase scale. Impairment of PRC1 enzymatic activity does not directly disrupt these interactions. We demonstrate that PcG targets coalesce in vivo, and that developmentally induced expression of one of the target loci disrupts this spatial arrangement. Finally, we show that transcriptional activation and the loss of PRC1-mediated interactions are separable events. These findings provide important insights into the function of PRC1, while highlighting the complexity of this regulatory system.
    Keywords:  embryonic stem cells; epigenetics; gene regulation; gene repression; histone modifications; nuclear organization; polycomb; topologically associating domains (TADs)
    DOI:  https://doi.org/10.1101/gad.336487.120
  4. Genome Res. 2020 May 18.
    MEDEA: analysis of transcription factor binding motifs in accessible chromatin.
    Luca Mariani, Kathryn Weinand, Stephen S Gisselbrecht, Martha L Bulyk.
      Deciphering the interplay between chromatin accessibility and transcription factor (TF) binding is fundamental to understanding transcriptional regulation, control of cellular states, and the establishment of new phenotypes. Recent genome-wide chromatin accessibility profiling studies have provided catalogs of putative open regions, where TFs can recognize their motifs and regulate gene expression programs. Here, we present motif enrichment in differential elements of accessibility (MEDEA), a computational tool that analyzes high-throughput chromatin accessibility genomic data to identify cell-type-specific accessible regions and lineage-specific motifs associated with TF binding therein. To benchmark MEDEA, we used a panel of reference cell lines profiled by ENCODE and curated by the ENCODE Project Consortium for the ENCODE-DREAM Challenge. By comparing results with RNA-seq data, ChIP-seq peaks, and DNase-seq footprints, we show that MEDEA improves the detection of motifs associated with known lineage specifiers. We then applied MEDEA to 610 ENCODE DNase-seq data sets, where it revealed significant motifs even when absolute enrichment was low and where it identified novel regulators, such as NRF1 in kidney development. Finally, we show that MEDEA performs well on both bulk and single-cell ATAC-seq data. MEDEA is publicly available as part of our Glossary-GENRE suite for motif enrichment analysis.
    DOI:  https://doi.org/10.1101/gr.260877.120
  5. Genome Biol. 2020 May 18. 21(1): 118
    Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance.
    Isaac Kremsky, Victor G Corces.
      BACKGROUND: A growing body of evidence suggests that certain epiphenotypes can be passed across generations via both the male and female germlines of mammals. These observations have been difficult to explain owing to a global loss of the majority of known epigenetic marks present in parental chromosomes during primordial germ cell development and after fertilization.RESULTS: By integrating previously published BS-seq, DNase-seq, ATAC-seq, and RNA-seq data collected during multiple stages of primordial germ cell and pre-implantation development, we find that the methylation status of the majority of CpGs genome-wide is restored after global de-methylation, despite the fact that global CpG methylation drops to 10% in primordial germ cells and 20% in the inner cell mass of the blastocyst. We estimate the proportion of such CpGs with preserved methylation status to be 78%. Further, we find that CpGs at sites bound by transcription factors during the global re-methylation phases of germline and embryonic development remain hypomethylated across all developmental stages observed. On the other hand, CpGs at sites not bound by transcription factors during the global re-methylation phase have high methylation levels prior to global de-methylation, become de-methylated during global de-methylation, and then become re-methylated.
    CONCLUSIONS: The results suggest that transcription factors can act as carriers of epigenetic information during germ cell and pre-implantation development by ensuring that the methylation status of CpGs is maintained. These findings provide the basis for a mechanistic description of trans-generational inheritance of epigenetic information in mammals.
    Keywords:  Chromatin; DNA methylation; Development; Embryo; Fertilization; Oogenesis; Spermatogenesis; Trans-generational inheritance; Transcription
    DOI:  https://doi.org/10.1186/s13059-020-02036-w
  6. Inflamm Regen. 2020 ;40 8
    Metabolic remodeling during somatic cell reprogramming to induced pluripotent stem cells: involvement of hypoxia-inducible factor 1.
    Tomoaki Ishida, Shu Nakao, Tomoe Ueyama, Yukihiro Harada, Teruhisa Kawamura.
      Induced pluripotent stem cells (iPSCs) were first established from differentiated somatic cells by gene introduction of key transcription factors, OCT4, SOX2, KLF4, and c-MYC, over a decade ago. Although iPSCs can be applicable for regenerative medicine, disease modeling and drug screening, several issues associated with the utilization of iPSCs such as low reprogramming efficiency and the risk of tumorigenesis, still need to be resolved. In addition, the molecular mechanisms involved in the somatic cell reprogramming to pluripotency are yet to be elucidated. Compared with their somatic counterparts, pluripotent stem cells, including embryonic stem cells and iPSCs, exhibit a high rate of glycolysis akin to aerobic glycolysis in cancer cells. This is known as the Warburg effect and is essential for maintaining stem cell properties. This unique glycolytic metabolism in iPSCs can provide energy and drive the pentose phosphate pathway, which is the preferred pathway for rapid cell proliferation. During reprogramming, somatic cells undergo a metabolic shift from oxidative phosphorylation (OXPHOS) to glycolysis trigged by a transient OXPHOS burst, resulting in the initiation and progression of reprogramming to iPSCs. Metabolic intermediates and mitochondrial functions are also involved in the epigenetic modification necessary for the process of iPSC reprogramming. Among the key regulatory molecules that have been reported to be involved in metabolic shift so far, hypoxia-inducible factor 1 (HIF1) controls the transcription of many target genes to initiate metabolic changes in the early stage and maintains glycolytic metabolism in the later phase of reprogramming. This review summarizes the current understanding of the unique metabolism of pluripotent stem cells and the metabolic shift during reprogramming, and details the relevance of HIF1 in the metabolic shift.
    Keywords:  Glycolysis; Hypoxia-inducible factor; Induced pluripotent stem cells; Metabolic shift; Oxidative phosphorylation; Regenerative medicine; Reprogramming
    DOI:  https://doi.org/10.1186/s41232-020-00117-8
  7. Am J Hum Genet. 2020 May 19. pii: S0002-9297(20)30124-5. [Epub ahead of print]
    De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas.
    Dara Tolchin, Jessica P Yeager, Priya Prasad, Naghmeh Dorrani, Alvaro Serrano Russi, Julian A Martinez-Agosto, Abdul Haseeb, Marco Angelozzi, G W E Santen, Claudia Ruivenkamp, Saadet Mercimek-Andrews, Christel Depienne, Alma Kuechler, Barbara Mikat, Hermann-Josef Ludecke, Frederic Bilan, Gwenael Le Guyader, Brigitte Gilbert-Dussardier, Boris Keren, Solveig Heide, Damien Haye, Hilde Van Esch, Liesbeth Keldermans, Damara Ortiz, Emily Lancaster, Ian D Krantz, Bryan L Krock, Kieran B Pechter, Alexandre Arkader, Livija Medne, Elizabeth T DeChene, Eduardo Calpena, Giada Melistaccio, Andrew O M Wilkie, Mohnish Suri, Nicola Foulds, , Amber Begtrup, Lindsay B Henderson, Cara Forster, Patrick Reed, Marie T McDonald, Allyn McConkie-Rosell, Julien Thevenon, Pauline Le Tanno, Charles Coutton, Anne C H Tsai, Sarah Stewart, Ales Maver, Rudolf Gorazd, Olivier Pichon, Mathilde Nizon, Benjamin Cogné, Bertrand Isidor, Dominique Martin-Coignard, Radka Stoeva, Véronique Lefebvre, Cédric Le Caignec.
      SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.
    Keywords:  ADHD; SOX6; SOXopathy; craniosynostosis; developmental delay; dysmorphism; genetic variant; human disease; intellectual disability; osteochondroma
    DOI:  https://doi.org/10.1016/j.ajhg.2020.04.015
  8. J Clin Invest. 2020 May 19. pii: 138577. [Epub ahead of print]
    Chemotherapy-induced S100A10 recruits KDM6A to facilitate OCT4-mediated breast cancer stemness.
    Haiquan Lu, Yangyiran Xie, Linh Tran, Jie Lan, Yongkang Yang, Naveena L Murugan, Ru Wang, Yueyang J Wang, Gregg L Semenza.
      Breast cancer stem cells (BCSCs) play a critical role in cancer recurrence and metastasis. Chemotherapy induces BCSC specification through increased expression of pluripotency factors, but how their expression is regulated is not fully understood. Here, we delineate a hypoxia-inducible factor 1 (HIF-1)-controlled pathway that epigenetically activates pluripotency factor gene transcription in response to chemotherapy. Paclitaxel induces HIF-1-dependent expression of S100A10, which forms a complex with ANXA2 that interacts with histone chaperone SPT6 and histone demethylase KDM6A. S100A10, ANXA2, SPT6, and KDM6A are recruited to OCT4 binding sites and KDM6A erases H3K27me3 chromatin marks, facilitating transcription of genes encoding the pluripotency factors NANOG, SOX2, and KLF4, which along with OCT4 are responsible for BCSC specification. Silencing of S100A10, ANXA2, SPT6, or KDM6A expression blocks chemotherapy-induced enrichment of BCSCs, impairs tumor initiation, and increases time to tumor recurrence after chemotherapy is discontinued. Pharmacological inhibition of KDM6A also impairs chemotherapy-induced BCSC enrichment. These results suggest that targeting HIF-1/S100A10-dependent and KDM6A-mediated epigenetic activation of pluripotency factor gene expression in combination with chemotherapy may block BCSC enrichment and improve clinical outcome.
    Keywords:  Breast cancer; Oncology; Transcription; hypoxia
    DOI:  https://doi.org/10.1172/JCI138577
  9. Mol Cell. 2020 May 12. pii: S1097-2765(20)30262-8. [Epub ahead of print]
    A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning.
    Ariel Erijman, Lukasz Kozlowski, Salma Sohrabi-Jahromi, James Fishburn, Linda Warfield, Jacob Schreiber, William S Noble, Johannes Söding, Steven Hahn.
      Acidic transcription activation domains (ADs) are encoded by a wide range of seemingly unrelated amino acid sequences, making it difficult to recognize features that promote their dynamic behavior, "fuzzy" interactions, and target specificity. We screened a large set of random 30-mer peptides for AD function in yeast and trained a deep neural network (ADpred) on the AD-positive and -negative sequences. ADpred identifies known acidic ADs within transcription factors and accurately predicts the consequences of mutations. Our work reveals that strong acidic ADs contain multiple clusters of hydrophobic residues near acidic side chains, explaining why ADs often have a biased amino acid composition. ADs likely use a binding mechanism similar to avidity where a minimum number of weak dynamic interactions are required between activator and target to generate biologically relevant affinity and in vivo function. This mechanism explains the basis for fuzzy binding observed between acidic ADs and targets.
    Keywords:  activator; allovalency; avidity; coactivator; deep learning; enhancer; intrinsically disordered protein; machine learning; transcription activation; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.molcel.2020.04.020
  10. Front Cell Dev Biol. 2020 ;8 289
    H3K4me1 Distribution Predicts Transcription State and Poising at Promoters.
    Sunhee Bae, Bluma J Lesch.
      Monomethylation on lysine 4 of histone H3 (H3K4me1) is commonly associated with distal enhancers, but H3K4me1 is also present at promoter regions proximal to transcription start sites. To assess a possible role for H3K4me1 in dictating gene regulatory states at promoters, we examined H3K4me1 peak density around promoters in human and mouse germ cells using an analytic strategy that allowed us to assess relationships between different epigenetic marks on a promoter-by-promoter basis. We found that H3K4me1 exhibits either a bimodal pattern at active promoters, where it flanks H3K4me3, or a unimodal pattern at poised promoters, where it coincides with both H3K4me3 and H3K27me3. This pattern is correlated with gene expression level, but is more strongly linked to a poised chromatin state, defined by the simultaneous presence of H3K4me3 and H3K27me3, than to transcriptional activity. The pattern is especially prominent in germ cells, but is also present in other cell types, including embryonic stem cells and differentiated somatic cells. We propose that H3K4me1 is a key feature of the poised epigenetic state, and suggest possible roles for this mark in epigenetic memory.
    Keywords:  bivalent; germ cell; histone; pluripotency; poised; promoter; spermatogenesis; stem cell
    DOI:  https://doi.org/10.3389/fcell.2020.00289
  11. iScience. 2020 Apr 29. pii: S2589-0042(20)30288-1. [Epub ahead of print]23(5): 101103
    Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage.
    Berkley E Gryder, Marco Wachtel, Kenneth Chang, Osama El Demerdash, Nicholas G Aboreden, Wardah Mohammed, Winston Ewert, Silvia Pomella, Rossella Rota, Jun S Wei, Young Song, Benjamin Z Stanton, Beat Schäfer, Christopher R Vakoc, Javed Khan.
      Core regulatory transcription factors (CR TFs) establish enhancers with logical ordering during embryogenesis and development. Here we report that in fusion-positive rhabdomyosarcoma, a cancer of the muscle lineage, the chief oncogene PAX3-FOXO1 is driven by a translocated FOXO1 super enhancer (SE) restricted to a late stage of myogenesis. Using chromatin conformation capture techniques, we demonstrate that the extensive FOXO1 cis-regulatory domain interacts with PAX3. Furthermore, RNA sequencing and chromatin immunoprecipitation sequencing data in tumors bearing rare PAX translocations implicate enhancer miswiring across all fusion-positive tumors. HiChIP of H3K27ac showed connectivity between the FOXO1 SE, additional intra-domain enhancers, and the PAX3 promoter. We show that PAX3-FOXO1 transcription is diminished when this network of enhancers is ablated by CRISPR. Our data reveal a hijacked enhancer network that disrupts the stepwise CR TF logic of normal skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an "infinite loop" enhancer logic that locks rhabdomyosarcoma in an undifferentiated stage.
    Keywords:  Biological Sciences; Cancer; Chromosome Organization; Molecular Mechanism of Gene Regulation
    DOI:  https://doi.org/10.1016/j.isci.2020.101103
  12. Am J Physiol Lung Cell Mol Physiol. 2020 May 20.
    The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells.
    Alekh Paranjapye, Michael J Mutolo, Jey Sabith Ebron, Shih-Hsing Leir, Ann Harris.
      The differentiated functions of the human airway epithelium are coordinated by a complex network of transcription factors. These include the pioneer factors Forkhead box A1 and A2 (FOXA1 and FOXA2), which are well studied in several tissues, but their role in airway epithelial cells is poorly characterized. Here we define the cistrome of FOXA1 and FOXA2 in primary human bronchial epithelial (HBE) cells by ChIP-seq. Next, siRNA- mediated depletion of each factor is used to investigate their transcriptome by RNA-seq. We found that, as predicted from their DNA-binding motifs, genome-wide occupancy of the two factors showed substantial overlap, however their global impact on gene expression differed. FOXA1 is an abundant transcript in HBE cells, while FOXA2 is expressed at low levels and both these factors likely exhibit auto-regulation and cross-regulation. FOXA1 regulated loci are involved in cell adhesion and the maintenance of epithelial cell identity, particularly through repression of genes associated with epithelial to mesenchymal transition (EMT). FOXA1 also directly targets other transcription factors with a known role in the airway epithelium such as SAM-pointed domain-containing Ets-like factor (SPDEF). The intersection of the cistrome and transcriptome for FOXA1 revealed enrichment of genes involved in epithelial development and tissue morphogenesis. Moreover, depletion of FOXA1 was shown to reduce the transepithelial resistance of HBE cells confirming the role of this factor in maintaining epithelial barrier integrity.
    Keywords:  FOXA1; human bronchial epithelial cells; transcriptional network
    DOI:  https://doi.org/10.1152/ajplung.00023.2020
  13. Cell Rep. 2020 May 19. pii: S2211-1247(20)30608-2. [Epub ahead of print]31(7): 107655
    Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors.
    Yuhki Nakatake, Shigeru B H Ko, Alexei A Sharov, Shunichi Wakabayashi, Miyako Murakami, Miki Sakota, Nana Chikazawa, Chiaki Ookura, Saeko Sato, Noriko Ito, Madoka Ishikawa-Hirayama, Siu Shan Mak, Lars Martin Jakt, Tomoo Ueno, Ken Hiratsuka, Misako Matsushita, Sravan Kumar Goparaju, Tomohiko Akiyama, Kei-Ichiro Ishiguro, Mayumi Oda, Norio Gouda, Akihiro Umezawa, Hidenori Akutsu, Kunihiro Nishimura, Ryo Matoba, Osamu Ohara, Minoru S H Ko.
      Transcription factors (TFs) play a pivotal role in determining cell states, yet our understanding of the causative relationship between TFs and cell states is limited. Here, we systematically examine the state changes of human pluripotent embryonic stem cells (hESCs) by the large-scale manipulation of single TFs. We establish 2,135 hESC lines, representing three clones each of 714 doxycycline (Dox)-inducible genes including 481 TFs, and obtain 26,998 microscopic cell images and 2,174 transcriptome datasets-RNA sequencing (RNA-seq) or microarrays-48 h after the presence or absence of Dox. Interestingly, the expression of essentially all the genes, including genes located in heterochromatin regions, are perturbed by these TFs. TFs are also characterized by their ability to induce differentiation of hESCs into specific cell lineages. These analyses help to provide a way of classifying TFs and identifying specific sets of TFs for directing hESC differentiation into desired cell types.
    Keywords:  cell differentiation; conditional induction; human embryonic stem cells; transcription factors; transcriptome
    DOI:  https://doi.org/10.1016/j.celrep.2020.107655
  14. Nat Commun. 2020 May 19. 11(1): 2491
    HOX13-dependent chromatin accessibility underlies the transition towards the digit development program.
    Ines Desanlis, Yacine Kherdjemil, Alexandre Mayran, Yasser Bouklouch, Claudia Gentile, Rushikesh Sheth, Rolf Zeller, Jacques Drouin, Marie Kmita.
      Hox genes encode transcription factors (TFs) that establish morphological diversity in the developing embryo. The similar DNA-binding motifs of the various HOX TFs contrast with the wide-range of HOX-dependent genetic programs. The influence of the chromatin context on HOX binding specificity remains elusive. Here, we used the developing limb as a model system to compare the binding specificity of HOXA13 and HOXD13 (HOX13 hereafter), which are required for digit formation, and HOXA11, involved in forearm/leg development. We find that upon ectopic expression in distal limb buds, HOXA11 binds sites normally HOX13-specific. Importantly, these sites are loci whose chromatin accessibility relies on HOX13. Moreover, we show that chromatin accessibility specific to the distal limb requires HOX13 function. Based on these results, we propose that HOX13 TFs pioneer the distal limb-specific chromatin accessibility landscape for the proper implementation of the distal limb developmental program.
    DOI:  https://doi.org/10.1038/s41467-020-16317-2
  15. Elife. 2020 May 20. pii: e56325. [Epub ahead of print]9
    Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms.
    Alessandro Scacchetti, Tamas Schauer, Alexander Reim, Zivkos Apostolou, Aline Campos Sparr, Silke Krause, Patrick Heun, Michael Wierer, Peter B Becker.
      Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene.
    Keywords:  D. melanogaster; chromatin; chromosomes; gene expression; genetics; genomics; histone acetylation; histone exchange; histone h2a.z; nucleosome remodeling; transcription
    DOI:  https://doi.org/10.7554/eLife.56325
  16. Nat Commun. 2020 May 18. 11(1): 2472
    Determinants of transcription factor regulatory range.
    Chen-Hao Chen, Rongbin Zheng, Collin Tokheim, Xin Dong, Jingyu Fan, Changxin Wan, Qin Tang, Myles Brown, Jun S Liu, Clifford A Meyer, X Shirley Liu.
      Characterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here we systematically examine the relationship between thousands of TF and histone modification ChIP-seq data sets with thousands of gene expression profiles. We develop a model for integrating these data, which reveals two classes of TFs with distinct ranges of regulatory influence, chromatin-binding preferences, and auto-regulatory properties. We find that the regulatory range of the same TF bound within different topologically associating domains (TADs) depend on intrinsic TAD properties such as local gene density and G/C content, but also on the TAD chromatin states. Our results suggest that considering TF type, binding distance to gene locus, as well as chromatin context is important in identifying implicated TFs from GWAS SNPs.
    DOI:  https://doi.org/10.1038/s41467-020-16106-x
  17. Cancer Cell. 2020 May 13. pii: S1535-6108(20)30213-0. [Epub ahead of print]
    SETD5-Coordinated Chromatin Reprogramming Regulates Adaptive Resistance to Targeted Pancreatic Cancer Therapy.
    Zhentian Wang, Simone Hausmann, Ruitu Lyu, Tie-Mei Li, Shane M Lofgren, Natasha M Flores, Mary E Fuentes, Marcello Caporicci, Ze Yang, Matthew Joseph Meiners, Marcus Adrian Cheek, Sarah Ann Howard, Lichao Zhang, Joshua Eric Elias, Michael P Kim, Anirban Maitra, Huamin Wang, Michael Cory Bassik, Michael-Christopher Keogh, Julien Sage, Or Gozani, Pawel K Mazur.
      Molecular mechanisms underlying adaptive targeted therapy resistance in pancreatic ductal adenocarcinoma (PDAC) are poorly understood. Here, we identify SETD5 as a major driver of PDAC resistance to MEK1/2 inhibition (MEKi). SETD5 is induced by MEKi resistance and its deletion restores refractory PDAC vulnerability to MEKi therapy in mouse models and patient-derived xenografts. SETD5 lacks histone methyltransferase activity but scaffolds a co-repressor complex, including HDAC3 and G9a. Gene silencing by the SETD5 complex regulates known drug resistance pathways to reprogram cellular responses to MEKi. Pharmacological co-targeting of MEK1/2, HDAC3, and G9a sustains PDAC tumor growth inhibition in vivo. Our work uncovers SETD5 as a key mediator of acquired MEKi therapy resistance in PDAC and suggests a context for advancing MEKi use in the clinic.
    Keywords:  KRAS; MEK inhibition; RAS signaling; SETD5; lysine methylation; pancreatic cancer; protein methylation
    DOI:  https://doi.org/10.1016/j.ccell.2020.04.014
  18. Nat Commun. 2020 May 18. 11(1): 2461
    TFEB regulates murine liver cell fate during development and regeneration.
    Nunzia Pastore, Tuong Huynh, Niculin J Herz, Alessia Calcagni', Tiemo J Klisch, Lorenzo Brunetti, Kangho Ho Kim, Marco De Giorgi, Ayrea Hurley, Annamaria Carissimo, Margherita Mutarelli, Niya Aleksieva, Luca D'Orsi, William R Lagor, David D Moore, Carmine Settembre, Milton J Finegold, Stuart J Forbes, Andrea Ballabio.
      It is well established that pluripotent stem cells in fetal and postnatal liver (LPCs) can differentiate into both hepatocytes and cholangiocytes. However, the signaling pathways implicated in the differentiation of LPCs are still incompletely understood. Transcription Factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy, is known to be involved in osteoblast and myeloid differentiation, but its role in lineage commitment in the liver has not been investigated. Here we show that during development and upon regeneration TFEB drives the differentiation status of murine LPCs into the progenitor/cholangiocyte lineage while inhibiting hepatocyte differentiation. Genetic interaction studies show that Sox9, a marker of precursor and biliary cells, is a direct transcriptional target of TFEB and a primary mediator of its effects on liver cell fate. In summary, our findings identify an unexplored pathway that controls liver cell lineage commitment and whose dysregulation may play a role in biliary cancer.
    DOI:  https://doi.org/10.1038/s41467-020-16300-x
  19. Nat Commun. 2020 May 22. 11(1): 2588
    KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain.
    Michal Lipinski, Rafael Muñoz-Viana, Beatriz Del Blanco, Angel Marquez-Galera, Juan Medrano-Relinque, José M Caramés, Andrzej A Szczepankiewicz, Jordi Fernandez-Albert, Carmen M Navarrón, Roman Olivares, Grzegorz M Wilczyński, Santiago Canals, Jose P Lopez-Atalaya, Angel Barco.
      The lysine acetyltransferases type 3 (KAT3) family members CBP and p300 are important transcriptional co-activators, but their specific functions in adult post-mitotic neurons remain unclear. Here, we show that the combined elimination of both proteins in forebrain excitatory neurons of adult mice resulted in a rapidly progressing neurological phenotype associated with severe ataxia, dendritic retraction and reduced electrical activity. At the molecular level, we observed the downregulation of neuronal genes, as well as decreased H3K27 acetylation and pro-neural transcription factor binding at the promoters and enhancers of canonical neuronal genes. The combined deletion of CBP and p300 in hippocampal neurons resulted in the rapid loss of neuronal molecular identity without de- or transdifferentiation. Restoring CBP expression or lysine acetylation rescued neuronal-specific transcription in cultured neurons. Together, these experiments show that KAT3 proteins maintain the excitatory neuron identity through the regulation of histone acetylation at cell type-specific promoter and enhancer regions.
    DOI:  https://doi.org/10.1038/s41467-020-16246-0
  20. Mol Syst Biol. 2020 May;16(5): e9438
    Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics.
    Carmen Bravo González-Blas, Xiao-Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime de Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts.
      Single-cell technologies allow measuring chromatin accessibility and gene expression in each cell, but jointly utilizing both layers to map bona fide gene regulatory networks and enhancers remains challenging. Here, we generate independent single-cell RNA-seq and single-cell ATAC-seq atlases of the Drosophila eye-antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering). To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~ 85% of enhancers in which chromatin accessibility and enhancer activity are coupled. Next, we infer enhancer-to-gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers. Exploiting cell type-specific enhancers, we deconvolute cell type-specific effects of bulk-derived chromatin accessibility QTLs. Finally, we discover that Prospero drives neuronal differentiation through the binding of a GGG motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue.
    Keywords:  enhancer detection; eye-antennal disc; gene regulation; single-cell omics; spatial integration
    DOI:  https://doi.org/10.15252/msb.20209438
  21. Sci Adv. 2020 May;6(20): eaba2489
    ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines.
    Pankaj Kumar, Shashi Kiran, Shekhar Saha, Zhangli Su, Teressa Paulsen, Ajay Chatrath, Yoshiyuki Shibata, Etsuko Shibata, Anindya Dutta.
      Extrachromosomal circular DNAs (eccDNAs) are somatically mosaic and contribute to intercellular heterogeneity in normal and tumor cells. Because short eccDNAs are poorly chromatinized, we hypothesized that they are sequenced by tagmentation in ATAC-seq experiments without any enrichment of circular DNA. Indeed, ATAC-seq identified thousands of eccDNAs in cell lines that were validated by inverse PCR and by metaphase FISH. ATAC-seq in gliomas and glioblastomas identify hundreds of eccDNAs, including one containing the well-known EGFR gene amplicon from chr7. More than 18,000 eccDNAs, many carrying known cancer driver genes, are identified in a pan-cancer analysis of ATAC-seq libraries from 23 tumor types. Somatically mosaic eccDNAs are identified by ATAC-seq even before amplification is recognized by genome-wide copy number variation measurements. Thus, ATAC-seq is a sensitive method to detect eccDNA present in a tumor at the pre-amplification stage and can be used to predict resistance to therapy.
    DOI:  https://doi.org/10.1126/sciadv.aba2489
  22. Cell Rep. 2020 May 19. pii: S2211-1247(20)30616-1. [Epub ahead of print]31(7): 107663
    Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks.
    Vikram Agarwal, Jay Shendure.
      Algorithms that accurately predict gene structure from primary sequence alone were transformative for annotating the human genome. Can we also predict the expression levels of genes based solely on genome sequence? Here, we sought to apply deep convolutional neural networks toward that goal. Surprisingly, a model that includes only promoter sequences and features associated with mRNA stability explains 59% and 71% of variation in steady-state mRNA levels in human and mouse, respectively. This model, termed Xpresso, more than doubles the accuracy of alternative sequence-based models and isolates rules as predictive as models relying on chromatic immunoprecipitation sequencing (ChIP-seq) data. Xpresso recapitulates genome-wide patterns of transcriptional activity, and its residuals can be used to quantify the influence of enhancers, heterochromatic domains, and microRNAs. Model interpretation reveals that promoter-proximal CpG dinucleotides strongly predict transcriptional activity. Looking forward, we propose cell-type-specific gene-expression predictions based solely on primary sequences as a grand challenge for the field.
    Keywords:  deep learning; gene regulation; predicting gene expression
    DOI:  https://doi.org/10.1016/j.celrep.2020.107663
  23. Development. 2020 May 21. pii: dev.186023. [Epub ahead of print]
    Pitx2-Sox2-Lef-1 interactions specify progenitor oral/dental epithelial cell signaling centers.
    Wenjie Yu, Zhao Sun, Yan Sweat, Mason Sweat, Shankar Rengasamy Venugopalan, Steven Eliason, Huojun Cao, Michael L Paine, Brad A Amendt.
      Epithelial signaling centers control epithelial invagination and organ development, but how these centers are specified remains unclear. We report that Pitx2 (the first transcriptional marker for tooth development) controls the embryonic formation and patterning of epithelial signaling centers during incisor development. We demonstrate using Krt14 Cre /Pitx2 flox/flox (Pitx2 cKO ) embryos, and Rosa26 CreERT /Pitx2 flox/flox mice that loss of Pitx2 delays epithelial invagination, decreases progenitor cell proliferation, and dental epithelium cell differentiation. Developmentally, Pitx2 regulates formation of the Sox2+ labial cervical loop (LaCL) stem cell niche in concert with two signaling centers, the initiation knot (IK) and enamel knot (EK). The loss of Pitx2 disrupted the patterning of these two signaling centers resulting in tooth arrest at E14.5. Mechanistically, Pitx2 transcriptional activity and DNA binding is inhibited by Sox2, and this interaction controls gene expression in specific Sox2 and Pitx2 co-expression progenitor cell domains. We demonstrate new transcriptional mechanisms regulating signaling centers by Pitx2, Sox2, Lef-1 and Irx1.
    Keywords:  Craniofacial/tooth development; Dental Epithelial Stem Cells; Enamel knot; Irx1; Pitx2; Shh; Signaling centers; Sox2; Stem cell niche; Transcriptional regulation
    DOI:  https://doi.org/10.1242/dev.186023
  24. Nat Cell Biol. 2020 May 18.
    Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance.
    Mingjun Bi, Zhao Zhang, Yi-Zhou Jiang, Pengya Xue, Hu Wang, Zhao Lai, Xiaoyong Fu, Carmine De Angelis, Yue Gong, Zhen Gao, Jianhua Ruan, Victor X Jin, Elisabetta Marangoni, Elodie Montaudon, Christopher K Glass, Wei Li, Tim Hui-Ming Huang, Zhi-Ming Shao, Rachel Schiff, Lizhen Chen, Zhijie Liu.
      Acquired therapy resistance is a major problem for anticancer treatment, yet the underlying molecular mechanisms remain unclear. Using an established breast cancer cellular model, we show that endocrine resistance is associated with enhanced phenotypic plasticity, indicated by a general downregulation of luminal/epithelial differentiation markers and upregulation of basal/mesenchymal invasive markers. Consistently, similar gene expression changes are found in clinical breast tumours and patient-derived xenograft samples that are resistant to endocrine therapies. Mechanistically, the differential interactions between oestrogen receptor α and other oncogenic transcription factors, exemplified by GATA3 and AP1, drive global enhancer gain/loss reprogramming, profoundly altering breast cancer transcriptional programs. Our functional studies in multiple culture and xenograft models reveal a coordinated role of GATA3 and AP1 in re-organizing enhancer landscapes and regulating cancer phenotypes. Collectively, our study suggests that differential high-order assemblies of transcription factors on enhancers trigger genome-wide enhancer reprogramming, resulting in transcriptional transitions that promote tumour phenotypic plasticity and therapy resistance.
    DOI:  https://doi.org/10.1038/s41556-020-0514-z
  25. iScience. 2020 Apr 29. pii: S2589-0042(20)30291-1. [Epub ahead of print]23(5): 101106
    RORγt-driven TH17 Cell Differentiation Requires Epigenetic Control by the Swi/Snf Chromatin Remodeling Complex.
    Sungkyu Lee, Jieun Kim, Hyungyu Min, Rho H Seong.
      Epigenetic regulation, including chromatin accessibility and posttranslational modifications of histones, is of importance for T cell lineage decision. TH17 cells play a critical role in protective mucosal immunity and pathogenic multiple autoimmune diseases. The differentiation of TH17 cells is dictated by a master transcription factor, RORγt. However, the epigenetic mechanism that controls TH17 cell differentiation remains poorly understood. Here we show that the Swi/Snf complex is required for TH17-mediated cytokine production both in vitro and in vivo. We demonstrate that RORγt recruits and forms a complex with the Swi/Snf complex to cooperate for the RORγt-mediated epigenetic modifications of target genes, including both permissive and repressive ones for TH17 cell differentiation. Our findings thus highlight the Swi/Snf complex as an essential epigenetic regulator of TH17 cell differentiation and provide a basis for the understanding of how a master transcription factor RORγt collaborates with the Swi/Snf complex to govern epigenetic regulation.
    Keywords:  Immunity; Molecular Mechanism of Gene Regulation; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2020.101106
  26. Nucleic Acids Res. 2020 May 22. pii: gkaa388. [Epub ahead of print]
    3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.
    Michal Wlasnowolski, Michal Sadowski, Tymon Czarnota, Karolina Jodkowska, Przemyslaw Szalaj, Zhonghui Tang, Yijun Ruan, Dariusz Plewczynski.
      Structural variants (SVs) that alter DNA sequence emerge as a driving force involved in the reorganisation of DNA spatial folding, thus affecting gene transcription. In this work, we describe an improved version of our integrated web service for structural modeling of three-dimensional genome (3D-GNOME), which now incorporates all types of SVs to model changes to the reference 3D conformation of chromatin. In 3D-GNOME 2.0, the default reference 3D genome structure is generated using ChIA-PET data from the GM12878 cell line and SVs data are sourced from the population-scale catalogue of SVs identified by the 1000 Genomes Consortium. However, users may also submit their own structural data to set a customized reference genome structure, and/or a custom input list of SVs. 3D-GNOME 2.0 provides novel tools to inspect, visualize and compare 3D models for regions that differ in terms of their linear genomic sequence. Contact diagrams are displayed to compare the reference 3D structure with the one altered by SVs. In our opinion, 3D-GNOME 2.0 is a unique online tool for modeling and analyzing conformational changes to the human genome induced by SVs across populations. It can be freely accessed at https://3dgnome.cent.uw.edu.pl/.
    DOI:  https://doi.org/10.1093/nar/gkaa388
  27. Development. 2020 May 21. pii: dev.175141. [Epub ahead of print]
    Cdk8 is required for establishment of H3K27me3 and gene repression by Xist and mouse development.
    Andreas Postlmayr, Charles Etienne Dumeau, Anton Wutz.
      We previously identified the cyclin dependent kinase Cdk8 as a putative silencing factor for Xist To investigate its role in X inactivation, we engineered a Cdk8 mutation in mouse embryonic stem cells (ESCs) carrying an inducible system for studying Xist function. We find that Xist represses X-linked genes to half the expression level in Cdk8 mutant cells, whereas near complete silencing is observed in controls. Lack of Cdk8 impairs Ezh2 recruitment and establishment of histone H3 lysine 27 tri-methylation but not PRC1 recruitment by Xist Transgenic expression of wild-type but not catalytically inactive Cdk8 restores efficient gene repression and PRC2 recruitment. Mutation of the paralogous kinase Cdk19 does not affect Xist function and combined mutations of Cdk8 and Cdk19 resemble the Cdk8 mutation. In mice a Cdk8 mutation causes post-implantation lethality. We observe that homozygous Cdk8 mutant female embryos show a greater developmental delay than males on day 10.5. Together with inefficient repression of X-linked genes in differentiating Cdk8 mutant female ESCs these data show a requirement of Cdk8 for the initiation of X inactivation.
    Keywords:  Cdk8; Cyclin dependent kinase; Gene regulation; Polycomb; X inactivation; Xist
    DOI:  https://doi.org/10.1242/dev.175141
  28. Nat Commun. 2020 May 22. 11(1): 2560
    Methylation of a CGATA element inhibits binding and regulation by GATA-1.
    Lu Yang, Zhiliang Chen, Elizabeth S Stout, Fabien Delerue, Lars M Ittner, Marc R Wilkins, Kate G R Quinlan, Merlin Crossley.
      Alterations in DNA methylation occur during development, but the mechanisms by which they influence gene expression remain uncertain. There are few examples where modification of a single CpG dinucleotide directly affects transcription factor binding and regulation of a target gene in vivo. Here, we show that the erythroid transcription factor GATA-1 - that typically binds T/AGATA sites - can also recognise CGATA elements, but only if the CpG dinucleotide is unmethylated. We focus on a single CGATA site in the c-Kit gene which progressively becomes unmethylated during haematopoiesis. We observe that methylation attenuates GATA-1 binding and gene regulation in cell lines. In mice, converting the CGATA element to a TGATA site that cannot be methylated leads to accumulation of megakaryocyte-erythroid progenitors. Thus, the CpG dinucleotide is essential for normal erythropoiesis and this study illustrates how a single methylated CpG can directly affect transcription factor binding and cellular regulation.
    DOI:  https://doi.org/10.1038/s41467-020-16388-1
  29. Nat Genet. 2020 May 18.
    Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium.
    Bartomeu Colom, Maria P Alcolea, Gabriel Piedrafita, Michael W J Hall, Agnieszka Wabik, Stefan C Dentro, Joanna C Fowler, Albert Herms, Charlotte King, Swee Hoe Ong, Roshan K Sood, Moritz Gerstung, Inigo Martincorena, Benjamin A Hall, Philip H Jones.
      During aging, progenitor cells acquire mutations, which may generate clones that colonize the surrounding tissue. By middle age, normal human tissues, including the esophageal epithelium (EE), become a patchwork of mutant clones. Despite their relevance for understanding aging and cancer, the processes that underpin mutational selection in normal tissues remain poorly understood. Here, we investigated this issue in the esophageal epithelium of mutagen-treated mice. Deep sequencing identified numerous mutant clones with multiple genes under positive selection, including Notch1, Notch2 and Trp53, which are also selected in human esophageal epithelium. Transgenic lineage tracing revealed strong clonal competition that evolved over time. Clone dynamics were consistent with a simple model in which the proliferative advantage conferred by positively selected mutations depends on the nature of the neighboring cells. When clones with similar competitive fitness collide, mutant cell fate reverts towards homeostasis, a constraint that explains how selection operates in normal-appearing epithelium.
    DOI:  https://doi.org/10.1038/s41588-020-0624-3
  30. Genome Biol. 2020 May 18. 21(1): 120
    RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function.
    Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong, Ting Zhang, Pan Li, Bao-Fa Sun, Ying Yang, Ning Zhang, Yong-Liang Zhao, Hai-Lin Wang, Feng Liu, Qiangfeng Cliff Zhang, Yun-Gui Yang.
      BACKGROUND: Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined.RESULTS: Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis. Strikingly, we observe that RNA structurally variable regions are enriched in the 3' UTR and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We find that the RNA-binding protein Elavl1a stabilizes maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppresses Elavl1a's binding leading to the decay of its maternal targets.
    CONCLUSIONS: Our study finds that RNA structurally variable regions are enriched in mRNA 3' UTRs and contain cis-regulatory elements during zebrafish early embryogenesis. We reveal that Elavl1a regulates maternal RNA stability in an RNA structure-dependent fashion. Overall, our findings reveal a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.
    Keywords:  Elavl1a; RNA structure; Structure-based regulome; Zebrafish early embryogenesis
    DOI:  https://doi.org/10.1186/s13059-020-02022-2
  31. Cell Rep. 2020 May 19. pii: S2211-1247(20)30609-4. [Epub ahead of print]31(7): 107656
    Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing.
    Emily C Freund, Anne L Sapiro, Qin Li, Sandra Linder, James J Moresco, John R Yates, Jin Billy Li.
      Adenosine-to-inosine RNA editing is catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes that deaminate adenosine to inosine. Although many RNA editing sites are known, few trans regulators have been identified. We perform BioID followed by mass spectrometry to identify trans regulators of ADAR1 and ADAR2 in HeLa and M17 neuroblastoma cells. We identify known and novel ADAR-interacting proteins. Using ENCODE data, we validate and characterize a subset of the novel interactors as global or site-specific RNA editing regulators. Our set of novel trans regulators includes all four members of the DZF-domain-containing family of proteins: ILF3, ILF2, STRBP, and ZFR. We show that these proteins interact with each ADAR and modulate RNA editing levels. We find ILF3 is a broadly influential negative regulator of editing. This work demonstrates the broad roles that RNA binding proteins play in regulating editing levels, and establishes DZF-domain-containing proteins as a group of highly influential RNA editing regulators.
    Keywords:  A-to-I RNA editing; ADAR; BioID; BirA; DZF-domain; ILF2; ILF3; STRBP; ZFR
    DOI:  https://doi.org/10.1016/j.celrep.2020.107656
  32. Nat Commun. 2020 May 22. 11(1): 2578
    N6-methyladenosine regulates glycolysis of cancer cells through PDK4.
    Zihan Li, Yanxi Peng, Jiexin Li, Zhuojia Chen, Feng Chen, Jian Tu, Shuibin Lin, Hongsheng Wang.
      Studies on biological functions of N6-methyladenosine (m6A) modification in mRNA have sprung up in recent years. We find m6A can positively regulate the glycolysis of cancer cells. Specifically, m6A-sequencing and functional studies confirm that pyruvate dehydrogenase kinase 4 (PDK4) is involved in m6A regulated glycolysis and ATP generation. The m6A modified 5'UTR of PDK4 positively regulates its translation elongation and mRNA stability via binding with YTHDF1/eEF-2 complex and IGF2BP3, respectively. Targeted specific demethylation of PDK4 m6A by dm6ACRISPR system can significantly decrease the expression of PDK4 and glycolysis of cancer cells. Further, TATA-binding protein (TBP) can transcriptionally increase the expression of Mettl3 in cervical cancer cells via binding to its promoter. In vivo and clinical data confirm the positive roles of m6A/PDK4 in tumor growth and progression of cervical and liver cancer. Our study reveals that m6A regulates glycolysis of cancer cells through PDK4.
    DOI:  https://doi.org/10.1038/s41467-020-16306-5
  33. Phys Rev E. 2020 Apr;101(4-1): 040401
    Pioneer transcription factors in chromatin remodeling: The kinetic proofreading view.
    Helmut Schiessel, Ralf Blossey.
      Pioneer transcription factors are a recently defined class of transcription factors which can bind directly to nucleosomal DNA; they play a key role in gene activation in certain pathways. Here we quantify their role in the initiation of nucleosome displacement within the kinetic proofreading scenario of chromatin remodeling. The model allows one to perform remodeling efficiency comparisons for scenarios involving different types of transcription factors and remodelers as a function of their binding and unbinding rates and concentrations. Our results demonstrate a way to fine-tune the specificity of processes that modify the chromatin structure in transcriptional initiation.
    DOI:  https://doi.org/10.1103/PhysRevE.101.040401
  34. Nucleic Acids Res. 2020 May 18. pii: gkaa334. [Epub ahead of print]
    Transcriptome-wide organization of subcellular microenvironments revealed by ATLAS-Seq.
    Danielle A Adekunle, Eric T Wang.
      Subcellular organization of RNAs and proteins is critical for cell function, but we still lack global maps and conceptual frameworks for how these molecules are localized in cells and tissues. Here, we introduce ATLAS-Seq, which generates transcriptomes and proteomes from detergent-free tissue lysates fractionated across a sucrose gradient. Proteomic analysis of fractions confirmed separation of subcellular compartments. Unexpectedly, RNAs tended to co-sediment with other RNAs in similar protein complexes, cellular compartments, or with similar biological functions. With the exception of those encoding secreted proteins, most RNAs sedimented differently than their encoded protein counterparts. To identify RNA binding proteins potentially driving these patterns, we correlated their sedimentation profiles to all RNAs, confirming known interactions and predicting new associations. Hundreds of alternative RNA isoforms exhibited distinct sedimentation patterns across the gradient, despite sharing most of their coding sequence. These observations suggest that transcriptomes can be organized into networks of co-segregating mRNAs encoding functionally related proteins and provide insights into the establishment and maintenance of subcellular organization.
    DOI:  https://doi.org/10.1093/nar/gkaa334
  35. Nat Commun. 2020 May 22. 11(1): 2564
    Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs.
    Marco Di Stefano, Ralph Stadhouders, Irene Farabella, David Castillo, François Serra, Thomas Graf, Marc A Marti-Renom.
      Chromosome structure is a crucial regulatory factor for a wide range of nuclear processes. Chromosome conformation capture (3C)-based experiments combined with computational modelling are pivotal for unveiling 3D chromosome structure. Here, we introduce TADdyn, a tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci in a completely data-driven way. We apply TADdyn on in situ Hi-C time-course experiments studying the reprogramming of murine B cells to pluripotent cells, and characterize the structural rearrangements that take place upon changes in the transcriptional state of 21 genomic loci of diverse expression dynamics. By measuring various structural and dynamical properties, we find that during gene activation, the transcription starting site contacts with open and active regions in 3D chromatin domains. We propose that these 3D hubs of open and active chromatin may constitute a general feature to trigger and maintain gene transcription.
    DOI:  https://doi.org/10.1038/s41467-020-16396-1
  36. Development. 2020 May 21. pii: dev.186999. [Epub ahead of print]
    MLL4 is required after implantation whereas MLL3 becomes essential during late gestation.
    Deepthi Ashokkumar, Qinyu Zhang, Christian Much, Anita S Bledau, Ronald Naumann, Dimitra Alexopoulou, Andreas Dahl, Neha Goveas, Jun Fu, Konstantinos Anastassiadis, A Francis Stewart, Andrea Kranz.
      Methylation of histone 3 lysine 4 (H3K4) is a major epigenetic system associated with gene expression. In mammals there are six H3K4 methyltransferases related to yeast Set1 and fly Trithorax, including two orthologs of fly Trithorax-related: MLL3 and MLL4. Exome sequencing has documented high frequencies of MLL3 and MLL4 mutations in many types of human cancer. Despite this emerging importance, the requirements of these paralogs in mammalian development have only been incompletely reported. Here we examined the null phenotypes to establish that MLL3 is first required for lung maturation whereas MLL4 is first required for migration of the anterior visceral endoderm (AVE) that initiates gastrulation. This collective cell migration is preceded by a columnar to squamous transition in visceral endoderm cells that depends on MLL4. Furthermore, Mll4 mutants display incompletely penetrant, sex distorted, embryonic haploinsufficiency and adult heterozygous mutants show aspects of Kabuki syndrome, indicating that MLL4 action, unlike MLL3, is dosage dependent. The highly specific and discordant functions of these paralogs in mouse development argues against their action as general enhancer factors.
    Keywords:  Cell migration; Epigenetic regulation; Exencephaly; Gastrulation; Lung maturation
    DOI:  https://doi.org/10.1242/dev.186999
  37. Bioinformatics. 2020 May 16. pii: btaa293. [Epub ahead of print]
    scVAE: Variational auto-encoders for single-cell gene expression data.
    Christopher Heje Grønbech, Maximillian Fornitz Vording, Pascal Timshel, Casper Kaae Sønderby, Tune Hannes Pers, Ole Winther.
      MOTIVATION: Models for analysing and making relevant biological inferences from massive amounts of complex single-cell transcriptomic data typically require several individual data-processing steps, each with their own set of hyperparameter choices. With deep generative models one can work directly with count data, make likelihood-based model comparison, learn a latent representation of the cells and capture more of the variability in different cell populations.RESULTS: We propose a novel method based on variational auto-encoders (VAEs) for analysis of single-cell RNA sequencing (scRNA-seq) data. It avoids data preprocessing by using raw count data as input and can robustly estimate the expected gene expression levels and a latent representation for each cell. We tested several count likelihood functions and a variant of the VAE that has a priori clustering in the latent space. We show for several scRNA-seq data sets that our method outperforms recently proposed scRNA-seq methods in clustering cells and that the resulting clusters reflect cell types.
    AVAILABILITY AND IMPLEMENTATION: Our method, called scVAE, is implemented in Python using the TensorFlow machine-learning library, and it is freely available at https://github.com/scvae/scvae.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa293
  38. Genome Res. 2020 May 18.
    Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains.
    Ekaterina Khrameeva, Ilia Kurochkin, Dingding Han, Patricia Guijarro, Sabina Kanton, Malgorzata Santel, Zhengzong Qian, Shen Rong, Pavel Mazin, Marat Sabirov, Matvei Bulat, Olga Efimova, Anna Tkachev, Song Guo, Chet C Sherwood, J Gray Camp, Svante Pääbo, Barbara Treutlein, Philipp Khaitovich.
      Identification of gene expression traits unique to the human brain sheds light on the molecular mechanisms underlying human evolution. Here, we searched for uniquely human gene expression traits by analyzing 422 brain samples from humans, chimpanzees, bonobos, and macaques representing 33 anatomical regions, as well as 88,047 cell nuclei composing three of these regions. Among 33 regions, cerebral cortex areas, hypothalamus, and cerebellar gray and white matter evolved rapidly in humans. At the cellular level, astrocytes and oligodendrocyte progenitors displayed more differences in the human evolutionary lineage than the neurons. Comparison of the bulk tissue and single-nuclei sequencing revealed that conventional RNA sequencing did not detect up to two-thirds of cell-type-specific evolutionary differences.
    DOI:  https://doi.org/10.1101/gr.256958.119
  39. Bioinformatics. 2020 May 21. pii: btaa532. [Epub ahead of print]
    scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures.
    Yan Zhang, Yaru Zhang, Jun Hu, Ji Zhang, Fangjie Guo, Meng Zhou, Guijun Zhang, Fulong Yu, Jianzhong Su.
      MOTIVATION: At present, a fundamental challenge in single-cell RNA-sequencing data analysis is functional interpretation and annotation of cell clusters. Biological pathways in distinct cell types have different activation patterns, which facilitates the understanding of cell functions using single-cell transcriptomics. However, no effective web tool has been implemented for single-cell transcriptome data analysis based on prior biological pathway knowledge.RESULTS: Here, we present scTPA, a web-based platform for pathway-based analysis of single-cell RNA-seq data in human and mouse. scTPA incorporates four widely-used gene set enrichment methods to estimate the pathway activation scores of single cells based on a collection of available biological pathways with different functional and taxonomic classifications. The clustering analysis and cell-type-specific activation pathway identification were provided for the functional interpretation of cell types from a pathway-oriented perspective. An intuitive interface allows users to conveniently visualize and download single-cell pathway signatures. Overall, scTPA is a comprehensive tool for the identification of pathway activation signatures for the analysis of single cell heterogeneity.
    AVAILABILITY: http://sctpa.bio-data.cn/sctpa.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa532
  40. Nat Genet. 2020 May 18.
    Quantifying genetic effects on disease mediated by assayed gene expression levels.
    Douglas W Yao, Luke J O'Connor, Alkes L Price, Alexander Gusev.
      Disease variants identified by genome-wide association studies (GWAS) tend to overlap with expression quantitative trait loci (eQTLs), but it remains unclear whether this overlap is driven by gene expression levels 'mediating' genetic effects on disease. Here, we introduce a new method, mediated expression score regression (MESC), to estimate disease heritability mediated by the cis genetic component of gene expression levels. We applied MESC to GWAS summary statistics for 42 traits (average N = 323,000) and cis-eQTL summary statistics for 48 tissues from the Genotype-Tissue Expression (GTEx) consortium. Averaging across traits, only 11 ± 2% of heritability was mediated by assayed gene expression levels. Expression-mediated heritability was enriched in genes with evidence of selective constraint and genes with disease-appropriate annotations. Our results demonstrate that assayed bulk tissue eQTLs, although disease relevant, cannot explain the majority of disease heritability.
    DOI:  https://doi.org/10.1038/s41588-020-0625-2
  41. Nat Chem Biol. 2020 Jun;16(6): 620-629
    Chromatin as a key consumer in the metabolite economy.
    Katharine L Diehl, Tom W Muir.
      In eukaryotes, chromatin remodeling and post-translational modifications (PTMs) shape the local chromatin landscape to establish permissive and repressive regions within the genome, orchestrating transcription, replication, and DNA repair in concert with other epigenetic mechanisms. Though cellular nutrient signaling encompasses a huge number of pathways, recent attention has turned to the hypothesis that the metabolic state of the cell is communicated to the genome through the type and concentration of metabolites in the nucleus that are cofactors for chromatin-modifying enzymes. Importantly, both epigenetic and metabolic dysregulation are hallmarks of a range of diseases, and this metabolism-chromatin axis may yield a well of new therapeutic targets. In this Perspective, we highlight emerging themes in the inter-regulation of the genome and metabolism via chromatin, including nonenzymatic histone modifications arising from chemically reactive metabolites, the expansion of PTM diversity from cofactor-promiscuous chromatin-modifying enzymes, and evidence for the existence and importance of subnucleocytoplasmic metabolite pools.
    DOI:  https://doi.org/10.1038/s41589-020-0517-x
  42. Nat Commun. 2020 May 18. 11(1): 2484
    HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer's disease.
    Ping-Chieh Pao, Debasis Patnaik, L Ashley Watson, Fan Gao, Ling Pan, Jun Wang, Chinnakkaruppan Adaikkan, Jay Penney, Hugh P Cam, Wen-Chin Huang, Lorena Pantano, Audrey Lee, Alexi Nott, Trongha X Phan, Elizabeta Gjoneska, Sara Elmsaouri, Stephen J Haggarty, Li-Huei Tsai.
      DNA damage contributes to brain aging and neurodegenerative diseases. However, the factors stimulating DNA repair to stave off functional decline remain obscure. We show that HDAC1 modulates OGG1-initated 8-oxoguanine (8-oxoG) repair in the brain. HDAC1-deficient mice display age-associated DNA damage accumulation and cognitive impairment. HDAC1 stimulates OGG1, a DNA glycosylase known to remove 8-oxoG lesions that are associated with transcriptional repression. HDAC1 deficiency causes impaired OGG1 activity, 8-oxoG accumulation at the promoters of genes critical for brain function, and transcriptional repression. Moreover, we observe elevated 8-oxoG along with reduced HDAC1 activity and downregulation of a similar gene set in the 5XFAD mouse model of Alzheimer's disease. Notably, pharmacological activation of HDAC1 alleviates the deleterious effects of 8-oxoG in aged wild-type and 5XFAD mice. Our work uncovers important roles for HDAC1 in 8-oxoG repair and highlights the therapeutic potential of HDAC1 activation to counter functional decline in brain aging and neurodegeneration.
    DOI:  https://doi.org/10.1038/s41467-020-16361-y
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