bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020–06–07
forty papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Dynamics of the 4D genome during in vivo lineage specification and differentiation.
  2. CTCF loss mediates unique DNA hypermethylation landscapes in human cancers.
  3. Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells.
  4. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation.
  5. Machine learning uncovers cell identity regulator by histone code.
  6. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae.
  7. Selective Mediator dependence of cell-type-specifying transcription.
  8. BRD4 promotes metastatic potential in oral squamous cell carcinoma through the epigenetic regulation of the MMP2 gene.
  9. Targeted Perturb-seq enables genome-scale genetic screens in single cells.
  10. Proximity Labeling Techniques to Study Chromatin.
  11. Evolving methodologies and concepts in 4D nucleome research.
  12. The transcriptional repressor Blimp1/PRDM1 regulates the maternal decidual response in mice.
  13. Single-cell transcriptomic analysis identifies the conversion of zebrafish Etv2-deficient vascular progenitors into skeletal muscle.
  14. Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription.
  15. Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity.
  16. Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation.
  17. A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing.
  18. The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression.
  19. The transcription factor E2A drives neural differentiation in pluripotent cells.
  20. Regulatory sharing between estrogen receptor α bound enhancers.
  21. Diverse nucleosome site-selectivity among histone deacetylase complexes.
  22. SETDB1 is required for intestinal epithelial differentiation and the prevention of intestinal inflammation.
  23. A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin.
  24. Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering.
  25. DAMEfinder: a method to detect differential allele-specific methylation.
  26. Unresolved Complexity in the Gene Regulatory Network Underlying EMT.
  27. A HIF1a-dependent pro-oxidant state disrupts synaptic plasticity and impairs spatial memory in response to intermittent hypoxia.
  28. RIC-seq for global in situ profiling of RNA-RNA spatial interactions.
  29. Specialization of the chromatin remodeler RSC to mobilize partially-unwrapped nucleosomes.
  30. PHF20L1 as a H3K27me2 reader coordinates with transcriptional repressors to promote breast tumorigenesis.
  31. Loss of the transcription factor MAFB limits β-cell derivation from human PSCs.
  32. Reproducibility-optimized detection of differential DNA methylation.
  33. BRM-SWI/SNF chromatin remodeling complex enables functional telomeres by promoting co-expression of TRF2 and TRF1.
  34. Enhancement of gene expression noise from transcription factor binding to genomic decoy sites.
  35. The EMT transcription factor ZEB2 promotes proliferation of primary and metastatic melanoma while suppressing an invasive, mesenchymal-like phenotype.
  36. poly(UG)-tailed RNAs in genome protection and epigenetic inheritance.
  37. MYC protein stability is negatively regulated by BRD4.
  38. SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update).
  39. Oncometabolites suppress DNA repair by disrupting local chromatin signalling.
  40. MYC functions as a switch for natural killer cell-mediated immune surveillance of lymphoid malignancies.
  1. Nat Commun. 2020 Jun 01. 11(1): 2722
    Dynamics of the 4D genome during in vivo lineage specification and differentiation.
    A Marieke Oudelaar, Robert A Beagrie, Matthew Gosden, Sara de Ornellas, Emily Georgiades, Jon Kerry, Daniel Hidalgo, Joana Carrelha, Arun Shivalingam, Afaf H El-Sagheer, Jelena M Telenius, Tom Brown, Veronica J Buckle, Merav Socolovsky, Douglas R Higgs, Jim R Hughes.
      Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. Our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.
    DOI:  https://doi.org/10.1038/s41467-020-16598-7
  2. Clin Epigenetics. 2020 Jun 05. 12(1): 80
    CTCF loss mediates unique DNA hypermethylation landscapes in human cancers.
    Nathan A Damaschke, Joseph Gawdzik, Mele Avilla, Bing Yang, John Svaren, Avtar Roopra, Jian-Hua Luo, Yan P Yu, Sunduz Keles, David F Jarrard.
       BACKGROUND: The chromatin insulator CCCTC-binding factor (CTCF) displays tissue-specific DNA binding sites that regulate transcription and chromatin organization. Despite evidence linking CTCF to the protection of epigenetic states through barrier insulation, the impact of CTCF loss on genome-wide DNA methylation sites in human cancer remains undefined.
    RESULTS: Here, we demonstrate that prostate and breast cancers within The Cancer Genome Atlas (TCGA) exhibit frequent copy number loss of CTCF and that this loss is associated with increased DNA methylation events that occur preferentially at CTCF binding sites. CTCF sites differ among tumor types and result in tissue-specific methylation patterns with little overlap between breast and prostate cancers. DNA methylation and transcriptome profiling in vitro establish that forced downregulation of CTCF leads to spatially distinct DNA hypermethylation surrounding CTCF binding sites, loss of CTCF binding, and decreased gene expression that is also seen in human tumors. DNA methylation inhibition reverses loss of expression at these CTCF-regulated genes.
    CONCLUSION: These findings establish CTCF loss as a major mediator in directing localized DNA hypermethylation events in a tissue-specific fashion and further support its role as a driver of the cancer phenotype.
    Keywords:  CTCF; Cancer; DNA methylation
    DOI:  https://doi.org/10.1186/s13148-020-00869-7
  3. Genes Dev. 2020 Jun 04.
    Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells.
    Peng Gao, Changya Chen, Elizabeth D Howell, Yan Li, Joanna Tober, Yasin Uzun, Bing He, Long Gao, Qin Zhu, Arndt F Siekmann, Nancy A Speck, Kai Tan.
      Hematopoietic stem cell (HSC) ontogeny is accompanied by dynamic changes in gene regulatory networks. We performed RNA-seq and histone mark ChIP-seq to define the transcriptomes and epigenomes of cells representing key developmental stages of HSC ontogeny in mice. The five populations analyzed were embryonic day 10.5 (E10.5) endothelium and hemogenic endothelium from the major arteries, an enriched population of prehematopoietic stem cells (pre-HSCs), fetal liver HSCs, and adult bone marrow HSCs. Using epigenetic signatures, we identified enhancers for each developmental stage. Only 12% of enhancers are primed, and 78% are active, suggesting the vast majority of enhancers are established de novo without prior priming in earlier stages. We constructed developmental stage-specific transcriptional regulatory networks by linking enhancers and predicted bound transcription factors to their target promoters using a novel computational algorithm, target inference via physical connection (TIPC). TIPC predicted known transcriptional regulators for the endothelial-to-hematopoietic transition, validating our overall approach, and identified putative novel transcription factors, including the broadly expressed transcription factors SP3 and MAZ. Finally, we validated a role for SP3 and MAZ in the formation of hemogenic endothelium. Our data and computational analyses provide a useful resource for uncovering regulators of HSC formation.
    Keywords:  HSC; embryonic hematopoiesis; enhancer; epigenetics; hemogenic endothelium; regulatory network
    DOI:  https://doi.org/10.1101/gad.338202.120
  4. Genes Dev. 2020 Jun 04.
    Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation.
    Hyeseon Kang, Maxim N Shokhirev, Zhichao Xu, Sahaana Chandran, Jesse R Dixon, Martin W Hetzer.
      During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division.
    Keywords:  chromatin; mitosis; transcription
    DOI:  https://doi.org/10.1101/gad.335794.119
  5. Nat Commun. 2020 Jun 01. 11(1): 2696
    Machine learning uncovers cell identity regulator by histone code.
    Bo Xia, Dongyu Zhao, Guangyu Wang, Min Zhang, Jie Lv, Alin S Tomoiaga, Yanqiang Li, Xin Wang, Shu Meng, John P Cooke, Qi Cao, Lili Zhang, Kaifu Chen.
      Conversion between cell types, e.g., by induced expression of master transcription factors, holds great promise for cellular therapy. Our ability to manipulate cell identity is constrained by incomplete information on cell identity genes (CIGs) and their expression regulation. Here, we develop CEFCIG, an artificial intelligent framework to uncover CIGs and further define their master regulators. On the basis of machine learning, CEFCIG reveals unique histone codes for transcriptional regulation of reported CIGs, and utilizes these codes to predict CIGs and their master regulators with high accuracy. Applying CEFCIG to 1,005 epigenetic profiles, our analysis uncovers the landscape of regulation network for identity genes in individual cell or tissue types. Together, this work provides insights into cell identity regulation, and delivers a powerful technique to facilitate regenerative medicine.
    DOI:  https://doi.org/10.1038/s41467-020-16539-4
  6. Genome Biol. 2020 Jun 02. 21(1): 132
    Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae.
    Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M Visbisky, Scott L Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William K M Lai, Richard P Metz, Charles D Johnson, Sing-Hoi Sze, B Franklin Pugh, Bryce E Nickels, Craig D Kaplan.
       BACKGROUND: The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function.
    RESULTS: To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model.
    CONCLUSIONS: Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.
    DOI:  https://doi.org/10.1186/s13059-020-02040-0
  7. Nat Genet. 2020 Jun 01.
    Selective Mediator dependence of cell-type-specifying transcription.
    Martin G Jaeger, Björn Schwalb, Sebastian D Mackowiak, Taras Velychko, Alexander Hanzl, Hana Imrichova, Matthias Brand, Benedikt Agerer, Someth Chorn, Behnam Nabet, Fleur M Ferguson, André C Müller, Andreas Bergthaler, Nathanael S Gray, James E Bradner, Christoph Bock, Denes Hnisz, Patrick Cramer, Georg E Winter.
      The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase II (Pol II). Despite this pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. In agreement with a model of condensate-driven transcription initiation, large clusters of hypophosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell-type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Notably, the transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates across the genome. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell-type-specifying transcriptional networks.
    DOI:  https://doi.org/10.1038/s41588-020-0635-0
  8. Br J Cancer. 2020 Jun 05.
    BRD4 promotes metastatic potential in oral squamous cell carcinoma through the epigenetic regulation of the MMP2 gene.
    Tatsuro Yamamoto, Akiyuki Hirosue, Masafumi Nakamoto, Ryoji Yoshida, Junki Sakata, Yuichiro Matsuoka, Kenta Kawahara, Yuka Nagao, Masashi Nagata, Nozomu Takahashi, Akimitsu Hiraki, Masanori Shinohara, Mitsuyoshi Nakao, Noriko Saitoh, Hideki Nakayama.
       BACKGROUND: Oral squamous cell carcinoma (OSCC) has increased morbidity, and its high metastatic potential affects patient survival. Bromodomain containing 4 (BRD4) is a chromatin protein that associates with acetylated histone lysines and facilitates transcription. BRD4 has been implicated in cell proliferation, metastasis, and prognosis in several types of cancer. However, the role of BRD4 in OSCC remains to be elucidated.
    METHODS: We investigated the role of BRD4 and its potential utility as a therapeutic target in OSCC.
    RESULTS: JQ1, the BRD4 inhibitor, suppressed the cell proliferation, migration, and invasion in the OSCC cell lines and in vivo. JQ1 reduced the expression levels of 15 metastasis genes in OSCC, including matrix metallopeptidase 2 (MMP2). Our chromatin immunoprecipitation assay showed that JQ1 reduced the BRD4 binding to the histone H3 lysine 27 acetylation-enriched sites in the MMP2 locus. Analyses of biopsy specimens from OSCC patients revealed that the BRD4 and MMP2 expression levels were correlated in the cancerous regions, and both were highly expressed in lymph node metastasis cases, including delayed metastasis.
    CONCLUSIONS: BRD4 contributes to metastasis in OSCC, through the epigenetic regulation of the MMP2 gene, and thus BRD4 may represent a therapeutic target and a novel prediction indicator for metastasis.
    DOI:  https://doi.org/10.1038/s41416-020-0907-6
  9. Nat Methods. 2020 Jun;17(6): 629-635
    Targeted Perturb-seq enables genome-scale genetic screens in single cells.
    Daniel Schraivogel, Andreas R Gschwind, Jennifer H Milbank, Daniel R Leonce, Petra Jakob, Lukas Mathur, Jan O Korbel, Christoph A Merten, Lars Velten, Lars M Steinmetz.
      The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive and platform-independent method focusing single-cell RNA-seq coverage on genes of interest, thereby increasing the sensitivity and scale of genetic screens by orders of magnitude. TAP-seq permits routine analysis of thousands of CRISPR-mediated perturbations within a single experiment, detects weak effects and lowly expressed genes, and decreases sequencing requirements by up to 50-fold. We apply TAP-seq to generate perturbation-based enhancer-target gene maps for 1,778 enhancers within 2.5% of the human genome. We thereby show that enhancer-target association is jointly determined by three-dimensional contact frequency and epigenetic states, allowing accurate prediction of enhancer targets throughout the genome. In addition, we demonstrate that TAP-seq can identify cell subtypes with only 100 sequencing reads per cell.
    DOI:  https://doi.org/10.1038/s41592-020-0837-5
  10. Front Genet. 2020 ;11 450
    Proximity Labeling Techniques to Study Chromatin.
    Henning Ummethum, Stephan Hamperl.
      Mammals contain over 200 different cell types, yet nearly all have the same genomic DNA sequence. It is a key question in biology how the genetic instructions in DNA are selectively interpreted by cells to specify various transcriptional programs and therefore cellular identity. The structural and functional organization of chromatin governs the transcriptional state of individual genes. To understand how genomic loci adopt different levels of gene expression, it is critical to characterize all local chromatin factors as well as long-range interactions in the 3D nuclear compartment. Much of our current knowledge regarding protein interactions in a chromatin context is based on affinity purification of chromatin components coupled to mass spectrometry (AP-MS). AP-MS has been invaluable to map strong protein-protein interactions in the nucleus. However, the interaction is detected after cell lysis and biochemical enrichment, allowing for loss or gain of false positive or negative interaction partners. Recently, proximity-dependent labeling methods have emerged as powerful tools for studying chromatin in its native context. These methods take advantage of engineered enzymes that are fused to a chromatin factor of interest and can directly label all factors in proximity. Subsequent pull-down assays followed by mass spectrometry or sequencing approaches provide a comprehensive snapshot of the proximal chromatin interactome. By combining this method with dCas9, this approach can also be extended to study chromatin at specific genomic loci. Here, we review and compare current proximity-labeling approaches available for studying chromatin, with a particular focus on new emerging technologies that can provide important insights into the transcriptional and chromatin interaction networks essential for cellular identity.
    Keywords:  APEX2; BioID; ChIP; affinity purification; dCas9; mass spectrometry; protein-protein interactions; proxisome
    DOI:  https://doi.org/10.3389/fgene.2020.00450
  11. Curr Opin Cell Biol. 2020 May 27. pii: S0955-0674(20)30051-X. [Epub ahead of print]64 105-111
    Evolving methodologies and concepts in 4D nucleome research.
    Thomas M Sparks, Izabela Harabula, Ana Pombo.
      The genome requires tight regulation in space and time to maintain viable cell functions. Advances in our understanding of the 3D genome show a complex hierarchical network of structures, involving compartments, membraneless bodies, topologically associating domains, lamina associated domains, protein- or RNA-mediated loops, enhancer-promoter contacts, and accessible chromatin regions, with chromatin state regulation through epigenetic and transcriptional mechanisms. Further technology developments are poised to increase genomic resolution, dissect single-cell behaviors, including in vivo dynamics of genome folding, and provide mechanistic perspectives that identify further 3D genome players by integrating multiomics information. We highlight recent key developments in 4D nucleome methodologies and give a perspective on their future directions.
    Keywords:  3D topology; Genome; Imaging; Long-range chromatin contacts; Single-cell biology
    DOI:  https://doi.org/10.1016/j.ceb.2020.04.005
  12. Nat Commun. 2020 Jun 03. 11(1): 2782
    The transcriptional repressor Blimp1/PRDM1 regulates the maternal decidual response in mice.
    Mubeen Goolam, Maria-Eleni Xypolita, Ita Costello, John P Lydon, Francesco J DeMayo, Elizabeth K Bikoff, Elizabeth J Robertson, Arne W Mould.
      The transcriptional repressor Blimp1 controls cell fate decisions in the developing embryo and adult tissues. Here we describe Blimp1 expression and functional requirements within maternal uterine tissues during pregnancy. Expression is robustly up-regulated at early post-implantation stages in the primary decidual zone (PDZ) surrounding the embryo. Conditional inactivation results in defective formation of the PDZ barrier and abnormal trophectoderm invasion. RNA-Seq analysis demonstrates down-regulated expression of genes involved in cell adhesion and markers of decidualisation. In contrast, genes controlling immune responses including IFNγ are up-regulated. ChIP-Seq experiments identify candidate targets unique to the decidua as well as those shared across diverse cell types including a highly conserved peak at the Csf-1 gene promoter. Interestingly Blimp1 inactivation results in up-regulated Csf1 expression and macrophage recruitment into maternal decidual tissues. These results identify Blimp1 as a critical regulator of tissue remodelling and maternal tolerance during early stages of pregnancy.
    DOI:  https://doi.org/10.1038/s41467-020-16603-z
  13. Nat Commun. 2020 Jun 03. 11(1): 2796
    Single-cell transcriptomic analysis identifies the conversion of zebrafish Etv2-deficient vascular progenitors into skeletal muscle.
    Brendan Chestnut, Satish Casie Chetty, Andrew L Koenig, Saulius Sumanas.
      Cell fate decisions involved in vascular and hematopoietic embryonic development are still poorly understood. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we report a single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors are identified using an etv2ci32Gt gene trap line, in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. We observe a cell population with a skeletal muscle signature in etv2-deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells differentiate as skeletal muscle cells instead of contributing to vasculature in etv2-deficient embryos. Wnt and FGF signaling promote the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors, thus restricting these cells to a vascular endothelial fate.
    DOI:  https://doi.org/10.1038/s41467-020-16515-y
  14. Nucleic Acids Res. 2020 Jun 04. pii: gkaa474. [Epub ahead of print]
    Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription.
    Miriam Sansó, Pabitra K Parua, Daniel Pinto, J Peter Svensson, Viviane Pagé, Danny A Bitton, Sarah MacKinnon, Patricia Garcia, Elena Hidalgo, Jürg Bähler, Jason C Tanny, Robert P Fisher.
      Mono-ubiquitylation of histone H2B (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. It remained unclear whether Cdk9 and H2Bub1 cooperate to regulate the expression of individual genes. Here, we show that Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of ∼10% of fission yeast genes, with each perturbation affecting largely distinct subsets; ablation of both pathways de-represses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both modifications are enriched, and directly proportional to each other, in coding regions, and decrease abruptly around the cleavage and polyadenylation signal (CPS). Cdk9-dependence of antisense suppression at specific genes correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Genetic interactions link Cdk9, H2Bub1 and the histone deacetylase Clr6-CII, while combined Cdk9 inhibition and H2Bub1 loss impair Clr6-CII recruitment to chromatin and lead to decreased occupancy and increased acetylation of histones within gene coding regions. These results uncover novel interactions between co-transcriptional histone modification pathways, which link regulation of RNAPII transcription elongation to suppression of aberrant initiation.
    DOI:  https://doi.org/10.1093/nar/gkaa474
  15. Nat Commun. 2020 Jun 03. 11(1): 2795
    Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity.
    Lu Cui, Shih-Yu Chen, Tristan Lerbs, Jin-Wook Lee, Pablo Domizi, Sydney Gordon, Yong-Hun Kim, Garry Nolan, Paola Betancur, Gerlinde Wernig.
      The transcription factor JUN is highly expressed in pulmonary fibrosis. Its induction in mice drives lung fibrosis, which is abrogated by administration of anti-CD47. Here, we use high-dimensional mass cytometry to profile protein expression and secretome of cells from patients with pulmonary fibrosis. We show that JUN is activated in fibrotic fibroblasts that expressed increased CD47 and PD-L1. Using ATAC-seq and ChIP-seq, we found that activation of JUN rendered promoters and enhancers of CD47 and PD-L1 accessible. We further detect increased IL-6 that amplified JUN-mediated CD47 enhancer activity and protein expression. Using an in vivo mouse model of fibrosis, we found two distinct mechanisms by which blocking IL-6, CD47 and PD-L1 reversed fibrosis, by increasing phagocytosis of profibrotic fibroblasts and by eliminating suppressive effects on adaptive immunity. Our results identify specific immune mechanisms that promote fibrosis and suggest a therapeutic approach that could be used alongside conventional anti-fibrotics for pulmonary fibrosis.
    DOI:  https://doi.org/10.1038/s41467-020-16466-4
  16. Cell. 2020 Jun 03. pii: S0092-8674(20)30621-8. [Epub ahead of print]
    Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation.
    Maria Samata, Anastasios Alexiadis, Gautier Richard, Plamen Georgiev, Johannes Nuebler, Tanvi Kulkarni, Gina Renschler, M Felicia Basilicata, Fides Lea Zenk, Maria Shvedunova, Giuseppe Semplicio, Leonid Mirny, Nicola Iovino, Asifa Akhtar.
      Before zygotic genome activation (ZGA), the quiescent genome undergoes reprogramming to transition into the transcriptionally active state. However, the mechanisms underlying euchromatin establishment during early embryogenesis remain poorly understood. Here, we show that histone H4 lysine 16 acetylation (H4K16ac) is maintained from oocytes to fertilized embryos in Drosophila and mammals. H4K16ac forms large domains that control nucleosome accessibility of promoters prior to ZGA in flies. Maternal depletion of MOF acetyltransferase leading to H4K16ac loss causes aberrant RNA Pol II recruitment, compromises the 3D organization of the active genomic compartments during ZGA, and causes downregulation of post-zygotically expressed genes. Germline depletion of histone deacetylases revealed that other acetyl marks cannot compensate for H4K16ac loss in the oocyte. Moreover, zygotic re-expression of MOF was neither able to restore embryonic viability nor onset of X chromosome dosage compensation. Thus, maternal H4K16ac provides an instructive function to the offspring, priming future gene activation.
    Keywords:  H4K16ac; MOF; X chromosome; ZGA; bookmarking; dosage compensation initiation; epigenetics; memory; nucleosome accessibility; pronuclei apposition; zygotic genome activation
    DOI:  https://doi.org/10.1016/j.cell.2020.05.026
  17. PLoS One. 2020 ;15(6): e0233800
    A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing.
    Wendell Jacinto Pereira, Marília de Castro Rodrigues Pappas, Dario Grattapaglia, Georgios Joannis Pappas.
      Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).
    DOI:  https://doi.org/10.1371/journal.pone.0233800
  18. Cell Rep. 2020 Jun 02. pii: S2211-1247(20)30701-4. [Epub ahead of print]31(9): 107724
    The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression.
    Hiroki Michida, Hiroaki Imoto, Hisaaki Shinohara, Noriko Yumoto, Masahide Seki, Mana Umeda, Tetsutaro Hayashi, Itoshi Nikaido, Takeya Kasukawa, Yutaka Suzuki, Mariko Okada-Hatakeyama.
      NF-κB is a transcription factor that activates super enhancers (SEs) and typical enhancers (TEs) and triggers threshold and graded gene expression, respectively. However, the mechanisms by which NF-κB selectively participates in these enhancers remain unclear. Here we show using mouse primary B lymphocytes that SE activity simultaneously associates with chromatin opening and enriched NF-κB binding, resulting in a higher fold change and threshold expression upon B cell receptor (BCR) activation. The higher fold change results from longer DNA, whereas the threshold response is explained by synergy in DNA-NF-κB binding and is supported by the coexistence of PU.1 and NF-κB in a SE before cell stimulation. This model indicates that the pre-existing NF-κB functions as a seed and triggers its processive binding upon BCR activation. Our mathematical modeling of the single-cell transcriptome reveals an additional role for SEs in divergent clonal responses in B cells.
    Keywords:  B cell; NF-κB; enhancer; mathematical model; quantitative analysis; single cell; transcription factor; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.celrep.2020.107724
  19. Development. 2020 Jun 02. pii: dev.184093. [Epub ahead of print]
    The transcription factor E2A drives neural differentiation in pluripotent cells.
    Chandrika Rao, Mattias Malaguti, John O Mason, Sally Lowell.
      The intrinsic mechanisms that link extracellular signalling to the onset of neural differentiation are not well understood. In pluripotent mouse cells, BMP blocks entry into the neural lineage via transcriptional upregulation of Inhibitor of Differentiation (Id) factors. We have previously identified that the major binding partner of Id proteins in pluripotent cells is the basic helix-loop-helix (bHLH) transcription factor (TF), E2A. Id1 can prevent E2A from forming heterodimers with bHLH TFs or from forming homodimers. Here, we show that overexpression of a forced E2A homodimer is sufficient to drive robust neural commitment in pluripotent cells, even under non-permissive conditions. Conversely, we find that E2A null cells display a defect in their neural differentiation capacity. E2A acts as an upstream activator of neural lineage genes, including Sox1 and Foxd4, and as a repressor of Nodal signalling. Our results suggest a crucial role for E2A in establishing neural lineage commitment in pluripotent cells.
    Keywords:  E2A; bHLH; neural development; pluripotent
    DOI:  https://doi.org/10.1242/dev.184093
  20. Nucleic Acids Res. 2020 Jun 01. pii: gkaa454. [Epub ahead of print]
    Regulatory sharing between estrogen receptor α bound enhancers.
    Julia B Carleton, Matthew Ginley-Hidinger, Kristofer C Berrett, Ryan M Layer, Aaron R Quinlan, Jason Gertz.
      The human genome encodes an order of magnitude more gene expression enhancers than promoters, suggesting that most genes are regulated by the combined action of multiple enhancers. We have previously shown that neighboring estrogen-responsive enhancers exhibit complex synergistic contributions to the production of an estrogenic transcriptional response. Here we sought to determine the molecular underpinnings of this enhancer cooperativity. We generated genetic deletions of four estrogen receptor α (ER) bound enhancers that regulate two genes and found that enhancers containing full estrogen response element (ERE) motifs control ER binding at neighboring sites, while enhancers with pre-existing histone acetylation/accessibility confer a permissible chromatin environment to the neighboring enhancers. Genome engineering revealed that two enhancers with half EREs could not compensate for the lack of a full ERE site within the cluster. In contrast, two enhancers with full EREs produced a transcriptional response greater than the wild-type locus. By swapping genomic sequences, we found that the genomic location of a full ERE strongly influences enhancer activity. Our results lead to a model in which a full ERE is required for ER recruitment, but the presence of a pre-existing permissible chromatin environment can also be needed for estrogen-driven gene regulation to occur.
    DOI:  https://doi.org/10.1093/nar/gkaa454
  21. Elife. 2020 Jun 05. pii: e57663. [Epub ahead of print]9
    Diverse nucleosome site-selectivity among histone deacetylase complexes.
    Zhipeng A Wang, Christopher J Millard, Chia-Liang Lin, Jennifer E Gurnett, Mingxuan Wu, Kwangwoon Lee, Louise Fairall, John W R Schwabe, Philip A Cole.
      Histone acetylation regulates chromatin structure and gene expression and is removed by histone deacetylases (HDACs). HDACs are commonly found in various protein complexes to confer distinct cellular functions, but how the multi-subunit complexes influence deacetylase activities and site-selectivities in chromatin is poorly understood. Previously we reported the results of studies on the HDAC1 containing CoREST complex and acetylated nucleosome substrates which revealed a notable preference for deacetylation of histone H3 acetyl-Lys9 vs. acetyl-Lys14 (M. Wu et al, 2018). Here we analyze the enzymatic properties of five class I HDAC complexes: CoREST, NuRD, Sin3B, MiDAC and SMRT with site-specific acetylated nucleosome substrates. Our results demonstrate that these HDAC complexes show a wide variety of deacetylase rates in a site-selective manner. A Gly13 in the histone H3 tail is responsible for a sharp reduction in deacetylase activity of the CoREST complex for H3K14ac. These studies provide a framework for connecting enzymatic and biological functions of specific HDAC complexes.
    Keywords:  biochemistry; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.57663
  22. Gut. 2020 Jun 05. pii: gutjnl-2020-321339. [Epub ahead of print]
    SETDB1 is required for intestinal epithelial differentiation and the prevention of intestinal inflammation.
    Lea Južnić, Kenneth Peuker, Anne Strigli, Mario Brosch, Alexander Herrmann, Robert Häsler, Michael Koch, Liz Matthiesen, Yvonne Zeissig, Britt-Sabina Löscher, Alexander Nuber, Gunnar Schotta, Volker Neumeister, Triantafyllos Chavakis, Thomas Kurth, Mathias Lesche, Andreas Dahl, Anne von Mässenhausen, Andreas Linkermann, Stefan Schreiber, Konrad Aden, Philip C Rosenstiel, Andre Franke, Jochen Hampe, Sebastian Zeissig.
       OBJECTIVE: The intestinal epithelium is a rapidly renewing tissue which plays central roles in nutrient uptake, barrier function and the prevention of intestinal inflammation. Control of epithelial differentiation is essential to these processes and is dependent on cell type-specific activity of transcription factors which bind to accessible chromatin. Here, we studied the role of SET Domain Bifurcated Histone Lysine Methyltransferase 1, also known as ESET (SETDB1), a histone H3K9 methyltransferase, in intestinal epithelial homeostasis and IBD.
    DESIGN: We investigated mice with constitutive and inducible intestinal epithelial deletion of Setdb1, studied the expression of SETDB1 in patients with IBD and mouse models of IBD, and investigated the abundance of SETDB1 variants in healthy individuals and patients with IBD.
    RESULTS: Deletion of intestinal epithelial Setdb1 in mice was associated with defects in intestinal epithelial differentiation, barrier disruption, inflammation and mortality. Mechanistic studies showed that loss of SETDB1 leads to de-silencing of endogenous retroviruses, DNA damage and intestinal epithelial cell death. Predicted loss-of-function variants in human SETDB1 were considerably less frequently observed than expected, consistent with a critical role of SETDB1 in human biology. While the vast majority of patients with IBD showed unimpaired mucosal SETDB1 expression, comparison of IBD and non-IBD exomes revealed over-representation of individual rare missense variants in SETDB1 in IBD, some of which are predicted to be associated with loss of function and may contribute to the pathogenesis of intestinal inflammation.
    CONCLUSION: SETDB1 plays an essential role in intestinal epithelial homeostasis. Future work is required to investigate whether rare variants in SETDB1 contribute to the pathogenesis of IBD.
    Keywords:  IBD; IBD - genetics; epithelial differentiation; gut inflammation; intestinal epithelium
    DOI:  https://doi.org/10.1136/gutjnl-2020-321339
  23. Elife. 2020 Jun 03. pii: e54341. [Epub ahead of print]9
    A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin.
    Gergana Shipkovenska, Alexander Durango, Marian Kalocsay, Steven P Gygi, Danesh Moazed.
      Heterochromatic domains containing histone H3 lysine 9 methylation (H3K9me) can be epigenetically inherited independently of underlying DNA sequence. To gain insight into the mechanisms that mediate epigenetic inheritance, we used a Schizosaccharomyces pombe inducible heterochromatin formation system to perform a genetic screen for mutations that abolish heterochromatin inheritance without affecting its establishment. We identified mutations in several pathways, including the conserved and essential Rix1-associated complex (henceforth the rixosome), which contains RNA endonuclease and polynucleotide kinase activities with known roles in ribosomal RNA processing. We show that the rixosome is required for spreading and epigenetic inheritance of heterochromatin in fission yeast. Viable rixosome mutations that disrupt its association with Swi6/HP1 fail to localize to heterochromatin, lead to accumulation of heterochromatic RNAs, and block spreading of H3K9me and silencing into actively transcribed regions. These findings reveal a new pathway for degradation of heterochromatic RNAs with essential roles in heterochromatin spreading and inheritance.
    Keywords:  H3K9 methylation; RNA degradation; Rix1; S. pombe; cell biology; chromosomes; epigenetics; gene expression; heterochromatin; rixosome
    DOI:  https://doi.org/10.7554/eLife.54341
  24. Sci Adv. 2020 Apr;6(16): eaay6515
    Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering.
    Mian Wei, Xiaoying Fan, Miao Ding, Ruifeng Li, Shipeng Shao, Yingping Hou, Shaoshuai Meng, Fuchou Tang, Cheng Li, Yujie Sun.
      Gene expression in response to stimuli underlies many fundamental processes. However, how transcription is regulated under these scenarios is largely unknown. Here, we find a previously unknown role of nuclear actin in transcriptional regulation. The RNA-seq data reveal that nuclear actin is required for the serum-induced transcriptional program. Using super-resolution imaging, we found a remarkable enhancement of RNA polymerase II (Pol II) clustering upon serum stimulation, and this enhancement requires nuclear actin. Pol II clusters colocalized with the serum-response genes and nuclear actin filaments upon serum stimulation. Furthermore, N-WASP is required for serum-enhanced Pol II clustering. N-WASP phase-separated with Pol II and nuclear actin. In addition to serum stimulation, nuclear actin also enhanced Pol II clustering upon interferon-γ treatment. Together, our work unveils that nuclear actin promotes the formation of transcription factory on inducible genes, acting as a general mechanism underlying the rapid response to environmental cues.
    DOI:  https://doi.org/10.1126/sciadv.aay6515
  25. Epigenetics Chromatin. 2020 Jun 01. 13(1): 25
    DAMEfinder: a method to detect differential allele-specific methylation.
    Stephany Orjuela, Dania Machlab, Mirco Menigatti, Giancarlo Marra, Mark D Robinson.
       BACKGROUND: DNA methylation is a highly studied epigenetic signature that is associated with regulation of gene expression, whereby genes with high levels of promoter methylation are generally repressed. Genomic imprinting occurs when one of the parental alleles is methylated, i.e., when there is inherited allele-specific methylation (ASM). A special case of imprinting occurs during X chromosome inactivation in females, where one of the two X chromosomes is silenced, to achieve dosage compensation between the sexes. Another more widespread form of ASM is sequence dependent (SD-ASM), where ASM is linked to a nearby heterozygous single nucleotide polymorphism (SNP).
    RESULTS: We developed a method to screen for genomic regions that exhibit loss or gain of ASM in samples from two conditions (treatments, diseases, etc.). The method relies on the availability of bisulfite sequencing data from multiple samples of the two conditions. We leverage other established computational methods to screen for these regions within a new R package called DAMEfinder. It calculates an ASM score for all CpG sites or pairs in the genome of each sample, and then quantifies the change in ASM between conditions. It then clusters nearby CpG sites with consistent change into regions. In the absence of SNP information, our method relies only on reads to quantify ASM. This novel ASM score compares favorably to current methods that also screen for ASM. Not only does it easily discern between imprinted and non-imprinted regions, but also females from males based on X chromosome inactivation. We also applied DAMEfinder to a colorectal cancer dataset and observed that colorectal cancer subtypes are distinguishable according to their ASM signature. We also re-discover known cases of loss of imprinting.
    CONCLUSION: We have designed DAMEfinder to detect regions of differential ASM (DAMEs), which is a more refined definition of differential methylation, and can therefore help in breaking down the complexity of DNA methylation and its influence in development and disease.
    Keywords:  Allele-specific methylation (ASM); DNA methylation; Differential methylation; Imprinting
    DOI:  https://doi.org/10.1186/s13072-020-00346-8
  26. Front Oncol. 2020 ;10 554
    Unresolved Complexity in the Gene Regulatory Network Underlying EMT.
    Deborah P Lavin, Vijay K Tiwari.
      Epithelial to mesenchymal transition (EMT) is the process whereby a polarized epithelial cell ceases to maintain cell-cell contacts, loses expression of characteristic epithelial cell markers, and acquires mesenchymal cell markers and properties such as motility, contractile ability, and invasiveness. A complex process that occurs during development and many disease states, EMT involves a plethora of transcription factors (TFs) and signaling pathways. Whilst great advances have been made in both our understanding of the progressive cell-fate changes during EMT and the gene regulatory networks that drive this process, there are still gaps in our knowledge. Epigenetic modifications are dynamic, chromatin modifying enzymes are vast and varied, transcription factors are pleiotropic, and signaling pathways are multifaceted and rarely act alone. Therefore, it is of great importance that we decipher and understand each intricate step of the process and how these players at different levels crosstalk with each other to successfully orchestrate EMT. A delicate balance and fine-tuned cooperation of gene regulatory mechanisms is required for EMT to occur successfully, and until we resolve the unknowns in this network, we cannot hope to develop effective therapies against diseases that involve aberrant EMT such as cancer. In this review, we focus on data that challenge these unknown entities underlying EMT, starting with EMT stimuli followed by intracellular signaling through to epigenetic mechanisms and chromatin remodeling.
    Keywords:  EMT; cancer; chromatin; epigenetics; gene regulation; signaling; transcription factors
    DOI:  https://doi.org/10.3389/fonc.2020.00554
  27. eNeuro. 2020 Jun 03. pii: ENEURO.0024-20.2020. [Epub ahead of print]
    A HIF1a-dependent pro-oxidant state disrupts synaptic plasticity and impairs spatial memory in response to intermittent hypoxia.
    Alejandra Arias-Cavieres, Maggie A Khuu, Chinwendu U Nwakudu, Jasmine E Barnard, Gokhan Dalgin, Alfredo J Garcia.
      Sleep apnea causes cognitive deficits and is associated with several neurologic diseases. Intermittent hypoxia (IH) is recognized as a principal mediator of pathophysiology associated with sleep apnea, yet the basis by which IH contributes to impaired cognition remains poorly defined. Using a mouse model exposed to IH, this study examines how the transcription factor, Hypoxia Inducible Factor 1a (HIF1a), contributes to disrupted synaptic physiology and spatial memory. In wildtype mice, impaired performance in the Barnes maze caused by IH coincided with a loss of NMDA receptor dependent Long Term Potentiation (LTP) in area CA1 and increased nuclear HIF1a within the hippocampus. IH-dependent HIF1a signaling caused a two-fold increase in expression of the reactive oxygen species generating enzyme NADPH oxidase 4 (NOX4). These changes promoted a pro-oxidant state and the downregulation of GLUN1 within the hippocampus. The IH-dependent effects were not present in either mice heterozygous for Hif1a (HIF1a+/-) or wild type mice treated with the antioxidant MnTMPyP. Our findings indicate that HIF1a dependent changes in redox state are central to the mechanism by which IH disrupts hippocampal synaptic plasticity and impairs spatial memory. This mechanism may enhance the vulnerability for cognitive deficit and lower the threshold for neurologic diseases associated untreated sleep apnea.Significance: Sleep apnea is associated with cognitive decline and neurological disease. Intermittent hypoxia, a hallmark consequence of sleep apnea, yet the mechanisms by which IH affects cognition is poorly understood. We show that a pro-oxidant state produced by HIF1a is a central factor causing IH-dependent impairment to spatial memory and synaptic plasticity. This work identifies potential targets for intervention in mitigating cognitive decline associated with sleep apnea.
    Keywords:  Hypoxia inducible facto; NADPH oxidas; NMDA recepto; Oxidative stres; sleep apnea
    DOI:  https://doi.org/10.1523/ENEURO.0024-20.2020
  28. Nature. 2020 May 06.
    RIC-seq for global in situ profiling of RNA-RNA spatial interactions.
    Zhaokui Cai, Changchang Cao, Lei Ji, Rong Ye, Di Wang, Cong Xia, Sui Wang, Zongchang Du, Naijing Hu, Xiaohua Yu, Juan Chen, Lei Wang, Xianguang Yang, Shunmin He, Yuanchao Xue.
      Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA-RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L-a super-enhancer hub RNA-interacts with the RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA.
    DOI:  https://doi.org/10.1038/s41586-020-2249-1
  29. Elife. 2020 Jun 04. pii: e58130. [Epub ahead of print]9
    Specialization of the chromatin remodeler RSC to mobilize partially-unwrapped nucleosomes.
    Alisha Schlichter, Margaret M Kasten, Timothy J Parnell, Bradley R Cairns.
      SWI/SNF-family chromatin remodeling complexes, such as S. cerevisiae RSC, slide and eject nucleosomes to regulate transcription. Within nucleosomes, stiff DNA sequences confer spontaneous partial unwrapping, prompting whether and how SWI/SNF-family remodelers are specialized to remodel partially-unwrapped nucleosomes. RSC1 and RSC2 are orthologs of mammalian PBRM1 (polybromo) which define two separate RSC sub-complexes. Remarkably, in vitro the Rsc1-containing complex remodels partially-unwrapped nucleosomes much better than does the Rsc2-containing complex. Moreover, a rsc1Δ mutation, but not rsc2Δ, is lethal with histone mutations that confer partial unwrapping. Rsc1/2 isoforms both cooperate with the DNA-binding proteins Rsc3/30 and the HMG protein, Hmo1, to remodel partially-unwrapped nucleosomes, but show differential reliance on these factors. Notably, genetic impairment of these factors strongly reduces the expression of genes with wide nucleosome-deficient regions (e.g. ribosomal protein genes), known to harbor partially-unwrapped nucleosomes. Taken together, Rsc1/2 isoforms are specialized through composition and interactions to manage and remodel partially-unwrapped nucleosomes.
    Keywords:  S. cerevisiae; biochemistry; chemical biology; chromosomes; gene expression
    DOI:  https://doi.org/10.7554/eLife.58130
  30. Sci Adv. 2020 Apr;6(16): eaaz0356
    PHF20L1 as a H3K27me2 reader coordinates with transcriptional repressors to promote breast tumorigenesis.
    Yongqiang Hou, Wei Liu, Xianfu Yi, Yang Yang, Dongxue Su, Wei Huang, Hefen Yu, Xu Teng, Ying Yang, Wei Feng, Tao Zhang, Jie Gao, Kai Zhang, Rongfang Qiu, Yan Wang.
      TUDOR domain-containing proteins (TDRDs) are chiefly responsible for recognizing methyl-lysine/arginine residue. However, how TDRD dysregulation contributes to breast tumorigenesis is poorly understood. Here, we report that TUDOR domain-containing PHF20L1 as a H3K27me2 reader exerts transcriptional repression by recruiting polycomb repressive complex 2 (PRC2) and Mi-2/nucleosome remodeling and deacetylase (NuRD) complex, linking PRC2-mediated methylation and NuRD-mediated deacetylation of H3K27. Furthermore, PHF20L1 was found to serve as a potential MYC and hypoxia-driven oncogene, promoting glycolysis, proliferation, and metastasis of breast cancer cells by directly inhibiting tumor suppressors such as HIC1, KISS1, and BRCA1. PHF20L1 expression was also strongly correlated with higher histologic grades of breast cancer and markedly up-regulated in several cancers. Meanwhile, Phf20l1 deletion not only induces growth retardation and mammary ductal outgrowth delay but also inhibits tumorigenesis in vivo. Our data indicate that PHF20L1 promotes tumorigenesis, supporting the pursuit of PHF20L1 as a target for cancer therapy.
    DOI:  https://doi.org/10.1126/sciadv.aaz0356
  31. Nat Commun. 2020 Jun 02. 11(1): 2742
    Loss of the transcription factor MAFB limits β-cell derivation from human PSCs.
    Ronan Russell, Phichitpol P Carnese, Thomas G Hennings, Emily M Walker, Holger A Russ, Jennifer S Liu, Simone Giacometti, Roland Stein, Matthias Hebrok.
      Next generation sequencing studies have highlighted discrepancies in β-cells which exist between mice and men. Numerous reports have identified MAF BZIP Transcription Factor B (MAFB) to be present in human β-cells postnatally, while its expression is restricted to embryonic and neo-natal β-cells in mice. Using CRISPR/Cas9-mediated gene editing, coupled with endocrine cell differentiation strategies, we dissect the contribution of MAFB to β-cell development and function specifically in humans. Here we report that MAFB knockout hPSCs have normal pancreatic differentiation capacity up to the progenitor stage, but favor somatostatin- and pancreatic polypeptide-positive cells at the expense of insulin- and glucagon-producing cells during endocrine cell development. Our results describe a requirement for MAFB late in the human pancreatic developmental program and identify it as a distinguishing transcription factor within islet cell subtype specification. We propose that hPSCs represent a powerful tool to model human pancreatic endocrine development and associated disease pathophysiology.
    DOI:  https://doi.org/10.1038/s41467-020-16550-9
  32. Epigenomics. 2020 Jun 04.
    Reproducibility-optimized detection of differential DNA methylation.
    Veronika Suni, Fatemeh Seyednasrollah, Bishwa Ghimire, Sini Junttila, Asta Laiho, Laura L Elo.
      Aim: DNA methylation is a key epigenetic mechanism regulating gene expression. Identifying differentially methylated regions is integral to DNA methylation analysis and there is a need for robust tools reliably detecting regions with significant differences in their methylation status. Materials & methods: We present here a reproducibility-optimized test statistic (ROTS) for detection of differential DNA methylation from high-throughput sequencing or array-based data. Results: Using both simulated and real data, we demonstrate the ability of ROTS to identify differential methylation between sample groups. Conclusion: Compared with state-of-the-art methods, ROTS shows competitive sensitivity and specificity in detecting consistently differentially methylated regions.
    Keywords:  DNA methylation; ROTS; differential methylation; reduced representation bisulfite sequencing; reproducibility
    DOI:  https://doi.org/10.2217/epi-2019-0289
  33. PLoS Genet. 2020 Jun 05. 16(6): e1008799
    BRM-SWI/SNF chromatin remodeling complex enables functional telomeres by promoting co-expression of TRF2 and TRF1.
    Shu Wu, Yuanlong Ge, Xiaocui Li, Yiding Yang, Haoxian Zhou, Kaixuan Lin, Zepeng Zhang, Yong Zhao.
      TRF2 and TRF1 are a key component in shelterin complex that associates with telomeric DNA and protects chromosome ends. BRM is a core ATPase subunit of SWI/SNF chromatin remodeling complex. Whether and how BRM-SWI/SNF complex is engaged in chromatin end protection by telomeres is unknown. Here, we report that depletion of BRM does not affect heterochromatin state of telomeres, but results in telomere dysfunctional phenomena including telomere uncapping and replication defect. Mechanistically, expression of TRF2 and TRF1 is jointly regulated by BRM-SWI/SNF complex, which is localized to promoter region of both genes and facilitates their transcription. BRM-deficient cells bear increased TRF2-free or TRF1-free telomeres due to insufficient expression. Importantly, BRM depletion-induced telomere uncapping or replication defect can be rescued by compensatory expression of exogenous TRF2 or TRF1, respectively. Together, these results identify a new function of BRM-SWI/SNF complex in enabling functional telomeres for maintaining genome stability.
    DOI:  https://doi.org/10.1371/journal.pgen.1008799
  34. Sci Rep. 2020 Jun 04. 10(1): 9126
    Enhancement of gene expression noise from transcription factor binding to genomic decoy sites.
    Supravat Dey, Mohammad Soltani, Abhyudai Singh.
      The genome contains several high-affinity non-functional binding sites for transcription factors (TFs) creating a hidden and unexplored layer of gene regulation. We investigate the role of such "decoy sites" in controlling noise (random fluctuations) in the level of a TF that is synthesized in stochastic bursts. Prior studies have assumed that decoy-bound TFs are protected from degradation, and in this case decoys function to buffer noise. Relaxing this assumption to consider arbitrary degradation rates for both bound/unbound TF states, we find rich noise behaviors. For low-affinity decoys, noise in the level of unbound TF always monotonically decreases to the Poisson limit with increasing decoy numbers. In contrast, for high-affinity decoys, noise levels first increase with increasing decoy numbers, before decreasing back to the Poisson limit. Interestingly, while protection of bound TFs from degradation slows the time-scale of fluctuations in the unbound TF levels, the decay of bound TFs leads to faster fluctuations and smaller noise propagation to downstream target proteins. In summary, our analysis reveals stochastic dynamics emerging from nonspecific binding of TFs and highlights the dual role of decoys as attenuators or amplifiers of gene expression noise depending on their binding affinity and stability of the bound TF.
    DOI:  https://doi.org/10.1038/s41598-020-65750-2
  35. Cancer Res. 2020 Jun 05. pii: canres.2373.2019. [Epub ahead of print]
    The EMT transcription factor ZEB2 promotes proliferation of primary and metastatic melanoma while suppressing an invasive, mesenchymal-like phenotype.
    Niels Vandamme, Geertrui Denecker, Kenneth Bruneel, Gillian Blancke, Özden Akay, Joachim Taminau, Jordy De Coninck, Eva De Smedt, Nicolas Skrypek, Wouter Van Loocke, Jasper Wouters, David Nittner, Corinna Köhler, Douglas S Darling, Phil F Cheng, Marieke I G Raaijmakers, Mitchell P Levesque, Udupi Girish Mallya, Mairin Rafferty, Balazs Balint, William M Gallagher, Lieve Brochez, Danny Huylebroeck, Jody J Haigh, Vanessa Andries, Florian Rambow, Pieter Van Vlierberghe, Steven Goossens, Joost J van den Oord, Jean-Christophe Marine, Geert Berx.
      EMT-inducing transcription factors (TF) are well known for their ability to induce mesenchymal states associated with increased migratory and invasive properties. Unexpectedly, nuclear expression of the EMT-TF ZEB2 in human primary melanoma has been shown to correlate with reduced invasion. We report here that ZEB2 is required for outgrowth for primary melanomas and metastases at secondary sites. Ablation of Zeb2 hampered outgrowth of primary melanomas in vivo, whereas ectopic expression enhanced proliferation and growth at both primary and secondary sites. Gain of Zeb2 expression in pulmonary-residing melanoma cells promoted the development of macroscopic lesions. In vivo fate mapping made clear that melanoma cells undergo a conversion in state where ZEB2 expression is replaced by ZEB1 expression associated with gain of an invasive phenotype. These findings suggest that reversible switching of the ZEB2/ZEB1 ratio enhances melanoma metastatic dissemination.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-19-2373
  36. Nature. 2020 May 20.
    poly(UG)-tailed RNAs in genome protection and epigenetic inheritance.
    Aditi Shukla, Jenny Yan, Daniel J Pagano, Anne E Dodson, Yuhan Fei, Josh Gorham, J G Seidman, Marvin Wickens, Scott Kennedy.
      Mobile genetic elements threaten genome integrity in all organisms. RDE-3 (also known as MUT-2) is a ribonucleotidyltransferase that is required for transposon silencing and RNA interference in Caenorhabditis elegans1-4. When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3' termini of these RNAs (designated poly(UG) or pUG tails)5. Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNA interference, as well as to transposon RNAs. RNA fragments attached to pUG tails with more than 16 perfectly alternating 3' U and G nucleotides become gene-silencing agents. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases, which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA-templated siRNA synthesis and siRNA-directed pUG RNA biogenesis underlie double-stranded-RNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA-siRNA silencing loop enables parents to inoculate progeny against the expression of unwanted or parasitic genetic elements.
    DOI:  https://doi.org/10.1038/s41586-020-2323-8
  37. Proc Natl Acad Sci U S A. 2020 Jun 01. pii: 201919507. [Epub ahead of print]
    MYC protein stability is negatively regulated by BRD4.
    Ballachanda N Devaiah, Jie Mu, Ben Akman, Sheetal Uppal, Jocelyn D Weissman, Dan Cheng, Laura Baranello, Zuqin Nie, David Levens, Dinah S Singer.
      The protooncogene MYC regulates a variety of cellular processes, including proliferation and metabolism. Maintaining MYC at homeostatic levels is critical to normal cell function; overexpression drives many cancers. MYC stability is regulated through phosphorylation: phosphorylation at Thr58 signals degradation while Ser62 phosphorylation leads to its stabilization and functional activation. The bromodomain protein 4 (BRD4) is a transcriptional and epigenetic regulator with intrinsic kinase and histone acetyltransferase (HAT) activities that activates transcription of key protooncogenes, including MYC We report that BRD4 phosphorylates MYC at Thr58, leading to MYC ubiquitination and degradation, thereby regulating MYC target genes. Importantly, BRD4 degradation, but not inhibition, results in increased levels of MYC protein. Conversely, MYC inhibits BRD4's HAT activity, suggesting that MYC regulates its own transcription by limiting BRD4-mediated chromatin remodeling of its locus. The MYC stabilizing kinase, ERK1, regulates MYC levels directly and indirectly by inhibiting BRD4 kinase activity. These findings demonstrate that BRD4 negatively regulates MYC levels, which is counteracted by ERK1 activation.
    Keywords:  BRD4 histone acetyltransferase; BRD4 kinase; ERK1; MYC phosphorylation; MYC stability
    DOI:  https://doi.org/10.1073/pnas.1919507117
  38. Nucleic Acids Res. 2020 Jun 04. pii: gkaa420. [Epub ahead of print]
    SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update).
    Jorge Oscanoa, Lavanya Sivapalan, Emanuela Gadaleta, Abu Z Dayem Ullah, Nicholas R Lemoine, Claude Chelala.
      SNPnexus is a web-based annotation tool for the analysis and interpretation of both known and novel sequencing variations. Since its last release, SNPnexus has received continual updates to expand the range and depth of annotations provided. SNPnexus has undergone a complete overhaul of the underlying infrastructure to accommodate faster computational times. The scope for data annotation has been substantially expanded to enhance biological interpretations of queried variants. This includes the addition of pathway analysis for the identification of enriched biological pathways and molecular processes. We have further expanded the range of user directed annotation fields available for the study of cancer sequencing data. These new additions facilitate investigations into cancer driver variants and targetable molecular alterations within input datasets. New user directed filtering options have been coupled with the addition of interactive graphical and visualization tools. These improvements streamline the analysis of variants derived from large sequencing datasets for the identification of biologically and clinically significant subsets in the data. SNPnexus is the most comprehensible web-based application currently available and these new set of updates ensures that it remains a state-of-the-art tool for researchers. SNPnexus is freely available at https://www.snp-nexus.org.
    DOI:  https://doi.org/10.1093/nar/gkaa420
  39. Nature. 2020 Jun 03.
    Oncometabolites suppress DNA repair by disrupting local chromatin signalling.
    Parker L Sulkowski, Sebastian Oeck, Jonathan Dow, Nicholas G Economos, Lily Mirfakhraie, Yanfeng Liu, Katelyn Noronha, Xun Bao, Jing Li, Brian M Shuch, Megan C King, Ranjit S Bindra, Peter M Glazer.
      Deregulation of metabolism and disruption of genome integrity are hallmarks of cancer1. Increased levels of the metabolites 2-hydroxyglutarate, succinate and fumarate occur in human malignancies owing to somatic mutations in the isocitrate dehydrogenase-1 or -2 (IDH1 or IDH2) genes, or germline mutations in the fumarate hydratase (FH) and succinate dehydrogenase genes (SDHA, SDHB, SDHC and SDHD), respectively2-4. Recent work has made an unexpected connection between these metabolites and DNA repair by showing that they suppress the pathway of homology-dependent repair (HDR)5,6 and confer an exquisite sensitivity to inhibitors of poly (ADP-ribose) polymerase (PARP) that are being tested in clinical trials. However, the mechanism by which these oncometabolites inhibit HDR remains poorly understood. Here we determine the pathway by which these metabolites disrupt DNA repair. We show that oncometabolite-induced inhibition of the lysine demethylase KDM4B results in aberrant hypermethylation of histone 3 lysine 9 (H3K9) at loci surrounding DNA breaks, masking a local H3K9 trimethylation signal that is essential for the proper execution of HDR. Consequently, recruitment of TIP60 and ATM, two key proximal HDR factors, is substantially impaired at DNA breaks, with reduced end resection and diminished recruitment of downstream repair factors. These findings provide a mechanistic basis for oncometabolite-induced HDR suppression and may guide effective strategies to exploit these defects for therapeutic gain.
    DOI:  https://doi.org/10.1038/s41586-020-2363-0
  40. Nat Commun. 2020 Jun 05. 11(1): 2860
    MYC functions as a switch for natural killer cell-mediated immune surveillance of lymphoid malignancies.
    Srividya Swaminathan, Aida S Hansen, Line D Heftdal, Renumathy Dhanasekaran, Anja Deutzmann, Wadie D M Fernandez, Daniel F Liefwalker, Crista Horton, Adriane Mosley, Mariola Liebersbach, Holden T Maecker, Dean W Felsher.
      The MYC oncogene drives T- and B- lymphoid malignancies, including Burkitt's lymphoma (BL) and Acute Lymphoblastic Leukemia (ALL). Here, we demonstrate a systemic reduction in natural killer (NK) cell numbers in SRα-tTA/Tet-O-MYCON mice bearing MYC-driven T-lymphomas. Residual mNK cells in spleens of MYCON T-lymphoma-bearing mice exhibit perturbations in the terminal NK effector differentiation pathway. Lymphoma-intrinsic MYC arrests NK maturation by transcriptionally repressing STAT1/2 and secretion of Type I Interferons (IFNs). Treating T-lymphoma-bearing mice with Type I IFN improves survival by rescuing NK cell maturation. Adoptive transfer of mature NK cells is sufficient to delay both T-lymphoma growth and recurrence post MYC inactivation. In MYC-driven BL patients, low expression of both STAT1 and STAT2 correlates significantly with the absence of activated NK cells and predicts unfavorable clinical outcomes. Our studies thus provide a rationale for developing NK cell-based therapies to effectively treat MYC-driven lymphomas in the future.
    DOI:  https://doi.org/10.1038/s41467-020-16447-7
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