bims-crepig 2021-08-22 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2021‒08‒22
thirty-five papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution.
Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes.
Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation.
Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations.
Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells.
Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences.
CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes.
Chromatin accessibility profiling identifies evolutionary conserved loci in activated human satellite cells.
A simple and robust method for simultaneous dual-omics profiling with limited numbers of cells.
Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4.
Genome-Wide Enhancer Analysis Reveals the Role of AP-1 Transcription Factor in Head and Neck Squamous Cell Carcinoma.
A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination.
Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma.
Tet2 Controls the Responses of β cells to Inflammation in Autoimmune Diabetes.
Lineages of embryonic stem cells show non-Markovian state transitions.
Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome length and individualization.
The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency.
An in vitro stem cell model of human epiblast and yolk sac interaction.
CoCoA-diff: counterfactual inference for single-cell gene expression analysis.
Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons.
Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network.
Two secured FACT recruitment mechanisms are essential for heterochromatin maintenance.
Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization.
A unified model of human hemoglobin switching through single-cell genome editing.
Nhp2 is a reader of H2AQ105me and part of a network integrating metabolism with rRNA synthesis.
De novo DNA methyltransferases DNMT3A and DNMT3B are essential for XIST silencing for erosion of dosage compensation in pluripotent stem cells.
NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1.
Bedshift: perturbation of genomic interval sets.
DMRT1-mediated reprogramming drives development of cancer resembling human germ cell tumors with features of totipotency.
ESA1 regulates meiotic chromosome axis and crossover frequency via acetylating histone H4.
The histone chaperone Anp32e regulates memory formation, transcription, and dendritic morphology by regulating steady-state H2A.Z binding in neurons.
Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development.
CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis.
LineageOT is a unified framework for lineage tracing and trajectory inference.
Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index.

Cell. 2021 Aug 11. pii: S0092-8674(21)00942-9. [Epub ahead of print]

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution.

Alexandro E Trevino, Fabian Müller, Jimena Andersen, Laksshman Sundaram, Arwa Kathiria, Anna Shcherbina, Kyle Farh, Howard Y Chang, Anca M Pașca, Anshul Kundaje, Sergiu P Pașca, William J Greenleaf.

  Genetic perturbations of cortical development can lead to neurodevelopmental disease, including autism spectrum disorder (ASD). To identify genomic regions crucial to corticogenesis, we mapped the activity of gene-regulatory elements generating a single-cell atlas of gene expression and chromatin accessibility both independently and jointly. This revealed waves of gene regulation by key transcription factors (TFs) across a nearly continuous differentiation trajectory, distinguished the expression programs of glial lineages, and identified lineage-determining TFs that exhibited strong correlation between linked gene-regulatory elements and expression levels. These highly connected genes adopted an active chromatin state in early differentiating cells, consistent with lineage commitment. Base-pair-resolution neural network models identified strong cell-type-specific enrichment of noncoding mutations predicted to be disruptive in a cohort of ASD individuals and identified frequently disrupted TF binding sites. This approach illustrates how cell-type-specific mapping can provide insights into the programs governing human development and disease.

Keywords:  autism spectrum disoder; development; human cerebral cortex; multiome; single-cell ATAC-seq; single-cell RNA-seq

DOI:  https://doi.org/10.1016/j.cell.2021.07.039
Nat Commun. 2021 Aug 20. 12(1): 4800

Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes.

Muhammad Shoaib, Qinming Chen, Xiangyan Shi, Nidhi Nair, Chinmayi Prasanna, Renliang Yang, David Walter, Klaus S Frederiksen, Hjorleifur Einarsson, J Peter Svensson, Chuan Fa Liu, Karl Ekwall, Mads Lerdrup, Lars Nordenskiöld, Claus S Sørensen.

Histone lysine methylations have primarily been linked to selective recruitment of reader or effector proteins that subsequently modify chromatin regions and mediate genome functions. Here, we describe a divergent role for histone H4 lysine 20 mono-methylation (H4K20me1) and demonstrate that it directly facilitates chromatin openness and accessibility by disrupting chromatin folding. Thus, accumulation of H4K20me1 demarcates highly accessible chromatin at genes, and this is maintained throughout the cell cycle. In vitro, H4K20me1-containing nucleosomal arrays with nucleosome repeat lengths (NRL) of 187 and 197 are less compact than unmethylated (H4K20me0) or trimethylated (H4K20me3) arrays. Concordantly, and in contrast to trimethylated and unmethylated tails, solid-state NMR data shows that H4K20 mono-methylation changes the H4 conformational state and leads to more dynamic histone H4-tails. Notably, the increased chromatin accessibility mediated by H4K20me1 facilitates gene expression, particularly of housekeeping genes. Altogether, we show how the methylation state of a single histone H4 residue operates as a focal point in chromatin structure control. While H4K20me1 directly promotes chromatin openness at highly transcribed genes, it also serves as a stepping-stone for H4K20me3-dependent chromatin compaction.

DOI: https://doi.org/10.1038/s41467-021-25051-2
Nucleic Acids Res. 2021 Aug 17. pii: gkab697. [Epub ahead of print]

Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation.

Athena Sklias, Andrea Halaburkova, Ludovica Vanzan, Nora Fernandez Jimenez, Cyrille Cuenin, Liacine Bouaoun, Vincent Cahais, Victor Ythier, Aurélie Sallé, Claire Renard, Geoffroy Durand, Florence Le Calvez-Kelm, Rita Khoueiry, Rabih Murr, Zdenko Herceg.

Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. These interactions take place in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.

DOI: https://doi.org/10.1093/nar/gkab697
Nat Commun. 2021 08 18. 12(1): 5013

Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations.

Christopher Chase Bolt, Lucille Lopez-Delisle, Bénédicte Mascrez, Denis Duboule.

Human families with chromosomal rearrangements at 2q31, where the human HOXD locus maps, display mesomelic dysplasia, a severe shortening and bending of the limb. In mice, the dominant Ulnaless inversion of the HoxD cluster produces a similar phenotype suggesting the same origin for these malformations in humans and mice. Here we engineer 1 Mb inversion including the HoxD gene cluster, which positioned Hoxd13 close to proximal limb enhancers. Using this model, we show that these enhancers contact and activate Hoxd13 in proximal cells, inducing the formation of mesomelic dysplasia. We show that a secondary Hoxd13 null mutation in-cis with the inversion completely rescues the alterations, demonstrating that ectopic HOXD13 is directly responsible for this bone anomaly. Single-cell expression analysis and evaluation of HOXD13 binding sites suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.

DOI: https://doi.org/10.1038/s41467-021-25330-y
Genes Dev. 2021 Aug 19.

Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells.

Masaki Yagi, Fei Ji, Jocelyn Charlton, Simona Cristea, Kathleen Messemer, Naftali Horwitz, Bruno Di Stefano, Nikolaos Tsopoulidis, Michael S Hoetker, Aaron J Huebner, Ori Bar-Nur, Albert E Almada, Masakazu Yamamoto, Anthony Patelunas, David J Goldhamer, Amy J Wagers, Franziska Michor, Alexander Meissner, Ruslan I Sadreyev, Konrad Hochedlinger.

  The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of transcription factor-induced reprogramming. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced myogenic progenitor cells (iMPCs). Here, we dissected the transcriptional and epigenetic dynamics of mouse fibroblasts undergoing reprogramming to either myotubes or iMPCs using a MyoD-inducible transgenic model. Induction of MyoD in fibroblasts combined with small molecules generated Pax7+ iMPCs with high similarity to primary muscle stem cells. Analysis of intermediate stages of iMPC induction revealed that extinction of the fibroblast program preceded induction of the stem cell program. Moreover, key stem cell genes gained chromatin accessibility prior to their transcriptional activation, and these regions exhibited a marked loss of DNA methylation dependent on the Tet enzymes. In contrast, myotube generation was associated with few methylation changes, incomplete and unstable reprogramming, and an insensitivity to Tet depletion. Finally, we showed that MyoD's ability to bind to unique bHLH targets was crucial for generating iMPCs but dispensable for generating myotubes. Collectively, our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity.

Keywords:  DNA methylation; MyoD; dedifferentiation; epigenetic reprogramming; induced myogenic progenitor cells (iMPCs); satellite cells; transdifferentiation

DOI:  https://doi.org/10.1101/gad.348678.121
Genome Biol. 2021 Aug 16. 22(1): 226

Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences.

Fan Cao, Yu Zhang, Yichao Cai, Sambhavi Animesh, Ying Zhang, Semih Can Akincilar, Yan Ping Loh, Xinya Li, Wee Joo Chng, Vinay Tergaonkar, Chee Keong Kwoh, Melissa J Fullwood.

  Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interaction neural network (ChINN), to predict chromatin interactions between open chromatin regions using only DNA sequences. ChINN predicts CTCF- and RNA polymerase II-associated and Hi-C chromatin interactions. ChINN shows good across-sample performances and captures various sequence features for chromatin interaction prediction. We apply ChINN to 6 chronic lymphocytic leukemia (CLL) patient samples and a published cohort of 84 CLL open chromatin samples. Our results demonstrate extensive heterogeneity in chromatin interactions among CLL patient samples.

Keywords:  3D genome organization; Bioinformatics; ChIA-PET; Chromatin interactions; DNA sequence; Hi-C; Leukemia; Machine learning

DOI:  https://doi.org/10.1186/s13059-021-02453-5
BMC Bioinformatics. 2021 Aug 17. 22(1): 407

CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes.

Lélia Polit, Gwenneg Kerdivel, Sebastian Gregoricchio, Michela Esposito, Christel Guillouf, Valentina Boeva.

  BACKGROUND: Multiple studies rely on ChIP-seq experiments to assess the effect of gene modulation and drug treatments on protein binding and chromatin structure. However, most methods commonly used for the normalization of ChIP-seq binding intensity signals across conditions, e.g., the normalization to the same number of reads, either assume a constant signal-to-noise ratio across conditions or base the estimates of correction factors on genomic regions with intrinsically different signals between conditions. Inaccurate normalization of ChIP-seq signal may, in turn, lead to erroneous biological conclusions.RESULTS: We developed a new R package, CHIPIN, that allows normalizing ChIP-seq signals across different conditions/samples when spike-in information is not available, but gene expression data are at hand. Our normalization technique is based on the assumption that, on average, no differences in ChIP-seq signals should be observed in the regulatory regions of genes whose expression levels are constant across samples/conditions. In addition to normalizing ChIP-seq signals, CHIPIN provides as output a number of graphs and calculates statistics allowing the user to assess the efficiency of the normalization and qualify the specificity of the antibody used. In addition to ChIP-seq, CHIPIN can be used without restriction on open chromatin ATAC-seq or DNase hypersensitivity data. We validated the CHIPIN method on several ChIP-seq data sets and documented its superior performance in comparison to several commonly used normalization techniques.
CONCLUSIONS: The CHIPIN method provides a new way for ChIP-seq signal normalization across conditions when spike-in experiments are not available. The method is implemented in a user-friendly R package available on GitHub: https://github.com/BoevaLab/CHIPIN.

Keywords:  Algorithm; ChIP-seq; Density profiles; Gene expression; Normalization; Open chromatin; R package

DOI:  https://doi.org/10.1186/s12859-021-04320-3
Stem Cell Res. 2021 Aug 11. pii: S1873-5061(21)00343-3. [Epub ahead of print]55 102496

Chromatin accessibility profiling identifies evolutionary conserved loci in activated human satellite cells.

Lisa S Chow, Darko Bosnakovski, Douglas G Mashek, Michael Kyba, Rita C R Perlingeiro, Alessandro Magli.

  Satellite cells represent the main myogenic population accounting for skeletal muscle homeostasis and regeneration. While our knowledge of the signaling pathways controlling satellite cell regenerative capability is increasing, the underlying epigenetic mechanisms are still not clear, especially in the case of human satellite cells. Here, by performing chromatin accessibility profiling (ATAC-seq) in samples isolated from human and murine muscles, we investigated the changes in the epigenetic landscape occurring during the transition from activated satellite cells to myoblasts. Our analysis identifies a compendium of putative regulatory elements defining human activated satellite cells and myoblasts, respectively. A subset of these differentially accessible loci is shared by both murine and human satellite cells, includes elements associated with known self-renewal regulators, and is enriched for motifs bound by transcription factors participating in satellite cell regulation. Integration of transcriptional and epigenetic data reveals that known regulators of metabolic gene expression, such as PPARGC1A, represent potential PAX7 targets. Through characterization of genomic networks and the underlying effectors, our data represent an important starting point for decoding and manipulating the molecular mechanisms underlying human satellite cell muscle regenerative potential.

Keywords:  ATAC-seq; Human satellite cell; Muscle stem cell; PGC1 alpha; Pax7; Regulatory element

DOI:  https://doi.org/10.1016/j.scr.2021.102496
Cell Rep Methods. 2021 Jul 26. pii: 100041. [Epub ahead of print]1(3):

A simple and robust method for simultaneous dual-omics profiling with limited numbers of cells.

Ruifang Li, Sara A Grimm, Paul A Wade.

Deciphering epigenetic regulation of gene expression requires measuring the epigenome and transcriptome jointly. Single-cell multi-omics technologies have been developed for concurrent profiling of chromatin accessibility and gene expression. However, multi-omics profiling of low-input bulk samples remains challenging. Therefore, we developed low-input ATAC&mRNA-seq, a simple and robust method for studying the role of chromatin structure in gene regulation in a single experiment with thousands of cells, to maximize insights from limited input material by obtaining ATAC-seq and mRNA-seq data simultaneously from the same cells with data quality comparable to that of conventional mono-omics assays. Integrative data analysis revealed similar strong association between promoter accessibility and gene expression when using the data of low-input ATAC&mRNA-seq as when using single-assay data, underscoring the accuracy and reliability of our dual-omics assay to generate both datum types simultaneously with just thousands of cells. We envision our method to be widely applied in many biological disciplines with limited materials.

DOI: https://doi.org/10.1016/j.crmeth.2021.100041
Nat Commun. 2021 Aug 20. 12(1): 5056

Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4.

Johanna Diener, Arianna Baggiolini, Mattias Pernebrink, Damian Dalcher, Luigi Lerra, Phil F Cheng, Sandra Varum, Jessica Häusel, Salome Stierli, Mathias Treier, Lorenz Studer, Konrad Basler, Mitchell P Levesque, Reinhard Dummer, Raffaella Santoro, Claudio Cantù, Lukas Sommer.

Melanoma cells rely on developmental programs during tumor initiation and progression. Here we show that the embryonic stem cell (ESC) factor Sall4 is re-expressed in the Tyr::NrasQ61K; Cdkn2a-/- melanoma model and that its expression is necessary for primary melanoma formation. Surprisingly, while Sall4 loss prevents tumor formation, it promotes micrometastases to distant organs in this melanoma-prone mouse model. Transcriptional profiling and in vitro assays using human melanoma cells demonstrate that SALL4 loss induces a phenotype switch and the acquisition of an invasive phenotype. We show that SALL4 negatively regulates invasiveness through interaction with the histone deacetylase (HDAC) 2 and direct co-binding to a set of invasiveness genes. Consequently, SALL4 knock down, as well as HDAC inhibition, promote the expression of an invasive signature, while inhibition of histone acetylation partially reverts the invasiveness program induced by SALL4 loss. Thus, SALL4 appears to regulate phenotype switching in melanoma through an HDAC2-mediated mechanism.

DOI: https://doi.org/10.1038/s41467-021-25326-8
Front Mol Biosci. 2021 ;8 701531

Genome-Wide Enhancer Analysis Reveals the Role of AP-1 Transcription Factor in Head and Neck Squamous Cell Carcinoma.

Chen-Yu Wang, Guang-Tao Yu, Chuan Gao, Ji Chen, Qing-Lan Li, Lu Zhang, Min Wu, Zhi-Jun Sun, Lian-Yun Li.

  Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in the world, but its epigenomic features have not been determined. Here, we studied the chromatin landscape of active enhancers of HNSCC head tumor tissues by performing H3K27ac and H3K4me1 ChIP-Seq with a Tgfbr1/Pten double conditional knockout HNSCC mouse model. We identified 1,248 gain variant enhancer loci (VELs) and 2,188 lost VELs, as well as 153 gain variant super enhancer loci (VSELs) and 234 lost VSELs. Potentially involved transcription factors were predicted with motif analysis, and we identified AP-1 as one of the critical oncogenic transcription factors in HNSCC and many other types of cancer. Combining transcriptomic and epigenomic data, our analysis also showed that AP-1 and histone modifications coordinately regulate target gene expression in HNSCC. In conclusion, our study provides important epigenomic information for enhancer studies in HNSCC and reveals new mechanism for AP-1 regulating HNSCC.

Keywords:  AP-1; H3K27ac; H3K4me1; HNSCC; enhancer

DOI:  https://doi.org/10.3389/fmolb.2021.701531
Genome Res. 2021 Aug 18. pii: gr.275368.121. [Epub ahead of print]

A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination.

Desislava P Staneva, Roberta Carloni, Tatsiana Auchynnikava, Pin Tong, Jeyaprakash A Arulanandam, Juri Rappsilber, Keith R Matthews, Robin C Allshire.

Nucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by 'writer' and 'eraser' enzymes, respectively. Nucleosomal PTMs are recognised by a variety of 'reader' proteins which alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 65 predicted readers, writers and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 60 of them in the parasite's bloodstream form. ChIP-seq demonstrated that fifteen candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins exhibit a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identified distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Several SET-domain and Bromo-domain protein networks suggest parallels to RNAPII promoter-associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcriptional start regions. The systematic approach employed provides detail of the composition and organization of the chromatin regulatory machinery in Trypanosoma brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.

DOI: https://doi.org/10.1101/gr.275368.121
Genome Med. 2021 Aug 16. 13(1): 130

Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma.

Hemant Gujar, Arjun Mehta, Hong-Tao Li, Yvonne C Tsai, Xiangning Qiu, Daniel J Weisenberger, Miriam Galvonas Jasiulionis, Gino K In, Gangning Liang.

  BACKGROUND: Merkel cell carcinoma (MCC) is a rare but aggressive skin cancer with limited treatment possibilities. Merkel cell tumors display with neuroendocrine features and Merkel cell polyomavirus (MCPyV) infection in the majority (80%) of patients. Although loss of histone H3 lysine 27 trimethylation (H3K27me3) has been shown during MCC tumorigenesis, epigenetic dysregulation has largely been overlooked.METHODS: We conducted global DNA methylation profiling of clinically annotated MCC primary tumors, metastatic skin tumors, metastatic lymph node tumors, paired normal tissues, and two human MCC cell lines using the Illumina Infinium EPIC DNA methylation BeadArray platform.
RESULTS: Significant differential DNA methylation patterns across the genome are revealed between the four tissue types, as well as based on MCPyV status. Furthermore, 964 genes directly regulated by promoter or gene body DNA methylation were identified with high enrichment in neuro-related pathways. Finally, our findings suggest that loss of H3K27me3 occupancy in MCC is attributed to KDM6B and EZHIP overexpression as a consequence of promoter DNA hypomethylation.
CONCLUSIONS: We have demonstrated specific DNA methylation patterns for primary MCC tumors, metastatic MCCs, and adjacent-normal tissues. We have also identified DNA methylation markers that not only show potential diagnostic or prognostic utility in MCC management, but also correlate with MCC tumorigenesis, MCPyV expression, neuroendocrine features, and H3K27me3 status. The identification of DNA methylation alterations in MCC supports the need for further studies to understand the clinical implications of epigenetic dysregulation and potential therapeutic targets in MCC.

Keywords:  DNA methylation marker; EZHIP; Epigenetic driver; Epigenetic therapy; H3K27me3; KDM6B; MCC; MCPyV; Neuroendocrine; PD1; PDL1

DOI:  https://doi.org/10.1186/s13073-021-00946-3
Nat Commun. 2021 Aug 20. 12(1): 5074

Tet2 Controls the Responses of β cells to Inflammation in Autoimmune Diabetes.

Jinxiu Rui, Songyan Deng, Ana Luisa Perdigoto, Gerald Ponath, Romy Kursawe, Nathan Lawlor, Tomokazu Sumida, Maya Levine-Ritterman, Michael L Stitzel, David Pitt, Jun Lu, Kevan C Herold.

β cells may participate and contribute to their own demise during Type 1 diabetes (T1D). Here we report a role of their expression of Tet2 in regulating immune killing. Tet2 is induced in murine and human β cells with inflammation but its expression is reduced in surviving β cells. Tet2-KO mice that receive WT bone marrow transplants develop insulitis but not diabetes and islet infiltrates do not eliminate β cells even though immune cells from the mice can transfer diabetes to NOD/scid recipients. Tet2-KO recipients are protected from transfer of disease by diabetogenic immune cells.Tet2-KO β cells show reduced expression of IFNγ-induced inflammatory genes that are needed to activate diabetogenic T cells. Here we show that Tet2 regulates pathologic interactions between β cells and immune cells and controls damaging inflammatory pathways. Our data suggests that eliminating TET2 in β cells may reduce activating pathologic immune cells and killing of β cells.

DOI: https://doi.org/10.1038/s41467-021-25367-z
iScience. 2021 Aug 20. 24(8): 102879

Lineages of embryonic stem cells show non-Markovian state transitions.

Tee Udomlumleart, Sofia Hu, Salil Garg.

  Pluripotent embryonic stem cells (ESCs) constitute the cell types of the adult vertebrate through a series of developmental state transitions. These states can be defined by expression levels of marker genes, such as Nanog and Sox2. In culture, ESCs reversibly transition between states. However, whether ESCs retain memory of their previous states or transition in a memoryless (Markovian) process remains relatively unknown. Here, we show some highly dynamic lineages of ESCs do not exhibit the Markovian property: their previous states and kin relations influence future choices. Unexpectedly, the distribution of lineages across their composition between states is constant over time, contrasting with the predictions of a Markov model. Additionally, highly dynamic ESC lineages show skewed cell fate distributions after retinoic acid differentiation. Together, these data suggest ESC lineage is an important variable governing future cell states, with implications for stem cell function and development.

Keywords:  Cell biology; Developmental biology; Embryology; Stem cells research; Systems and computational biology

DOI:  https://doi.org/10.1016/j.isci.2021.102879
Elife. 2021 Aug 18. pii: e68918. [Epub ahead of print]10

Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome length and individualization.

Pavan Choppakatla, Bastiaan Dekker, Erin E Cutts, Alessandro Vannini, Job Dekker, Hironori Funabiki.

  DNA loop extrusion by condensins and decatenation by DNA topoisomerase II (topo II) are thought to drive mitotic chromosome compaction and individualization. Here, we reveal that the linker histone H1.8 antagonizes condensins and topo II to shape mitotic chromosome organization. In vitro chromatin reconstitution experiments demonstrate that H1.8 inhibits binding of condensins and topo II to nucleosome arrays. Accordingly, H1.8 depletion in Xenopus egg extracts increased condensins and topo II levels on mitotic chromatin. Chromosome morphology and Hi-C analyses suggest that H1.8 depletion makes chromosomes thinner and longer through shortening the average loop size and reducing the DNA amount in each layer of mitotic loops. Furthermore, excess loading of condensins and topo II to chromosomes by H1.8 depletion causes hyper-chromosome individualization and dispersion. We propose that condensins and topo II are essential for chromosome individualization, but their functions are tuned by the linker histone to keep chromosomes together until anaphase.

Keywords:  chromosomes; gene expression; xenopus

DOI:  https://doi.org/10.7554/eLife.68918
Development. 2021 Aug 16. pii: dev.199604. [Epub ahead of print]

The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency.

Nicola Festuccia, Nick Owens, Almira Chervova, Agnès Dubois, Pablo Navarro.

  The maintenance of pluripotency in mouse embryonic stem cells (ESCs) is governed by the action of an interconnected network of transcription factors. Among them, only Oct4 and Sox2 have been shown to be strictly required for the self-renewal of ESCs and pluripotency, particularly in culture conditions where differentiation cues are chemically inhibited. Here, we report that the conjunct activity of two orphan nuclear receptors, Esrrb and Nr5a2, parallels the importance of that of Oct4 and Sox2 in naïve ESCs. By occupying a large common set of regulatory elements, these two factors control the binding of Oct4, Sox2 and Nanog to DNA. Consequently, in their absence the pluripotency network collapses and the transcriptome is substantially deregulated, leading to the differentiation of ESCs. Altogether, this work identifies orphan nuclear receptors, previously thought to be performing supportive functions, as a new set of core regulators of naïve pluripotency.

Keywords:  Embryonic Stem Cells; Esrrb; Nr5a2; Orphan nuclear receptors; Pluripotency

DOI:  https://doi.org/10.1242/dev.199604
Elife. 2021 Aug 17. pii: e63930. [Epub ahead of print]10

An in vitro stem cell model of human epiblast and yolk sac interaction.

Kirsty Ml Mackinlay, Bailey At Weatherbee, Viviane Souza Rosa, Charlotte E Handford, George Hudson, Tim Coorens, Lygia V Pereira, Sam Behjati, Ludovic Vallier, Marta N Shahbazi, Magdalena Zernicka-Goetz.

  Human embryogenesis entails complex signalling interactions between embryonic and extra-embryonic cells. However, how extra-embryonic cells direct morphogenesis within the human embryo remains largely unknown due to a lack of relevant stem cell models. Here, we have established conditions to differentiate human pluripotent stem cells (hPSCs) into yolk sac-like cells (YSLCs) that resemble the post-implantation human hypoblast molecularly and functionally. YSLCs induce the expression of pluripotency and anterior ectoderm markers in human embryonic stem cells (hESCs) at the expense of mesoderm and endoderm markers. This activity is mediated by the release of BMP and WNT signalling pathway inhibitors, and, therefore, resembles the functioning of the anterior visceral endoderm signalling centre of the mouse embryo, which establishes the anterior-posterior axis. Our results implicate the yolk sac in epiblast cell fate specification in the human embryo and propose YSLCs as a tool for studying post-implantation human embryo development in vitro.

Keywords:  cell biology; developmental biology; embryology; epiblast; human; human development; hypoblast; mouse; pluripotency; stem cells

DOI:  https://doi.org/10.7554/eLife.63930
Genome Biol. 2021 Aug 17. 22(1): 228

CoCoA-diff: counterfactual inference for single-cell gene expression analysis.

Yongjin P Park, Manolis Kellis.

  Finding a causal gene is a fundamental problem in genomic medicine. We present a causal inference framework, CoCoA-diff, that prioritizes disease genes by adjusting confounders without prior knowledge of control variables in single-cell RNA-seq data. We demonstrate that our method substantially improves statistical power in simulations and real-world data analysis of 70k brain cells collected for dissecting Alzheimer's disease. We identify 215 differentially regulated causal genes in various cell types, including highly relevant genes with a proper cell type context. Genes found in different types enrich distinctive pathways, implicating the importance of cell types in understanding multifaceted disease mechanisms.

Keywords:  Alzheimer’s disease; Causal inference; Counterfactual inference; Single-cell RNA-seq

DOI:  https://doi.org/10.1186/s13059-021-02438-4
Sci Rep. 2021 Aug 20. 11(1): 16977

Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons.

César Meléndez-Ramírez, Raquel Cuevas-Diaz Duran, Tonatiuh Barrios-García, Mayela Giacoman-Lozano, Adolfo López-Ornelas, Jessica Herrera-Gamboa, Enrique Estudillo, Ernesto Soto-Reyes, Iván Velasco, Víctor Treviño.

Chromatin architecture influences transcription by modulating the physical access of regulatory factors to DNA, playing fundamental roles in cell identity. Studies on dopaminergic differentiation have identified coding genes, but the relationship with non-coding genes or chromatin accessibility remains elusive. Using RNA-Seq and ATAC-Seq we profiled differentially expressed transcripts and open chromatin regions during early dopaminergic neuron differentiation. Hierarchical clustering of differentially expressed genes, resulted in 6 groups with unique characteristics. Surprisingly, the abundance of long non-coding RNAs (lncRNAs) was high in the most downregulated transcripts, and depicted positive correlations with target mRNAs. We observed that open chromatin regions decrease upon differentiation. Enrichment analyses of accessibility depict an association between open chromatin regions and specific functional pathways and gene-sets. A bioinformatic search for motifs allowed us to identify transcription factors and structural nuclear proteins that potentially regulate dopaminergic differentiation. Interestingly, we also found changes in protein and mRNA abundance of the CCCTC-binding factor, CTCF, which participates in genome organization and gene expression. Furthermore, assays demonstrated co-localization of CTCF with Polycomb-repressed chromatin marked by H3K27me3 in pluripotent cells, progressively decreasing in neural precursor cells and differentiated neurons. Our work provides a unique resource of transcription factors and regulatory elements, potentially involved in the acquisition of human dopaminergic neuron cell identity.

DOI: https://doi.org/10.1038/s41598-021-96263-1
Genome Biol. 2021 Aug 19. 22(1): 233

Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network.

Zhonghua Du, Xue Wen, Yichen Wang, Lin Jia, Shilin Zhang, Yudi Liu, Lei Zhou, Hui Li, Wang Yang, Cong Wang, Jingcheng Chen, Yajing Hao, Huiling Chen, Dan Li, Naifei Chen, Ilkay Celik, Yanbo Zhu, Zi Yan, Changhao Fu, Shanshan Liu, Benzheng Jiao, Zhuo Wang, Hui Zhang, Günhan Gülsoy, Jianjun Luo, Baoming Qin, Sujun Gao, Philipp Kapranov, Miguel A Esteban, Songling Zhang, Wei Li, Ferhat Ay, Runsheng Chen, Andrew R Hoffman, Jiuwei Cui, Ji-Fan Hu.

  BACKGROUND: A specific 3-dimensional intrachromosomal architecture of core stem cell factor genes is required to reprogram a somatic cell into pluripotency. As little is known about the epigenetic readers that orchestrate this architectural remodeling, we used a novel chromatin RNA in situ reverse transcription sequencing (CRIST-seq) approach to profile long noncoding RNAs (lncRNAs) in the Oct4 promoter.RESULTS: We identify Platr10 as an Oct4 - Sox2 binding lncRNA that is activated in somatic cell reprogramming. Platr10 is essential for the maintenance of pluripotency, and lack of this lncRNA causes stem cells to exit from pluripotency. In fibroblasts, ectopically expressed Platr10 functions in trans to activate core stem cell factor genes and enhance pluripotent reprogramming. Using RNA reverse transcription-associated trap sequencing (RAT-seq), we show that Platr10 interacts with multiple pluripotency-associated genes, including Oct4, Sox2, Klf4, and c-Myc, which have been extensively used to reprogram somatic cells. Mechanistically, we demonstrate that Platr10 helps orchestrate intrachromosomal promoter-enhancer looping and recruits TET1, the enzyme that actively induces DNA demethylation for the initiation of pluripotency. We further show that Platr10 contains an Oct4 binding element that interacts with the Oct4 promoter and a TET1-binding element that recruits TET1. Mutation of either of these two elements abolishes Platr10 activity.
CONCLUSION: These data suggest that Platr10 functions as a novel chromatin RNA molecule to control pluripotency in trans by modulating chromatin architecture and regulating DNA methylation in the core stem cell factor network.

Keywords:  DNA methylation; Intrachromosomal loop; Long noncoding RNA; Oct4; Pluripotency; Sox2; Stem cell

DOI:  https://doi.org/10.1186/s13059-021-02444-6
Cell Rep. 2021 Aug 17. pii: S2211-1247(21)00974-8. [Epub ahead of print]36(7): 109540

Two secured FACT recruitment mechanisms are essential for heterochromatin maintenance.

Shinya Takahata, Saori Chida, Aoi Ohnuma, Motoyoshi Ando, Takahiro Asanuma, Yota Murakami.

  FACT (facilitate chromatin transcription) is involved in heterochromatic silencing, but its mechanisms and function remain unclear. We reveal that the Spt16 recruitment mechanism operates in two distinct ways in heterochromatin. First, Pob3 mediates Spt16 recruitment onto the heterochromatin through its Spt16 dimerization and tandem PH domains. Without Pob3, Spt16 recruitment is partially reduced, exhibiting a silencing defect and impaired H2A/H2B organization. Second, heterochromatin protein 1 (HP1)/Swi6 mediates Spt16 recruitment onto the heterochromatin by physical interaction of the Swi6 chromo-shadow domain (CSD) and Spt16 peptidase-like domains. Several CSD mutants are tested for Spt16 binding activity, and the charged loop connecting β1 and β2 is critical for Spt16 binding and heterochromatic silencing. Loss of these pathways causes a severe defect in H3K9 methylation and HP1/Swi6 localization in the pericentromeric region, exhibiting transcriptional silencing defects and disordered heterochromatin. Our findings suggest that FACT and HP1/Swi6 work intimately to regulate heterochromatin organization.

Keywords:  FACT; H2A/H2B; H3K9me; HP1; Nhp6; Pob3; Spt16; Swi6; heterochromatin; nucleosome

DOI:  https://doi.org/10.1016/j.celrep.2021.109540
Genome Biol. 2021 Aug 17. 22(1): 230

Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization.

Xinyi Liu, Shaoshuai Jiang, Lin Ma, Jiale Qu, Longying Zhao, Xing Zhu, Junjun Ding.

  BACKGROUND: Biomolecular condensates have been implicated in multiple cellular processes. However, the global role played by condensates in 3D chromatin organization remains unclear. At present, 1,6-hexanediol (1,6-HD) is the only available tool to globally disrupt condensates, yet the conditions of 1,6-HD vary considerably between studies and may even trigger apoptosis.RESULTS: In this study, we first analyzed the effects of different concentrations and treatment durations of 1,6-HD and found that short-term exposure to 1.5% 1,6-HD dissolved biomolecular condensates whereas long-term exposure caused aberrant aggregation without affecting cell viability. Based on this condition, we drew a time-resolved map of 3D chromatin organization and found that short-term treatment with 1.5% 1,6-HD resulted in reduced long-range interactions, strengthened compartmentalization, homogenized A-A interactions, B-to-A compartment switch and TAD reorganization, whereas longer exposure had the opposite effects. Furthermore, the long-range interactions between condensate-component-enriched regions were markedly weakened following 1,6-HD treatment.
CONCLUSIONS: In conclusion, our study finds a proper 1,6-HD condition and provides a resource for exploring the role of biomolecular condensates in 3D chromatin organization.

Keywords:  1,6-Hexanediol; 3D chromatin organization; Biomolecular condensates

DOI:  https://doi.org/10.1186/s13059-021-02455-3
Nat Commun. 2021 08 17. 12(1): 4991

A unified model of human hemoglobin switching through single-cell genome editing.

Yong Shen, Jeffrey M Verboon, Yuannyu Zhang, Nan Liu, Yoon Jung Kim, Samantha Marglous, Satish K Nandakumar, Richard A Voit, Claudia Fiorini, Ayesha Ejaz, Anindita Basak, Stuart H Orkin, Jian Xu, Vijay G Sankaran.

Key mechanisms of fetal hemoglobin (HbF) regulation and switching have been elucidated through studies of human genetic variation, including mutations in the HBG1/2 promoters, deletions in the β-globin locus, and variation impacting BCL11A. While this has led to substantial insights, there has not been a unified understanding of how these distinct genetically-nominated elements, as well as other key transcription factors such as ZBTB7A, collectively interact to regulate HbF. A key limitation has been the inability to model specific genetic changes in primary isogenic human hematopoietic cells to uncover how each of these act individually and in aggregate. Here, we describe a single-cell genome editing functional assay that enables specific mutations to be recapitulated individually and in combination, providing insights into how multiple mutation-harboring functional elements collectively contribute to HbF expression. In conjunction with quantitative modeling and chromatin capture analyses, we illustrate how these genetic findings enable a comprehensive understanding of how distinct regulatory mechanisms can synergistically modulate HbF expression.

DOI: https://doi.org/10.1038/s41467-021-25298-9
EMBO Rep. 2021 Aug 19. e52435

Nhp2 is a reader of H2AQ105me and part of a network integrating metabolism with rRNA synthesis.

Julia S P Mawer, Jennifer Massen, Christina Reichert, Niklas Grabenhorst, Constantine Mylonas, Peter Tessarz.

  Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signalling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105 (H2AQ105me), is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signalling pathway and acetylation of histone H3 at position K56, thus integrating metabolic and proliferative signals. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes H2AQ105me. Based on functional and proteomic data, we suggest that Nhp2 functions as an adapter to bridge rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post-transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of rRNA.

Keywords:  chromatin; epigenetic reader; rRNA; ribosome biogenesis; small subunit processome

DOI:  https://doi.org/10.15252/embr.202152435
Stem Cell Reports. 2021 Aug 05. pii: S2213-6711(21)00381-7. [Epub ahead of print]

De novo DNA methyltransferases DNMT3A and DNMT3B are essential for XIST silencing for erosion of dosage compensation in pluripotent stem cells.

Atsushi Fukuda, Dane Z Hazelbaker, Nami Motosugi, Jin Hao, Francesco Limone, Amanda Beccard, Patrizia Mazzucato, Angelica Messana, Chisa Okada, Irune Guerra San Juan, Menglu Qian, Akihiro Umezawa, Hidenori Akutsu, Lindy E Barrett, Kevin Eggan.

  Human pluripotent stem cells (hPSCs) have proven to be valuable tools for both drug discovery and the development of cell-based therapies. However, the long non-coding RNA XIST, which is essential for the establishment and maintenance of X chromosome inactivation, is repressed during culture, thereby causing erosion of dosage compensation in female hPSCs. Here, we report that the de novo DNA methyltransferases DNMT3A/3B are necessary for XIST repression in female hPSCs. We found that the deletion of both genes, but not the individual genes, inhibited XIST silencing, maintained the heterochromatin mark of H3K27me3, and did not cause global overdosage in X-linked genes. Meanwhile, DNMT3A/3B deletion after XIST repression failed to restore X chromosome inactivation. Our findings revealed that de novo DNA methyltransferases are primary factors responsible for initiating erosion of dosage compensation in female hPSCs, and XIST silencing is stably maintained in a de novo DNA-methylation-independent manner.

Keywords:  DNA methylation; DNMT3A/3B; Lnc RNA XIST; dosage compensation; pluripotent stem cells

DOI:  https://doi.org/10.1016/j.stemcr.2021.07.015
Elife. 2021 Aug 17. pii: e64846. [Epub ahead of print]10

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1.

Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito.

  The molecular basis underlying glioblastoma (GBM) heterogeneity and plasticity is not fully understood. Using transcriptomic data of human patient-derived brain tumor stem cell lines (BTSCs), classified based on GBM-intrinsic signatures, we identify the AP-1 transcription factor FOSL1 as a key regulator of the mesenchymal (MES) subtype. We provide a mechanistic basis to the role of the neurofibromatosis type 1 gene (NF1), a negative regulator of the RAS/MAPK pathway, in GBM mesenchymal transformation through the modulation of FOSL1 expression. Depletion of FOSL1 in NF1-mutant human BTSCs and Kras-mutant mouse neural stem cells results in loss of the mesenchymal gene signature and reduction in stem cell properties and in vivo tumorigenic potential. Our data demonstrate that FOSL1 controls GBM plasticity and aggressiveness in response to NF1 alterations.

Keywords:  FOSL1; FRA-1; GBM; NF1; cancer biology; human; mesenchymal; mouse

DOI:  https://doi.org/10.7554/eLife.64846
Genome Biol. 2021 Aug 20. 22(1): 238

Bedshift: perturbation of genomic interval sets.

Aaron Gu, Hyun Jae Cho, Nathan C Sheffield.

Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the effectiveness of region set similarity metrics. We present Bedshift, a tool for perturbing BED files by randomly shifting, adding, and dropping regions from a reference file. The perturbed files can be used to benchmark similarity metrics, as well as for other applications. We highlight differences in behavior between metrics, such as that the Jaccard score is most sensitive to added or dropped regions, while coverage score is most sensitive to shifted regions.

DOI: https://doi.org/10.1186/s13059-021-02440-w
Nat Commun. 2021 08 19. 12(1): 5041

DMRT1-mediated reprogramming drives development of cancer resembling human germ cell tumors with features of totipotency.

Jumpei Taguchi, Hirofumi Shibata, Mio Kabata, Masaki Kato, Kei Fukuda, Akito Tanaka, Sho Ohta, Tomoyo Ukai, Kanae Mitsunaga, Yosuke Yamada, So I Nagaoka, Sho Yamazawa, Kotaro Ohnishi, Knut Woltjen, Tetsuo Ushiku, Manabu Ozawa, Mitinori Saitou, Yoichi Shinkai, Takuya Yamamoto, Yasuhiro Yamada.

In vivo reprogramming provokes a wide range of cell fate conversion. Here, we discover that in vivo induction of higher levels of OSKM in mouse somatic cells leads to increased expression of primordial germ cell (PGC)-related genes and provokes genome-wide erasure of genomic imprinting, which takes place exclusively in PGCs. Moreover, the in vivo OSKM reprogramming results in development of cancer that resembles human germ cell tumors. Like a subgroup of germ cell tumors, propagated tumor cells can differentiate into trophoblasts. Moreover, these tumor cells give rise to induced pluripotent stem cells (iPSCs) with expanded differentiation potential into trophoblasts. Remarkably, the tumor-derived iPSCs are able to contribute to non-neoplastic somatic cells in adult mice. Mechanistically, DMRT1, which is expressed in PGCs, drives the reprogramming and propagation of the tumor cells in vivo. Furthermore, the DMRT1-related epigenetic landscape is associated with trophoblast competence of the reprogrammed cells and provides a therapeutic target for germ cell tumors. These results reveal an unappreciated route for somatic cell reprogramming and underscore the impact of reprogramming in development of germ cell tumors.

DOI: https://doi.org/10.1038/s41467-021-25249-4
Nucleic Acids Res. 2021 Aug 20. pii: gkab722. [Epub ahead of print]

ESA1 regulates meiotic chromosome axis and crossover frequency via acetylating histone H4.

Ying Wang, Binyuan Zhai, Taicong Tan, Xiao Yang, Jiaming Zhang, Meihui Song, Yingjin Tan, Xuan Yang, Tingting Chu, Shuxian Zhang, Shunxin Wang, Liangran Zhang.

Meiotic recombination is integrated into and regulated by meiotic chromosomes, which is organized as loop/axis architecture. However, the regulation of chromosome organization is poorly understood. Here, we show Esa1, the NuA4 complex catalytic subunit, is constitutively expressed and localizes on chromatin loops during meiosis. Esa1 plays multiple roles including homolog synapsis, sporulation efficiency, spore viability, and chromosome segregation in meiosis. Detailed analyses show the meiosis-specific depletion of Esa1 results in decreased chromosome axis length independent of another axis length regulator Pds5, which further leads to a decreased number of Mer2 foci, and consequently a decreased number of DNA double-strand breaks, recombination intermediates, and crossover frequency. However, Esa1 depletion does not impair the occurrence of the obligatory crossover required for faithful chromosome segregation, or the strength of crossover interference. Further investigations demonstrate Esa1 regulates chromosome axis length via acetylating the N-terminal tail of histone H4 but not altering transcription program. Therefore, we firstly show a non-chromosome axis component, Esa1, acetylates histone H4 on chromatin loops to regulate chromosome axis length and consequently recombination frequency but does not affect the basic meiotic recombination process. Additionally, Esa1 depletion downregulates middle induced meiotic genes, which probably causing defects in sporulation and chromosome segregation.

DOI: https://doi.org/10.1093/nar/gkab722
Cell Rep. 2021 Aug 17. pii: S2211-1247(21)00985-2. [Epub ahead of print]36(7): 109551

The histone chaperone Anp32e regulates memory formation, transcription, and dendritic morphology by regulating steady-state H2A.Z binding in neurons.

Gilda Stefanelli, Claire E Makowski, Mark A Brimble, Meaghan Hall, Anas Reda, Samantha D Creighton, Amanda M Leonetti, Timothy A B McLean, Jacqueline M Zakaria, Jennet Baumbach, Celeste B Greer, Andrew M Davidoff, Brandon J Walters, Patrick J Murphy, Iva B Zovkic.

  Rapid removal of histone H2A.Z from neuronal chromatin is a key step in learning-induced gene expression and memory formation, but mechanisms underlying learning-induced H2A.Z removal are unclear. Anp32e was recently identified as an H2A.Z-specific histone chaperone that removes H2A.Z from nucleosomes in dividing cells, but its role in non-dividing neurons is unclear. Moreover, prior studies investigated Anp32e function under steady-state rather than stimulus-induced conditions. Here, we show that Anp32e regulates H2A.Z binding in neurons under steady-state conditions, with lesser impact on stimulus-induced H2A.Z removal. Functionally, Anp32e depletion leads to H2A.Z-dependent impairment in transcription and dendritic arborization in cultured hippocampal neurons, as well as impaired recall of contextual fear memory and transcriptional regulation. Together, these data indicate that Anp32e regulates behavioral and morphological outcomes by preventing H2A.Z accumulation in chromatin rather than by regulating activity-mediated H2A.Z dynamics.

Keywords:  Anp32e; H2A.Z; brain; epigenetics; histone variants; learning; memory; mice

DOI:  https://doi.org/10.1016/j.celrep.2021.109551
Stem Cell Res. 2021 Aug 08. pii: S1873-5061(21)00340-8. [Epub ahead of print]55 102493

Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development.

G V Hancock, W Liu, L Peretz, D Chen, J J Gell, A J Collier, J R Zamudio, K Plath, A T Clark.

  During embryo development, human primordial germ cells (hPGCs) express a naive gene expression program with similarities to pre-implantation naive epiblast (EPI) cells and naive human embryonic stem cells (hESCs). Previous studies have shown that TFAP2C is required for establishing naive gene expression in these cell types, however the role of additional naive transcription factors in hPGC biology is not known. Here, we show that unlike TFAP2C, the naive transcription factors KLF4 and TFCP2L1 are not required for induction of hPGC-like cells (hPGCLCs) from hESCs, and they have no role in establishing and maintaining a naive-like gene expression program in hPGCLCs with extended time in culture. Taken together, our results suggest a model whereby the molecular mechanisms that drive naive gene expression in hPGCs/hPGCLCs are distinct from those in the naive EPI/hESCs.

Keywords:  KLF4; PGCs; Pluripotency; Primordial Germ Cells; Stem cells; TFCP2L1; hPGCs

DOI:  https://doi.org/10.1016/j.scr.2021.102493
BMC Genomics. 2021 Aug 20. 22(1): 624

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis.

Carlos Alberto Oliveira de Biagi, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo, Wilson Araújo Silva.

  BACKGROUND: Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining.RESULTS: Here, we developed the R package "CeTF" that integrates the Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factors (RIF) algorithms applied to gene expression data from microarray, RNA-seq, or single-cell RNA-seq platforms. This approach allows identifying the transcription factors most likely to regulate a given network in different biological systems - for example, regulation of gene pathways in tumor stromal cells and tumor cells of the same tumor. This pipeline can be easily integrated into the high-throughput analysis. To demonstrate the CeTF package application, we analyzed gastric cancer RNA-seq data obtained from TCGA (The Cancer Genome Atlas) and found the HOXB3 gene as the second most relevant TFs with a high regulatory impact (TFs-HRi) regulating gene pathways in the cell cycle.
CONCLUSION: This preliminary finding shows the potential of CeTF to list master regulators of gene networks. CeTF was designed as a user-friendly tool that provides many highly automated functions without requiring the user to perform many complicated processes. It is available on Bioconductor ( http://bioconductor.org/packages/CeTF ) and GitHub ( http://github.com/cbiagii/CeTF ).

Keywords:  Bioinformatics; Network; R; R package; Transcript factors

DOI:  https://doi.org/10.1186/s12864-021-07918-2
Nat Commun. 2021 08 16. 12(1): 4940

LineageOT is a unified framework for lineage tracing and trajectory inference.

Aden Forrow, Geoffrey Schiebinger.

Understanding the genetic and epigenetic programs that control differentiation during development is a fundamental challenge, with broad impacts across biology and medicine. Measurement technologies like single-cell RNA-sequencing and CRISPR-based lineage tracing have opened new windows on these processes, through computational trajectory inference and lineage reconstruction. While these two mathematical problems are deeply related, methods for trajectory inference are not typically designed to leverage information from lineage tracing and vice versa. Here, we present LineageOT, a unified framework for lineage tracing and trajectory inference. Specifically, we leverage mathematical tools from graphical models and optimal transport to reconstruct developmental trajectories from time courses with snapshots of both cell states and lineages. We find that lineage data helps disentangle complex state transitions with increased accuracy using fewer measured time points. Moreover, integrating lineage tracing with trajectory inference in this way could enable accurate reconstruction of developmental pathways that are impossible to recover with state-based methods alone.

DOI: https://doi.org/10.1038/s41467-021-25133-1
Genome Biol. 2021 Aug 17. 22(1): 229

Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index.

Minglei Shi, Kaiqiang You, Taoyu Chen, Chao Hou, Zhengyu Liang, Mingwei Liu, Jifeng Wang, Taotao Wei, Jun Qin, Yang Chen, Michael Q Zhang, Tingting Li.

BACKGROUND: Liquid-liquid phase separation (LLPS) is an important organizing principle for biomolecular condensation and chromosome compartmentalization. However, while many proteins have been reported to undergo LLPS, quantitative and global analysis of chromatin LLPS property remains absent.RESULTS: Here, by combining chromatin-associated protein pull-down, quantitative proteomics and 1,6-hexanediol (1,6-HD) treatment, we develop Hi-MS and define an anti-1,6-HD index of chromatin-associated proteins (AICAP) to quantify 1,6-HD sensitivity of chromatin-associated proteins under physiological conditions. Compared with known physicochemical properties involved in phase separation, we find that proteins with lower AICAP are associated with higher content of disordered regions, higher hydrophobic residue preference, higher mobility and higher predicted LLPS potential. We also construct BL-Hi-C libraries following 1,6-HD treatment to study the sensitivity of chromatin conformation to 1,6-HD treatment. We find that the active chromatin and high-order structures, as well as the proteins enriched in corresponding regions, are more sensitive to 1,6-HD treatment.
CONCLUSIONS: Our work provides a global quantitative measurement of LLPS properties of chromatin-associated proteins and higher-order chromatin structure. Hi-MS and AICAP data provide an experimental tool and quantitative resources valuable for future studies of biomolecular condensates.

DOI: https://doi.org/10.1186/s13059-021-02456-2