bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020–11–29
thirty-six papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence.
  2. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization.
  3. Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation.
  4. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals.
  5. A map of cis-regulatory elements and 3D genome structures in zebrafish.
  6. Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome.
  7. Identifying chromatin features that regulate gene expression distribution.
  8. DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis.
  9. Transcription factor C/EBPβ induces genome-wide H3K27ac and upregulates gene expression during decidualization of human endometrial stromal cells.
  10. The PWWP2A Histone Deacetylase Complex Represses Intragenic Spurious Transcription Initiation in mESCs.
  11. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
  12. HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells.
  13. Evidence for context-dependent functions of KDM5B in prostate development and prostate cancer.
  14. 3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome.
  15. Intestinal FGF15/19 physiologically repress hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A.
  16. An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets.
  17. Fast detection of differential chromatin domains with SCIDDO.
  18. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms.
  19. A developmental stage specific network approach for studying dynamic transcription factor-microRNA co-regulation during craniofacial development.
  20. Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming.
  21. In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes.
  22. Maternal DOT1L is dispensable for mouse development.
  23. Deep feature extraction of single-cell transcriptomes by generative adversarial network.
  24. Haematopoietic stem cell-dependent Notch transcription is mediated by p53 through the Histone chaperone Supt16h.
  25. Both EZH2 and JMJD6 regulate cell cycle genes in breast cancer.
  26. TET2 chemically modifies tRNAs and regulates tRNA fragment levels.
  27. Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
  28. Quantification of the effect of site-specific histone acetylation on chromatin transcription rate.
  29. Chromatin topology and the timing of enhancer function at the HoxD locus.
  30. Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture.
  31. Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency.
  32. Identification of transcription factor co-regulators that drive prostate cancer progression.
  33. Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation.
  34. Endometrial epithelial ARID1A is critical for uterine gland function in early pregnancy establishment.
  35. BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms.
  36. An Irf6-Esrp1/2 regulatory axis controls midface morphogenesis in vertebrates.
  1. Nat Commun. 2020 Nov 27. 11(1): 6049
    Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence.
    Ioana Olan, Aled J Parry, Stefan Schoenfelder, Masako Narita, Yoko Ito, Adelyne S L Chan, Guy St C Slater, Dóra Bihary, Masashige Bando, Katsuhiko Shirahige, Hiroshi Kimura, Shamith A Samarajiwa, Peter Fraser, Masashi Narita.
      Senescence is a state of stable proliferative arrest, generally accompanied by the senescence-associated secretory phenotype, which modulates tissue homeostasis. Enhancer-promoter interactions, facilitated by chromatin loops, play a key role in gene regulation but their relevance in senescence remains elusive. Here, we use Hi-C to show that oncogenic RAS-induced senescence in human diploid fibroblasts is accompanied by extensive enhancer-promoter rewiring, which is closely connected with dynamic cohesin binding to the genome. We find de novo cohesin peaks often at the 3' end of a subset of active genes. RAS-induced de novo cohesin peaks are transcription-dependent and enriched for senescence-associated genes, exemplified by IL1B, where de novo cohesin binding is involved in new loop formation. Similar IL1B induction with de novo cohesin appearance and new loop formation are observed in terminally differentiated macrophages, but not TNFα-treated cells. These results suggest that RAS-induced senescence represents a cell fate determination-like process characterised by a unique gene expression profile and 3D genome folding signature, mediated in part through cohesin redistribution on chromatin.
    DOI:  https://doi.org/10.1038/s41467-020-19878-4
  2. Cell Stem Cell. 2020 Nov 17. pii: S1934-5909(20)30539-7. [Epub ahead of print]
    The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization.
    Naoya Takayama, Alex Murison, Shin-Ichiro Takayanagi, Christopher Arlidge, Stanley Zhou, Laura Garcia-Prat, Michelle Chan-Seng-Yue, Sasan Zandi, Olga I Gan, Héléna Boutzen, Kerstin B Kaufmann, Aaron Trotman-Grant, Erwin Schoof, Ken Kron, Noelia Díaz, John J Y Lee, Tiago Medina, Daniel D De Carvalho, Michael D Taylor, Juan M Vaquerizas, Stephanie Z Xie, John E Dick, Mathieu Lupien.
      Lifelong blood production requires long-term hematopoietic stem cells (LT-HSCs), marked by stemness states involving quiescence and self-renewal, to transition into activated short-term HSCs (ST-HSCs) with reduced stemness. As few transcriptional changes underlie this transition, we used single-cell and bulk assay for transposase-accessible chromatin sequencing (ATAC-seq) on human HSCs and hematopoietic stem and progenitor cell (HSPC) subsets to uncover chromatin accessibility signatures, one including LT-HSCs (LT/HSPC signature) and another excluding LT-HSCs (activated HSPC [Act/HSPC] signature). These signatures inversely correlated during early hematopoietic commitment and differentiation. The Act/HSPC signature contains CCCTC-binding factor (CTCF) binding sites mediating 351 chromatin interactions engaged in ST-HSCs, but not LT-HSCs, enclosing multiple stemness pathway genes active in LT-HSCs and repressed in ST-HSCs. CTCF silencing derepressed stemness genes, restraining quiescent LT-HSCs from transitioning to activated ST-HSCs. Hence, 3D chromatin interactions centrally mediated by CTCF endow a gatekeeper function that governs the earliest fate transitions HSCs make by coordinating disparate stemness pathways linked to quiescence and self-renewal.
    Keywords:  4D nucleome; CTCF; chromatin accessibility; chromatin interactions; epigenetics; hematopoiesis; hematopoietic stem cells; low-C; single-cell ATAC-seq; topologically associated domain
    DOI:  https://doi.org/10.1016/j.stem.2020.11.001
  3. Nucleic Acids Res. 2020 Nov 24. pii: gkaa1093. [Epub ahead of print]
    Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation.
    Hong-Yeoul Ryu, Dejian Zhao, Jianhui Li, Dan Su, Mark Hochstrasser.
      Histones are substrates of the SUMO (small ubiquitin-like modifier) conjugation pathway. Several reports suggest histone sumoylation affects transcription negatively, but paradoxically, our genome-wide analysis shows the modification concentrated at many active genes. We find that trans-tail regulation of histone-H2B ubiquitylation and H3K4 di-methylation potentiates subsequent histone sumoylation. Consistent with the known control of the Set3 histone deacetylase complex (HDAC) by H3K4 di-methylation, histone sumoylation directly recruits the Set3 complex to both protein-coding and noncoding RNA (ncRNA) genes via a SUMO-interacting motif in the HDAC Cpr1 subunit. The altered gene expression profile caused by reducing histone sumoylation matches well to the profile in cells lacking Set3. Histone H2B sumoylation and the Set3 HDAC coordinately suppress cryptic ncRNA transcription initiation internal to mRNA genes. Our results reveal an elaborate co-transcriptional histone crosstalk pathway involving the consecutive ubiquitylation, methylation, sumoylation and deacetylation of histones, which maintains transcriptional fidelity by suppressing spurious transcription.
    DOI:  https://doi.org/10.1093/nar/gkaa1093
  4. Nat Commun. 2020 11 24. 11(1): 5972
    Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals.
    Christopher B Mulholland, Atsuya Nishiyama, Joel Ryan, Ryohei Nakamura, Merve Yiğit, Ivo M Glück, Carina Trummer, Weihua Qin, Michael D Bartoschek, Franziska R Traube, Edris Parsa, Enes Ugur, Miha Modic, Aishwarya Acharya, Paul Stolz, Christoph Ziegenhain, Michael Wierer, Wolfgang Enard, Thomas Carell, Don C Lamb, Hiroyuki Takeda, Makoto Nakanashi, Sebastian Bultmann, Heinrich Leonhardt.
      Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
    DOI:  https://doi.org/10.1038/s41467-020-19603-1
  5. Nature. 2020 Nov 25.
    A map of cis-regulatory elements and 3D genome structures in zebrafish.
    Hongbo Yang, Yu Luan, Tingting Liu, Hyung Joo Lee, Li Fang, Yanli Wang, Xiaotao Wang, Bo Zhang, Qiushi Jin, Khai Chung Ang, Xiaoyun Xing, Juan Wang, Jie Xu, Fan Song, Iyyanki Sriranga, Chachrit Khunsriraksakul, Tarik Salameh, Daofeng Li, Mayank N K Choudhary, Jacek Topczewski, Kai Wang, Glenn S Gerhard, Ross C Hardison, Ting Wang, Keith C Cheng, Feng Yue.
      The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species1. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.
    DOI:  https://doi.org/10.1038/s41586-020-2962-9
  6. Nat Commun. 2020 Nov 27. 11(1): 6053
    Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome.
    He Fang, Giancarlo Bonora, Jordan P Lewandowski, Jitendra Thakur, Galina N Filippova, Steven Henikoff, Jay Shendure, Zhijun Duan, John L Rinn, Xinxian Deng, William S Noble, Christine M Disteche.
      Firre encodes a lncRNA involved in nuclear organization. Here, we show that Firre RNA expressed from the active X chromosome maintains histone H3K27me3 enrichment on the inactive X chromosome (Xi) in somatic cells. This trans-acting effect involves SUZ12, reflecting interactions between Firre RNA and components of the Polycomb repressive complexes. Without Firre RNA, H3K27me3 decreases on the Xi and the Xi-perinucleolar location is disrupted, possibly due to decreased CTCF binding on the Xi. We also observe widespread gene dysregulation, but not on the Xi. These effects are measurably rescued by ectopic expression of mouse or human Firre/FIRRE transgenes, supporting conserved trans-acting roles. We also find that the compact 3D structure of the Xi partly depends on the Firre locus and its RNA. In common lymphoid progenitors and T-cells Firre exerts a cis-acting effect on maintenance of H3K27me3 in a 26 Mb region around the locus, demonstrating cell type-specific trans- and cis-acting roles of this lncRNA.
    DOI:  https://doi.org/10.1038/s41467-020-19879-3
  7. Sci Rep. 2020 Nov 25. 10(1): 20566
    Identifying chromatin features that regulate gene expression distribution.
    Thanutra Zhang, Robert Foreman, Roy Wollman.
      Gene expression variability, differences in the number of mRNA per cell across a population of cells, is ubiquitous across diverse organisms with broad impacts on cellular phenotypes. The role of chromatin in regulating average gene expression has been extensively studied. However, what aspects of the chromatin contribute to gene expression variability is still underexplored. Here we addressed this problem by leveraging chromatin diversity and using a systematic investigation of randomly integrated expression reporters to identify what aspects of chromatin microenvironment contribute to gene expression variability. Using DNA barcoding and split-pool decoding, we created a large library of isogenic reporter clones and identified reporter integration sites in a massive and parallel manner. By mapping our measurements of reporter expression at different genomic loci with multiple epigenetic profiles including the enrichment of transcription factors and the distance to different chromatin states, we identified new factors that impact the regulation of gene expression distributions.
    DOI:  https://doi.org/10.1038/s41598-020-77638-2
  8. Genome Biol. 2020 Nov 25. 21(1): 283
    DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis.
    Pierre Bourguet, Leticia López-González, Ángeles Gómez-Zambrano, Thierry Pélissier, Amy Hesketh, Magdalena E Potok, Marie-Noëlle Pouch-Pélissier, Magali Perez, Olivier Da Ines, David Latrasse, Charles I White, Steven E Jacobsen, Moussa Benhamed, Olivier Mathieu.
       BACKGROUND: Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear.
    RESULTS: We isolate a strong hypomorphic Arabidopsis thaliana mutant of the POL2A catalytic subunit of DNA polymerase epsilon and show that POL2A is required to stabilize heterochromatin silencing genome-wide, likely by preventing replicative stress. We reveal that POL2A inhibits DNA methylation and histone H3 lysine 9 methylation. Hence, the release of heterochromatin silencing in POL2A-deficient mutants paradoxically occurs in a chromatin context of increased levels of these two repressive epigenetic marks. At the nuclear level, the POL2A defect is associated with fragmentation of heterochromatin.
    CONCLUSION: These results indicate that POL2A is critical to heterochromatin structure and function, and that unhindered replisome progression is required for the faithful propagation of DNA methylation throughout the cell cycle.
    Keywords:  DNA methylation; DNA polymerase epsilon; Heterochromatin; Replication stress; Silencing
    DOI:  https://doi.org/10.1186/s13059-020-02190-1
  9. Mol Cell Endocrinol. 2020 Nov 21. pii: S0303-7207(20)30387-7. [Epub ahead of print] 111085
    Transcription factor C/EBPβ induces genome-wide H3K27ac and upregulates gene expression during decidualization of human endometrial stromal cells.
    Isao Tamura, Ryo Maekawa, Kosuke Jozaki, Yasuyuki Ohkawa, Haruka Takagi, Yumiko Doi-Tanaka, Yuichiro Shirafuta, Yumiko Mihara, Toshiaki Taketani, Shun Sato, Hiroshi Tamura, Norihiro Sugino.
      We previously reported that H3K27 acetylation (H3K27ac) increases throughout the genome during decidualization of human endometrial stromal cells (ESCs). However, its mechanisms have not been clarified. We also reported that C/EBPβ acts as a pioneer factor initiating chromatin remodeling by increasing H3K27ac of IGFBP-1 and PRL promoters. Therefore, C/EBPβ may be involved in the genome-wide increase of H3K27ac during decidualization. In this study, we investigated whether C/EBPβ causes genome-wide H3K27ac modifications and regulates gene expressions during decidualization. cAMP was used to induce decidualization. Three types of cells (control cells, cAMP-treated cells, and cAMP-treated + C/EBPβ-knockdowned cells by siRNA) were generated. Of 4,190 genes that were upregulated by cAMP, C/EBPβ knockdown inhibited these upregulation in 2,239 genes (53.4%), indicating that they are under the regulation of C/EBPβ. cAMP increased H3K27ac in 1,272 of the 2,239 genes. C/EBPβ knockdown abolished the increase of H3K27ac in almost all genes (1,263 genes, 99.3 %), suggesting that C/EBPβ can upregulate gene expression by increasing H3K27ac. To investigate how C/EBPβ regulates H3K27ac throughout the genome, we tested the hypothesis that C/EBPβ binds to its binding regions and recruits cofactors with histone acetyltransferase activities. To do this, we collated our ChIP-sequence data with public ChIP-sequence database of transcription factors, and found that p300 is the most likely cofactor that binds to the H3K27ac-increased-regions with C/EBPβ. ChIP-qPCR of several genes confirmed that C/EBPβ binds to the target regions, recruits p300, and increases H3K27ac. Our genome-wide analysis revealed that C/EBPβ induces H3K27ac throughout the genome and upregulates gene expressions during decidualization by recruiting p300 to the promoters.
    Keywords:  CCAAT enhancer-binding protein β (C/EBPβ); decidualization; endometrial stromal cells (ESCs); histone acetylation; p300
    DOI:  https://doi.org/10.1016/j.mce.2020.111085
  10. iScience. 2020 Nov 20. 23(11): 101741
    The PWWP2A Histone Deacetylase Complex Represses Intragenic Spurious Transcription Initiation in mESCs.
    Guifeng Wei, Neil Brockdorff, Tianyi Zhang.
      Transcriptional fidelity depends on accurate promoter selection and initiation from the correct sites. In yeast, H3K36me3-mediated recruitment of the Rpd3S HDAC complex to gene bodies suppresses spurious transcription initiation. Here we describe an equivalent pathway in metazoans. PWWP2A/B is an H3K36me3 reader that forms a stable complex with HDAC1/2. We used CAGE-seq to profile all transcription initiation sites in wild-type mESCs and cells lacking PWWP2A/B. Loss of PWWP2A/B enhances spurious initiation from intragenic sites present in wild-type mESCs, and this effect is associated with increased levels of initiating Pol-II and histone acetylation. Spurious initiation events in Pwwp2a/b DKO mESCs do not overlap in genomic location or chromatin features with spurious sites that arise in Dnmt3b KO mESCs, previously reported to function in the suppression of intragenic transcriptional initiation, suggesting these pathways function cooperatively in maintaining the fidelity of transcription initiation in metazoans.
    Keywords:  Molecular Biology; Molecular Mechanism of Gene Regulation; Stem Cells Research
    DOI:  https://doi.org/10.1016/j.isci.2020.101741
  11. Nat Methods. 2020 Nov 23.
    Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
    Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael Molnar, Ariel Gershman, Norah Sadowski, Fritz J Sedlazeck, Kasper D Hansen, Jared T Simpson, Winston Timp.
      Probing epigenetic features on DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we use nanopore sequencing to evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA by applying GpC methyltransferase to exogenously label open chromatin. We performed nanopore sequencing of nucleosome occupancy and methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7 and MDA-MB-231). The single-molecule resolution allows footprinting of protein and nucleosome binding, and determination of the combinatorial promoter epigenetic signature on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, allowing us to generate a fully phased human epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility. We further apply this to a breast cancer model to evaluate differential methylation and accessibility between cancerous and noncancerous cells.
    DOI:  https://doi.org/10.1038/s41592-020-01000-7
  12. Nucleic Acids Res. 2020 Nov 25. pii: gkaa1091. [Epub ahead of print]
    HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells.
    Nur Zafirah Zaidan, Rupa Sridharan.
      The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency.
    DOI:  https://doi.org/10.1093/nar/gkaa1091
  13. Oncotarget. 2020 Nov 17. 11(46): 4243-4252
    Evidence for context-dependent functions of KDM5B in prostate development and prostate cancer.
    Bigang Liu, Rahul Kumar, Hseuh-Ping Chao, Rashid Mehmood, Yibing Ji, Amanda Tracz, Dean G Tang.
      Prostate cancer (PCa) is one of the leading causes of cancer-related deaths worldwide. Prostate tumorigenesis and PCa progression involve numerous genetic as well as epigenetic perturbations. Histone modification represents a fundamental epigenetic mechanism that regulates diverse cellular processes, and H3K4 methylation, one such histone modification associated with active transcription, can be reversed by dedicated histone demethylase KDM5B (JARID1B). Abnormal expression and functions of KDM5B have been implicated in several cancer types including PCa. Consistently, our bioinformatics analysis reveals that the KDM5B mRNA levels are upregulated in PCa compared to benign prostate tissues, and correlate with increased tumor grade and poor patient survival, supporting an oncogenic function of KDM5B in PCa. Surprisingly, however, when we generated prostate-specific conditional Kdm5b knockout mice using probasin (Pb) promoter-driven Cre: loxP system, we observed that Kdm5b deletion did not affect normal prostate development but instead induced mild hyperplasia. These results suggest that KDM5B may possess context-dependent roles in normal prostate development vs. PCa development and progression.
    Keywords:  KDM5B; epigenetics; hyperplasia; prostate cancer; prostate development
    DOI:  https://doi.org/10.18632/oncotarget.27818
  14. Nucleic Acids Res. 2020 Nov 27. pii: gkaa1078. [Epub ahead of print]
    3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome.
    Kyukwang Kim, Insu Jang, Mooyoung Kim, Jinhyuk Choi, Min-Seo Kim, Byungwook Lee, Inkyung Jung.
      Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. '3DIV' is freely available at http://3div.kr.
    DOI:  https://doi.org/10.1093/nar/gkaa1078
  15. Nat Commun. 2020 11 24. 11(1): 5969
    Intestinal FGF15/19 physiologically repress hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A.
    Young-Chae Kim, Sunmi Seok, Yang Zhang, Jian Ma, Bo Kong, Grace Guo, Byron Kemper, Jongsook Kim Kemper.
      Hepatic lipogenesis is normally tightly regulated but is aberrantly elevated in obesity. Fibroblast Growth Factor-15/19 (mouse FGF15, human FGF19) are bile acid-induced late fed-state gut hormones that decrease hepatic lipid levels by unclear mechanisms. We show that FGF15/19 and FGF15/19-activated Small Heterodimer Partner (SHP/NR0B2) have a role in transcriptional repression of lipogenesis. Comparative genomic analyses reveal that most of the SHP cistrome, including lipogenic genes repressed by FGF19, have overlapping CpG islands. FGF19 treatment or SHP overexpression in mice inhibits lipogenesis in a DNA methyltransferase-3a (DNMT3A)-dependent manner. FGF19-mediated activation of SHP via phosphorylation recruits DNMT3A to lipogenic genes, leading to epigenetic repression via DNA methylation. In non-alcoholic fatty liver disease (NAFLD) patients and obese mice, occupancy of SHP and DNMT3A and DNA methylation at lipogenic genes are low, with elevated gene expression. In conclusion, FGF15/19 represses hepatic lipogenesis by activating SHP and DNMT3A physiologically, which is likely dysregulated in NAFLD.
    DOI:  https://doi.org/10.1038/s41467-020-19803-9
  16. Cell Rep. 2020 Nov 24. pii: S2211-1247(20)31422-4. [Epub ahead of print]33(8): 108433
    An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets.
    Huiyuan Zhang, Asaf Madi, Nir Yosef, Norio Chihara, Amit Awasthi, Caroline Pot, Conner Lambden, Amitabh Srivastava, Patrick R Burkett, Jackson Nyman, Elena Christian, Yasaman Etminan, Annika Lee, Helene Stroh, Junrong Xia, Katarzyna Karwacz, Pratiksha I Thakore, Nandini Acharya, Alexandra Schnell, Chao Wang, Lionel Apetoh, Orit Rozenblatt-Rosen, Ana C Anderson, Aviv Regev, Vijay K Kuchroo.
      Interleukin-27 (IL-27) is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms, including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, and Atf3) and 2 negative (Irf9 and Irf8) Il10 regulators, generating an experimentally refined regulatory network for Il10. We report two central regulators, Prdm1 and Maf, that cooperatively drive the expression of signature genes induced by IL-27 in type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3+ regulatory T cells. Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying ll10-deficient mice. Our work provides insights into IL-27-driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets.
    Keywords:  IL-10; IL-27; Maf; Prdm1; T helper cells; Tr1; Treg; colitis; transcriptional network
    DOI:  https://doi.org/10.1016/j.celrep.2020.108433
  17. Bioinformatics. 2020 Nov 24. pii: btaa960. [Epub ahead of print]
    Fast detection of differential chromatin domains with SCIDDO.
    Peter Ebert, Marcel H Schulz.
       MOTIVATION: The generation of genome-wide maps of histone modifications using chromatin immunoprecipitation sequencing is a standard approach to dissect the complexity of the epigenome. Interpretation and differential analysis of histone datasets remains challenging due to regulatory meaningful co-occurrences of histone marks and their difference in genomic spread. To ease interpretation, chromatin state segmentation maps are a commonly employed abstraction combining individual histone marks. We developed the tool SCIDDO as a fast, flexible and statistically sound method for the differential analysis of chromatin state segmentation maps.
    RESULTS: We demonstrate the utility of SCIDDO in a comparative analysis that identifies differential chromatin domains (DCD) in various regulatory contexts and with only moderate computational resources. We show that the identified DCDs correlate well with observed changes in gene expression and can recover a substantial number of differentially expressed genes (DEGs). We showcase SCIDDO's ability to directly interrogate chromatin dynamics, such as enhancer switches in downstream analysis, which simplifies exploring specific questions about regulatory changes in chromatin. By comparing SCIDDO to competing methods, we provide evidence that SCIDDO's performance in identifying DEGs via differential chromatin marking is more stable across a range of cell-type comparisons and parameter cut-offs.
    AVAILABILITY AND IMPLEMENTATION: The SCIDDO source code is openly available under github.com/ptrebert/sciddo.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa960
  18. Mol Cell. 2020 Nov 16. pii: S1097-2765(20)30772-3. [Epub ahead of print]
    Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms.
    Bing-Rui Zhou, Hanqiao Feng, Seyit Kale, Tara Fox, Htet Khant, Natalia de Val, Rodolfo Ghirlando, Anna R Panchenko, Yawen Bai.
      The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the flanking/linker DNAs displayed substantial distinct dynamic conformations. Nuclear magnetic resonance (NMR) and H1 tail-swapping cryo-EM experiments revealed that the C-terminal tails of the H1 isoforms mainly controlled the flanking DNA orientations. We also observed partial ordering of the core histone H2A C-terminal and H3 N-terminal tails in the chromatosomes. Our results provide insights into the structures and dynamics of the chromatosomes and have implications for the structure and function of chromatin.
    Keywords:  Cryo-EM; NMR; chromatin structure; chromatosome; chromatosome dynamics; chromatosome structure; linker histone isoform; linker histone tail; nucleosome; single-chain antibody
    DOI:  https://doi.org/10.1016/j.molcel.2020.10.038
  19. Development. 2020 Nov 24. pii: dev.192948. [Epub ahead of print]
    A developmental stage specific network approach for studying dynamic transcription factor-microRNA co-regulation during craniofacial development.
    Fangfang Yan, Peilin Jia, Hiroki Yoshioka, Akiko Suzuki, Junichi Iwata, Zhongming Zhao.
      Craniofacial development is regulated through dynamic and complex mechanisms that involve various signaling cascades and gene regulations. Disruption of such regulations may result in craniofacial birth defects. Here, we propose the first developmental stage-specific network approach by integrating two critical regulators, transcription factor (TF) and microRNA (miRNA), to study their co-regulation during craniofacial development. Specifically, we used TFs, miRNAs, and non-TF genes to form Feed-forward Loops (FFLs) using genomic data covering mouse embryonic days E10.5 to E14.5. We identified key novel regulators (TFs: Foxm1, Hif1a, Zbtb16, Myog, Myod1, and Tcf7, and miRNAs: miR-340-5p and miR-129-5p) and target genes (Col1a1, Sgms2, and Slc8a3) whose expression changed in a developmental stage-dependent manner. We found Wnt-FoxO-Hippo pathway (from E10.5 to E11.5), tissue remodeling (from E12.5 to E13.5), and miR-129-5p-mediated Col1a1 regulation (from E10.5 to E14.5) might play crucial roles in craniofacial development. Enrichment analyses further suggested their functions. Our experiments validated the regulatory roles of miR-340-5p and Foxm1 in Wnt-FoxO-Hippo subnetwork, as well as the role of miR-129-5p in the miR-129-5p-Col1a1 subnetwork. Thus, our study helps understand comprehensive regulatory mechanisms for craniofacial development.
    Keywords:  Craniofacial development; Feed-forward loop; Regulatory network; Transcription factor; microRNA
    DOI:  https://doi.org/10.1242/dev.192948
  20. Clin Epigenetics. 2020 Nov 23. 12(1): 181
    Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming.
    Karen L Leung, Smriti Sanchita, Catherine T Pham, Brett A Davis, Mariam Okhovat, Xiangming Ding, Phillip Dumesic, Tristan R Grogan, Kevin J Williams, Marco Morselli, Feiyang Ma, Lucia Carbone, Xinmin Li, Matteo Pellegrini, Daniel A Dumesic, Gregorio D Chazenbalk.
       BACKGROUND: Normal-weight polycystic ovary syndrome (PCOS) women exhibit adipose resistance in vivo accompanied by enhanced subcutaneous (SC) abdominal adipose stem cell (ASC) development to adipocytes with accelerated lipid accumulation per cell in vitro. The present study examines chromatin accessibility, RNA expression and fatty acid (FA) synthesis during SC abdominal ASC differentiation into adipocytes in vitro of normal-weight PCOS versus age- and body mass index-matched normoandrogenic ovulatory (control) women to study epigenetic/genetic characteristics as well as functional alterations of PCOS and control ASCs during adipogenesis.
    RESULTS: SC abdominal ASCs from PCOS women versus controls exhibited dynamic chromatin accessibility during adipogenesis, from significantly less chromatin accessibility at day 0 to greater chromatin accessibility by day 12, with enrichment of binding motifs for transcription factors (TFs) of the AP-1 subfamily at days 0, 3, and 12. In PCOS versus control cells, expression of genes governing adipocyte differentiation (PPARγ, CEBPα, AGPAT2) and function (ADIPOQ, FABP4, LPL, PLIN1, SLC2A4) was increased two-sixfold at days 3, 7, and 12, while that involving Wnt signaling (FZD1, SFRP1, and WNT10B) was decreased. Differential gene expression in PCOS cells at these time points involved triacylglycerol synthesis, lipid oxidation, free fatty acid beta-oxidation, and oxidative phosphorylation of the TCA cycle, with TGFB1 as a significant upstream regulator. There was a broad correspondence between increased chromatin accessibility and increased RNA expression of those 12 genes involved in adipocyte differentiation and function, Wnt signaling, as well as genes involved in the triacylglycerol synthesis functional group at day 12 of adipogenesis. Total content and de novo synthesis of myristic (C14:0), palmitic (C16:0), palmitoleic (C16:1), and oleic (C18:1) acid increased from day 7 to day 12 in all cells, with total content and de novo synthesis of FAs significantly greater in PCOS than controls cells at day 12.
    CONCLUSIONS: In normal-weight PCOS women, dynamic chromatin remodeling of SC abdominal ASCs during adipogenesis may enhance adipogenic gene expression as a programmed mechanism to promote greater fat storage.
    Keywords:  Adipogenesis; Adipose stem cells; Cellular programming; Chromatin accessibility; De novo synthesis of fatty acids; Fat storage; Gene expression; Polycystic ovary syndrome; Total content; Transcriptional factors
    DOI:  https://doi.org/10.1186/s13148-020-00970-x
  21. Science. 2020 Nov 27. pii: eaaz6063. [Epub ahead of print]370(6520):
    In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes.
    Xin Jin, Sean K Simmons, Amy Guo, Ashwin S Shetty, Michelle Ko, Lan Nguyen, Vahbiz Jokhi, Elise Robinson, Paul Oyler, Nathan Curry, Giulio Deangeli, Simona Lodato, Joshua Z Levin, Aviv Regev, Feng Zhang, Paola Arlotta.
      The number of disease risk genes and loci identified through human genetic studies far outstrips the capacity to systematically study their functions. We applied a scalable genetic screening approach, in vivo Perturb-Seq, to functionally evaluate 35 autism spectrum disorder/neurodevelopmental delay (ASD/ND) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing mouse brain in utero, followed by single-cell RNA-sequencing of perturbed cells in the postnatal brain. We identified cell type-specific and evolutionarily conserved gene modules from both neuronal and glial cell classes. Recurrent gene modules and cell types are affected across this cohort of perturbations, representing key cellular effects across sets of ASD/ND risk genes. In vivo Perturb-Seq allows us to investigate how diverse mutations affect cell types and states in the developing organism.
    DOI:  https://doi.org/10.1126/science.aaz6063
  22. Sci Rep. 2020 Nov 26. 10(1): 20636
    Maternal DOT1L is dispensable for mouse development.
    Ji Liao, Piroska E Szabó.
      A battery of chromatin modifying enzymes play essential roles in remodeling the epigenome in the zygote and cleavage stage embryos, when the maternal genome is the sole contributor. Here we identify an exemption. DOT1L methylates lysine 79 in the globular domain of histone H3 (H3K79). Dot1l is an essential gene, as homozygous null mutant mouse embryos exhibit multiple developmental abnormalities and die before 11.5 days of gestation. To test if maternally deposited DOT1L is required for embryo development, we carried out a conditional Dot1l knockout in growing oocytes using the Zona pellucida 3-Cre (Zp3-Cre) transgenic mice. We found that the resulting maternal mutant Dot1lmat-/+ offspring displayed normal development and fertility, suggesting that the expression of the paternally inherited copy of Dot1l in the embryo is sufficient to support development. In addition, Dot1l maternal deletion did not affect the parental allele-specific expression of imprinted genes, indicating that DOT1L is not needed for imprint establishment in the oocyte or imprint protection in the zygote. In summary, uniquely and as opposed to other histone methyltransferases and histone marks, maternal DOT1L deposition and H3K79 methylation in the zygote and in the preimplantation stage embryo is dispensable for mouse development.
    DOI:  https://doi.org/10.1038/s41598-020-77545-6
  23. Bioinformatics. 2020 Nov 23. pii: btaa976. [Epub ahead of print]
    Deep feature extraction of single-cell transcriptomes by generative adversarial network.
    Mojtaba Bahrami, Malosree Maitra, Corina Nagy, Gustavo Turecki, Hamid R Rabiee, Yue Li.
       MOTIVATION: Single-cell RNA-sequencing (scRNA-seq) offers the opportunity to dissect heterogeneous cellular compositions and interrogate the cell-type-specific gene expression patterns across diverse conditions. However, batch effects such as laboratory conditions and individual-variability hinder their usage in cross-condition designs.
    RESULTS: Here, we present a single-cell Generative Adversarial Network (scGAN) to simultaneously acquire patterns from raw data while minimizing the confounding effect driven by technical artifacts or other factors inherent to the data. Specifically, scGAN models the data likelihood of the raw scRNA-seq counts by projecting each cell onto a latent embedding. Meanwhile, scGAN attempts to minimize the correlation between the latent embeddings and the batch labels across all cells. We demonstrate scGAN on three public scRNA-seq datasets and show that our method confers superior performance over the state-of-the-art methods in forming clusters of known cell types and identifying known psychiatric genes that are associated with major depressive disorder.
    AVAILABILITY: The scGAN code and the information for the public scRNA-seq datasets are available at https://github.com/li-lab-mcgill/singlecell-deepfeature.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa976
  24. Nat Cell Biol. 2020 Nov 23.
    Haematopoietic stem cell-dependent Notch transcription is mediated by p53 through the Histone chaperone Supt16h.
    Sophia G Espanola, Hyemin Song, Eunjin Ryu, Aditya Saxena, Eun-Sun Kim, Jennifer E Manegold, Chanond A Nasamran, Debashis Sahoo, Chang-Kyu Oh, Cara Bickers, Unbeom Shin, Stephanie Grainger, Yong Hwan Park, Lauren Pandolfo, Mi-Sun Kang, Sukhyun Kang, Kyungjae Myung, Kimberly L Cooper, Deborah Yelon, David Traver, Yoonsung Lee.
      Haematopoietic stem and progenitor cells (HSPCs) have been the focus of developmental and regenerative studies, yet our understanding of the signalling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the Facilitates chromatin transcription (FACT) complex, is required for HSPC formation. Zebrafish supt16h mutants express reduced levels of Notch-signalling components, genes essential for HSPC development, due to abrogated transcription. Whereas global chromatin accessibility in supt16h mutants is not substantially altered, we observe a specific increase in p53 accessibility, causing an accumulation of p53. We further demonstrate that p53 influences expression of the Polycomb-group protein PHC1, which functions as a transcriptional repressor of Notch genes. Suppression of phc1 or its upstream regulator, p53, rescues the loss of both Notch and HSPC phenotypes in supt16h mutants. Our results highlight a relationship between supt16h, p53 and phc1 to specify HSPCs via modulation of Notch signalling.
    DOI:  https://doi.org/10.1038/s41556-020-00604-7
  25. BMC Cancer. 2020 Nov 27. 20(1): 1159
    Both EZH2 and JMJD6 regulate cell cycle genes in breast cancer.
    Antara Biswas, Geetashree Mukherjee, Paturu Kondaiah, Kartiki V Desai.
       BACKGROUND: Strong evidences support the critical role of Jumonji domain containing 6 (JMJD6) in progression of breast cancer. Here we explore potential partners that coregulate gene expression, to understand additional pathways that are activated by higher amounts of JMJD6.
    METHODS: We used Gene Set Enrichment Analysis (GSEA) data to identify factors that display gene expression similar to cells treated with JMJD6 siRNA. Using chromatin immunoprecipitations (ChIP) against genomic regions that bind JMJD6 identified by in house and public database Encyclopaedia of DNA Elements (ENCODE), we confirmed JMJD6 occupancy by ChIP PCR. We tested the association of co-regulated genes with patient prognosis using The Cancer Genome Atlas (TCGA) datasets.
    RESULTS: JMJD6 profiles overlapped with those of Enhancer of Zeste homolog 2 (EZH2) and together they appear to co-regulate a unique cassette of genes in both ER+ and ER- cells. 496 genes including aurora kinases, which are currently being tested as novel therapeutic targets in breast cancer were co-regulated in MDA MB 231 cells. JMJD6 and EZH2 neither inter-regulated nor physically interacted with one another. Since both proteins are chromatin modulators, we performed ChIP linked PCR analysis and show that JMJD6 bound in the neighbourhood of co-regulated genes, though EZH2 data did not show any peaks within 100 kb of these sites. Alignment of binding site sequences suggested that atleast two types of binding partners could offer their DNA binding properties to enrich JMJD6 at regulatory sites. In clinical samples, JMJD6 and EZH2 expression significantly correlated in both normal and tumor samples, however the strongest correlation was observed in triple-negative breast cancer (TNBC) subtype. Co-expression of JMJD6 and EZH2 imposed poorer prognosis in breast cancer.
    CONCLUSIONS: JMJD6 and EZH2 regulate the same crucial cell cycle regulatory and therapeutic targets but their mechanisms appear to be independent of each other. Blocking of a single molecule may not axe cell proliferation completely and blocking both JMJD6 and EZH2 simultaneously may be more effective in breast cancer patients.
    Keywords:  DREAM; Microarray; Prognosis; TNBC
    DOI:  https://doi.org/10.1186/s12885-020-07531-8
  26. Nat Struct Mol Biol. 2020 Nov 23.
    TET2 chemically modifies tRNAs and regulates tRNA fragment levels.
    Chongsheng He, Julianna Bozler, Kevin A Janssen, Jeremy E Wilusz, Benjamin A Garcia, Andrea J Schorn, Roberto Bonasio.
      The ten-eleven translocation 2 (TET2) protein, which oxidizes 5-methylcytosine in DNA, can also bind RNA; however, the targets and function of TET2-RNA interactions in vivo are not fully understood. Using stringent affinity tags introduced at the Tet2 locus, we purified and sequenced TET2-crosslinked RNAs from mouse embryonic stem cells (mESCs) and found a high enrichment for tRNAs. RNA immunoprecipitation with an antibody against 5-hydroxymethylcytosine (hm5C) recovered tRNAs that overlapped with those bound to TET2 in cells. Mass spectrometry (MS) analyses revealed that TET2 is necessary and sufficient for the deposition of the hm5C modification on tRNA. Tet2 knockout in mESCs affected the levels of several small noncoding RNAs originating from TET2-bound tRNAs that were enriched by hm5C immunoprecipitation. Thus, our results suggest a new function of TET2 in promoting the conversion of 5-methylcytosine to hm5C on tRNA and regulating the processing or stability of different classes of tRNA fragments.
    DOI:  https://doi.org/10.1038/s41594-020-00526-w
  27. Mol Cell. 2020 Nov 19. pii: S1097-2765(20)30792-9. [Epub ahead of print]
    Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
    Meredith Corley, Ryan A Flynn, Byron Lee, Steven M Blue, Howard Y Chang, Gene W Yeo.
      Discovering the interaction mechanism and location of RNA-binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts compared to protein-absent transcripts in four human cell lines to identify transcriptome-wide footprints (fSHAPE) on RNA. Structural analyses indicate that fSHAPE precisely detects nucleobases that hydrogen bond with protein. We demonstrate that fSHAPE patterns predict binding sites of known RBPs, such as iron response elements in both known loci and previously unknown loci in CDC34, SLC2A4RG, COASY, and H19. Furthermore, by integrating SHAPE and fSHAPE with crosslinking and immunoprecipitation (eCLIP) of desired RBPs, we interrogate specific RNA-protein complexes, such as histone stem-loop elements and their nucleotides that hydrogen bond with stem-loop-binding proteins. Together, these technologies greatly expand our ability to study and understand specific cellular RNA interactions in RNA-protein complexes.
    Keywords:  RNA footprinting; RNA secondary structure; RNA-protein interactions; crosslinking and immunoprecipitation; iron response element
    DOI:  https://doi.org/10.1016/j.molcel.2020.11.014
  28. Nucleic Acids Res. 2020 Nov 26. pii: gkaa1050. [Epub ahead of print]
    Quantification of the effect of site-specific histone acetylation on chromatin transcription rate.
    Masatoshi Wakamori, Kohki Okabe, Kiyoe Ura, Takashi Funatsu, Masahiro Takinoue, Takashi Umehara.
      Eukaryotic transcription is epigenetically regulated by chromatin structure and post-translational modifications (PTMs). For example, lysine acetylation in histone H4 is correlated with activation of RNA polymerase I-, II- and III-driven transcription from chromatin templates, which requires prior chromatin remodeling. However, quantitative understanding of the contribution of particular PTM states to the sequential steps of eukaryotic transcription has been hampered partially because reconstitution of a chromatin template with designed PTMs is difficult. In this study, we reconstituted a di-nucleosome with site-specifically acetylated or unmodified histone H4, which contained two copies of the Xenopus somatic 5S rRNA gene with addition of a unique sequence detectable by hybridization-assisted fluorescence correlation spectroscopy. Using a Xenopus oocyte nuclear extract, we analyzed the time course of accumulation of nascent 5S rRNA-derived transcripts generated on chromatin templates in vitro. Our mathematically described kinetic model and fitting analysis revealed that tetra-acetylation of histone H4 at K5/K8/K12/K16 increases the rate of transcriptionally competent chromatin formation ∼3-fold in comparison with the absence of acetylation. We provide a kinetic model for quantitative evaluation of the contribution of epigenetic modifications to chromatin transcription.
    DOI:  https://doi.org/10.1093/nar/gkaa1050
  29. Proc Natl Acad Sci U S A. 2020 Nov 23. pii: 202015083. [Epub ahead of print]
    Chromatin topology and the timing of enhancer function at the HoxD locus.
    Eddie Rodríguez-Carballo, Lucille Lopez-Delisle, Andréa Willemin, Leonardo Beccari, Sandra Gitto, Bénédicte Mascrez, Denis Duboule.
      The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different subgroups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate from two distinct topologically associating domains (TADs) flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory submodules. To understand the importance of this particular regulatory topology to control Hoxd gene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites, or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation of Hoxd genes illustrate the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts was eventually resumed, showing that the presence of enhancer sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavorable orientation of CTCF sites.
    Keywords:  Hox clusters; TAD boundary; chromatin architecture; enhancers; gene regulation
    DOI:  https://doi.org/10.1073/pnas.2015083117
  30. Nat Commun. 2020 11 24. 11(1): 5963
    Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture.
    Katla Kristjánsdóttir, Alexis Dziubek, Hyun Min Kang, Hojoong Kwak.
      Enhancer RNAs (eRNA) are unstable non-coding RNAs, transcribed bidirectionally from active regulatory sequences, whose expression levels correlate with enhancer activity. We use capped-nascent-RNA sequencing to efficiently capture bidirectional transcription initiation across several human lymphoblastoid cell lines (Yoruba population) and detect ~75,000 eRNA transcription sites with high sensitivity and specificity. The use of nascent-RNA sequencing sidesteps the confounding effect of eRNA instability. We identify quantitative trait loci (QTLs) associated with the level and directionality of eRNA expression. High-resolution analyses of these two types of QTLs reveal distinct positions of enrichment at the central transcription factor (TF) binding regions and at the flanking eRNA initiation regions, both of which are associated with mRNA expression QTLs. These two regions-the central TF-binding footprint and the eRNA initiation cores-define a bipartite architecture of enhancers, inform enhancer function, and can be used as an indicator of the significance of non-coding regulatory variants.
    DOI:  https://doi.org/10.1038/s41467-020-19829-z
  31. Stem Cell Reports. 2020 Nov 10. pii: S2213-6711(20)30422-7. [Epub ahead of print]
    Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency.
    Bobbie Pelham-Webb, Dylan Murphy, Effie Apostolou.
      Higher-order chromatin structure is tightly linked to gene expression and therefore cell identity. In recent years, the chromatin landscape of pluripotent stem cells has become better characterized, and unique features at various architectural levels have been revealed. However, the mechanisms that govern establishment and maintenance of these topological characteristics and the temporal and functional relationships with transcriptional or epigenetic features are still areas of intense study. Here, we will discuss progress and limitations of our current understanding regarding how the 3D chromatin topology of pluripotent stem cells is established during somatic cell reprogramming and maintained during cell division. We will also discuss evidence and theories about the driving forces of topological reorganization and the functional links with key features and properties of pluripotent stem cell identity.
    Keywords:  3D chromatin organization; ESC; bookmarking; enhancer-promoter interaction; iPSC; mitosis; reprogramming; transcription factors
    DOI:  https://doi.org/10.1016/j.stemcr.2020.10.012
  32. Sci Rep. 2020 Nov 23. 10(1): 20332
    Identification of transcription factor co-regulators that drive prostate cancer progression.
    Manjunath Siddappa, Sajad A Wani, Mark D Long, Damien A Leach, Ewy A Mathé, Charlotte L Bevan, Moray J Campbell.
      In prostate cancer (PCa), and many other hormone-dependent cancers, there is clear evidence for distorted transcriptional control as disease driver mechanisms. Defining which transcription factor (TF) and coregulators are altered and combine to become oncogenic drivers remains a challenge, in part because of the multitude of TFs and coregulators and the diverse genomic space on which they function. The current study was undertaken to identify which TFs and coregulators are commonly altered in PCa. We generated unique lists of TFs (n = 2662), coactivators (COA; n = 766); corepressors (COR; n = 599); mixed function coregulators (MIXED; n = 511), and to address the challenge of defining how these genes are altered we tested how expression, copy number alterations and mutation status varied across seven prostate cancer (PCa) cohorts (three of localized and four advanced disease). Testing of significant changes was undertaken by bootstrapping approaches and the most significant changes were identified. For one commonly and significantly altered gene were stably knocked-down expression and undertook cell biology experiments and RNA-Seq to identify differentially altered gene networks and their association with PCa progression risks. COAS, CORS, MIXED and TFs all displayed significant down-regulated expression (q.value < 0.1) and correlated with protein expression (r 0.4-0.55). In localized PCa, stringent expression filtering identified commonly altered TFs and coregulator genes, including well-established (e.g. ERG) and underexplored (e.g. PPARGC1A, encodes PGC1α). Reduced PPARGC1A expression significantly associated with worse disease-free survival in two cohorts of localized PCa. Stable PGC1α knockdown in LNCaP cells increased growth rates and invasiveness and RNA-Seq revealed a profound basal impact on gene expression (~ 2300 genes; FDR < 0.05, logFC > 1.5), but only modestly impacted PPARγ responses. GSEA analyses of the PGC1α transcriptome revealed that it significantly altered the AR-dependent transcriptome, and was enriched for epigenetic modifiers. PGC1α-dependent genes were overlapped with PGC1α-ChIP-Seq genes and significantly associated in TCGA with higher grade tumors and worse disease-free survival. These methods and data demonstrate an approach to identify cancer-driver coregulators in cancer, and that PGC1α expression is clinically significant yet underexplored coregulator in aggressive early stage PCa.
    DOI:  https://doi.org/10.1038/s41598-020-77055-5
  33. Commun Biol. 2020 Nov 25. 3(1): 696
    Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation.
    Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim.
      Gene transcription is regulated by distant regulatory elements via combinatorial binding of transcription factors. It is increasingly recognized that alterations in chromatin state and transcription factor binding in these distant regulatory elements may have key roles in cancer development. Here we focused on the first stages of oncogene-induced carcinogenic transformation, and characterized the regulatory network underlying transcriptional changes associated with this process. Using Hi-C data, we observe spatial coupling between differentially expressed genes and their differentially accessible regulatory elements and reveal two candidate transcription factors, p53 and CTCF, as determinants of transcriptional alterations at the early stages of oncogenic HRas-induced transformation in human mammary epithelial cells. Strikingly, the malignant transcriptional reprograming is promoted by redistribution of chromatin binding of these factors without major variation in their expression level. Our results demonstrate that alterations in the regulatory landscape have a major role in driving oncogene-induced transcriptional reprogramming.
    DOI:  https://doi.org/10.1038/s42003-020-01398-y
  34. FASEB J. 2020 Nov 22.
    Endometrial epithelial ARID1A is critical for uterine gland function in early pregnancy establishment.
    Ryan M Marquardt, Tae Hoon Kim, Jung-Yoon Yoo, Hanna E Teasley, Asgerally T Fazleabas, Steven L Young, Bruce A Lessey, Ripla Arora, Jae-Wook Jeong.
      Though endometriosis and infertility are clearly associated, the pathophysiological mechanism remains unclear. Previous work has linked endometrial ARID1A loss to endometriosis-related endometrial non-receptivity. Here, we show in mice that ARID1A binds and regulates transcription of the Foxa2 gene required for endometrial gland function. Uterine-specific deletion of Arid1a compromises gland development and diminishes Foxa2 and Lif expression. Deletion of Arid1a with Ltf-iCre in the adult mouse endometrial epithelium preserves the gland development while still compromising the gland function. Mice lacking endometrial epithelial Arid1a are severely sub-fertile due to defects in implantation, decidualization, and endometrial receptivity from disruption of the LIF-STAT3-EGR1 pathway. FOXA2 is also reduced in the endometrium of women with endometriosis in correlation with diminished ARID1A, and both ARID1A and FOXA2 are reduced in nonhuman primates induced with endometriosis. Our findings describe a role for ARID1A in the endometrial epithelium supporting early pregnancy establishment through the maintenance of gland function.
    Keywords:  ARID1A; FOXA2; endometriosis; endometrium; infertility
    DOI:  https://doi.org/10.1096/fj.202002178R
  35. Am J Hum Genet. 2020 Nov 14. pii: S0002-9297(20)30400-6. [Epub ahead of print]
    BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms.
    Undiagnosed Diseases Network
      SWI/SNF-related intellectual disability disorders (SSRIDDs) are rare neurodevelopmental disorders characterized by developmental disability, coarse facial features, and fifth digit/nail hypoplasia that are caused by pathogenic variants in genes that encode for members of the SWI/SNF (or BAF) family of chromatin remodeling complexes. We have identified 12 individuals with rare variants (10 loss-of-function, 2 missense) in the BICRA (BRD4 interacting chromatin remodeling complex-associated protein) gene, also known as GLTSCR1, which encodes a subunit of the non-canonical BAF (ncBAF) complex. These individuals exhibited neurodevelopmental phenotypes that include developmental delay, intellectual disability, autism spectrum disorder, and behavioral abnormalities as well as dysmorphic features. Notably, the majority of individuals lack the fifth digit/nail hypoplasia phenotype, a hallmark of most SSRIDDs. To confirm the role of BICRA in the development of these phenotypes, we performed functional characterization of the zebrafish and Drosophila orthologs of BICRA. In zebrafish, a mutation of bicra that mimics one of the loss-of-function variants leads to craniofacial defects possibly akin to the dysmorphic facial features seen in individuals harboring putatively pathogenic BICRA variants. We further show that Bicra physically binds to other non-canonical ncBAF complex members, including the BRD9/7 ortholog, CG7154, and is the defining member of the ncBAF complex in flies. Like other SWI/SNF complex members, loss of Bicra function in flies acts as a dominant enhancer of position effect variegation but in a more context-specific manner. We conclude that haploinsufficiency of BICRA leads to a unique SSRIDD in humans whose phenotypes overlap with those previously reported.
    Keywords:  BAFopathy; CG11873; Drosophila; GLTSCR1; chromatin; developmental delay; intellectual disability; ncBAF complex; position effect variegation; zebrafish
    DOI:  https://doi.org/10.1016/j.ajhg.2020.11.003
  36. Development. 2020 Nov 24. pii: dev.194498. [Epub ahead of print]
    An Irf6-Esrp1/2 regulatory axis controls midface morphogenesis in vertebrates.
    Shannon H Carroll, Claudio Macias Trevino, Edward B Li, Kenta Kawasaki, Nikita Myers, Shawn A Hallett, Nora Alhazmi, Justin Cotney, Russ P Carstens, Eric C Liao.
      Irf6 and Esrp1 are important for palate development across vertebrates. In zebrafish, we found that irf6 regulates the expression of esrp1 We detailed overlapping Irf6 and Esrp1/2 expression in mouse orofacial epithelium. In zebrafish, irf6 and esrp1/2 share expression in periderm, frontonasal ectoderm, and oral epithelium. Genetic disruption of irf6 and esrp1/2 in zebrafish resulted in cleft of the anterior neurocranium. The esrp1/2 mutant also developed cleft of the mouth opening. Lineage tracing of cranial neural crest cells revealed that cleft resulted not from migration defect, but from impaired chondrogenesis. Analysis of aberrant cells within the cleft revealed expression of sox10, col1a1 and irf6 and were adjacent to cells krt4 and krt5 positive. Breeding of mouse Irf6;Esrp1;Esrp2 compound mutants suggested genetic interaction, as the triple homozygote and the Irf6;Esrp1 double homozygote was not observed. Further, Irf6 heterozygosity reduced Esrp1/2 cleft severity. These studies highlight the complementary analysis of Irf6 and Esrp1/2 in mouse and zebrafish and captured a unique aberrant cell population expressing sox10, col1a1 and irf6 Future work characterizing this cell population will yield additional insight into cleft pathogenesis.
    Keywords:  Cleft; Craniofacial; Development; ESRP1; IRF6
    DOI:  https://doi.org/10.1242/dev.194498
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