bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020–08–09
twenty-two papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. The Dynamics of Transcriptional Activation by Hepatic Reprogramming Factors.
  2. The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma.
  3. The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation.
  4. An integrative multi-omics analysis to identify candidate DNA methylation biomarkers related to prostate cancer risk.
  5. The functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma.
  6. Comprehensive analysis of the transcriptome-wide m6A methylome in colorectal cancer by MeRIP sequencing.
  7. FoxA factors: the chromatin key and doorstop essential for liver development and function.
  8. NuRD subunit CHD4 regulates super-enhancer accessibility in Rhabdomyosarcoma and represents a general tumor dependency.
  9. Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome.
  10. Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation.
  11. The discovery of SWI/SNF chromatin remodeling activity as a novel and targetable dependency in uveal melanoma.
  12. Haspin kinase modulates nuclear architecture and Polycomb-dependent gene silencing.
  13. Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility.
  14. Dynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disorders.
  15. ATF4 Regulates MYB to Increase γ-Globin in Response to Loss of β-Globin.
  16. Two Functional Axes of Feedback-Enforced PRC2 Recruitment in Mouse Embryonic Stem Cells.
  17. Metabolic stress regulates genome-wide transcription in a PTEN-dependent manner.
  18. XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing.
  19. TET1 downregulates epithelial-mesenchymal transition and chemoresistance in PDAC by demethylating CHL1 to inhibit the Hedgehog signaling pathway.
  20. A limited set of transcriptional programs define major cell types.
  21. Stem cell regionalization during olfactory bulb neurogenesis depends on regulatory interactions between Vax1 and Pax6.
  22. Systematized reporter assays reveal ZIC protein regulatory abilities are Subclass-specific and dependent upon transcription factor binding site context.
  1. Mol Cell. 2020 Jul 27. pii: S1097-2765(20)30502-5. [Epub ahead of print]
    The Dynamics of Transcriptional Activation by Hepatic Reprogramming Factors.
    Kenichi Horisawa, Miyako Udono, Kazuko Ueno, Yasuyuki Ohkawa, Masao Nagasaki, Sayaka Sekiya, Atsushi Suzuki.
      Specific combinations of two transcription factors (Hnf4α plus Foxa1, Foxa2, or Foxa3) can induce direct conversion of mouse fibroblasts into hepatocyte-like cells. However, the molecular mechanisms underlying hepatic reprogramming are largely unknown. Here, we show that the Foxa protein family members and Hnf4α sequentially and cooperatively bind to chromatin to activate liver-specific gene expression. Although all Foxa proteins bind to and open regions of closed chromatin as pioneer factors, Foxa3 has the unique potential of transferring from the distal to proximal regions of the transcription start site of target genes, binding RNA polymerase II, and co-traversing target genes. These distinctive characteristics of Foxa3 are essential for inducing the hepatic fate in fibroblasts. Similar functional coupling of transcription factors to RNA polymerase II may occur in other contexts whereby transcriptional activation can induce cell differentiation.
    Keywords:  RNA polymerase II; cell proliferation; direct reprogramming; gene expression; hepatocyte; liver; pioneer factor; transactivation domain; transcription factor; transcriptional activation
    DOI:  https://doi.org/10.1016/j.molcel.2020.07.012
  2. Nat Struct Mol Biol. 2020 Aug 03.
    The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma.
    Matthew J McBride, Nazar Mashtalir, Evan B Winter, Hai T Dao, Martin Filipovski, Andrew R D'Avino, Hyuk-Soo Seo, Neil T Umbreit, Roodolph St Pierre, Alfredo M Valencia, Kristin Qian, Hayley J Zullow, Jacob D Jaffe, Sirano Dhe-Paganon, Tom W Muir, Cigall Kadoch.
      Interactions between chromatin-associated proteins and the histone landscape play major roles in dictating genome topology and gene expression. Cancer-specific fusion oncoproteins, which display unique chromatin localization patterns, often lack classical DNA-binding domains, presenting challenges in identifying mechanisms governing their site-specific chromatin targeting and function. Here we identify a minimal region of the human SS18-SSX fusion oncoprotein (the hallmark driver of synovial sarcoma) that mediates a direct interaction between the mSWI/SNF complex and the nucleosome acidic patch. This binding results in altered mSWI/SNF composition and nucleosome engagement, driving cancer-specific mSWI/SNF complex targeting and gene expression. Furthermore, the C-terminal region of SSX confers preferential affinity to repressed, H2AK119Ub-marked nucleosomes, underlying the selective targeting to polycomb-marked genomic regions and synovial sarcoma-specific dependency on PRC1 function. Together, our results describe a functional interplay between a key nucleosome binding hub and a histone modification that underlies the disease-specific recruitment of a major chromatin remodeling complex.
    DOI:  https://doi.org/10.1038/s41594-020-0466-9
  3. Genome Biol. 2020 Aug 06. 21(1): 195
    The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation.
    Adam Kosti, Patricia Rosa de Araujo, Wei-Qing Li, Gabriela D A Guardia, Jennifer Chiou, Caihong Yi, Debashish Ray, Fabiana Meliso, Yi-Ming Li, Talia Delambre, Mei Qiao, Suzanne S Burns, Franziska K Lorbeer, Fanny Georgi, Markus Flosbach, Sarah Klinnert, Anne Jenseit, Xiufen Lei, Carolina Romero Sandoval, Kevin Ha, Hong Zheng, Renu Pandey, Aleksandra Gruslova, Yogesh K Gupta, Andrew Brenner, Erzsebet Kokovay, Timothy R Hughes, Quaid D Morris, Pedro A F Galante, Stefano Tiziani, Luiz O F Penalva.
       BACKGROUND: RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in RBP expression and function are often observed in cancer and influence critical pathways implicated in tumor initiation and growth. Identification and characterization of oncogenic RBPs and their regulatory networks provide new opportunities for targeted therapy.
    RESULTS: We identify the RNA-binding protein SERBP1 as a novel regulator of glioblastoma (GBM) development. High SERBP1 expression is prevalent in GBMs and correlates with poor patient survival and poor response to chemo- and radiotherapy. SERBP1 knockdown causes delay in tumor growth and impacts cancer-relevant phenotypes in GBM and glioma stem cell lines. RNAcompete identifies a GC-rich region as SERBP1-binding motif; subsequent genomic and functional analyses establish SERBP1 regulation role in metabolic routes preferentially used by cancer cells. An important consequence of these functions is SERBP1 impact on methionine production. SERBP1 knockdown decreases methionine levels causing a subsequent reduction in histone methylation as shown for H3K27me3 and upregulation of genes associated with neurogenesis, neuronal differentiation, and function. Further analysis demonstrates that several of these genes are downregulated in GBM, potentially through epigenetic silencing as indicated by the presence of H3K27me3 sites.
    CONCLUSIONS: SERBP1 is the first example of an RNA-binding protein functioning as a central regulator of cancer metabolism and indirect modulator of epigenetic regulation in GBM. By bridging these two processes, SERBP1 enhances glioma stem cell phenotypes and contributes to GBM poorly differentiated state.
    Keywords:  Cancer metabolism; Epigenetic regulation; GBM; One carbon cycle; RNA-binding protein; SERBP1
    DOI:  https://doi.org/10.1186/s13059-020-02115-y
  4. Nat Commun. 2020 Aug 06. 11(1): 3905
    An integrative multi-omics analysis to identify candidate DNA methylation biomarkers related to prostate cancer risk.
    PRACTICAL consortium
      It remains elusive whether some of the associations identified in genome-wide association studies of prostate cancer (PrCa) may be due to regulatory effects of genetic variants on CpG sites, which may further influence expression of PrCa target genes. To search for CpG sites associated with PrCa risk, here we establish genetic models to predict methylation (N = 1,595) and conduct association analyses with PrCa risk (79,194 cases and 61,112 controls). We identify 759 CpG sites showing an association, including 15 located at novel loci. Among those 759 CpG sites, methylation of 42 is associated with expression of 28 adjacent genes. Among 22 genes, 18 show an association with PrCa risk. Overall, 25 CpG sites show consistent association directions for the methylation-gene expression-PrCa pathway. We identify DNA methylation biomarkers associated with PrCa, and our findings suggest that specific CpG sites may influence PrCa via regulating expression of candidate PrCa target genes.
    DOI:  https://doi.org/10.1038/s41467-020-17673-9
  5. J Hematol Oncol. 2020 Aug 06. 13(1): 108
    The functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma.
    Samrat Roy Choudhury, Cody Ashby, Ruslana Tytarenko, Michael Bauer, Yan Wang, Shayu Deshpande, Judith Den, Carolina Schinke, Maurizio Zangari, Sharmilan Thanendrarajan, Faith E Davies, Frits van Rhee, Gareth J Morgan, Brian A Walker.
       BACKGROUND: Multiple Myeloma (MM) is a hematological malignancy with genomic heterogeneity and poor survival outcome. Apart from the central role of genetic lesions, epigenetic anomalies have been identified as drivers in the development of the disease.
    METHODS: Alterations in the DNA methylome were mapped in 52 newly diagnosed MM (NDMM) patients of six molecular subgroups and matched with loci-specific chromatin marks to define their impact on gene expression. Differential DNA methylation analysis was performed using DMAP with a ≥10% increase (hypermethylation) or decrease (hypomethylation) in NDMM subgroups, compared to control samples, considered significant for all the subsequent analyses with p<0.05 after adjusting for a false discovery rate.
    RESULTS: We identified differentially methylated regions (DMRs) within the etiological cytogenetic subgroups of myeloma, compared to control plasma cells. Using gene expression data we identified genes that are dysregulated and correlate with DNA methylation levels, indicating a role for DNA methylation in their transcriptional control. We demonstrated that 70% of DMRs in the MM epigenome were hypomethylated and overlapped with repressive H3K27me3. In contrast, differentially expressed genes containing hypermethylated DMRs within the gene body or hypomethylated DMRs at the promoters overlapped with H3K4me1, H3K4me3, or H3K36me3 marks. Additionally, enrichment of BRD4 or MED1 at the H3K27ac enriched DMRs functioned as super-enhancers (SE), controlling the overexpression of genes or gene-cassettes.
    CONCLUSIONS: Therefore, this study presents the underlying epigenetic regulatory networks of gene expression dysregulation in NDMM patients and identifies potential targets for future therapies.
    Keywords:  DNA methylation; epigenetics; gene regulation; myeloma
    DOI:  https://doi.org/10.1186/s13045-020-00933-y
  6. Epigenetics. 2020 Aug 04.
    Comprehensive analysis of the transcriptome-wide m6A methylome in colorectal cancer by MeRIP sequencing.
    Zhen Zhang, Quan Wang, Mengmeng Zhang, Wei Zhang, Long Zhao, Changjiang Yang, Bo Wang, Kewei Jiang, Yingjiang Ye, Zhanlong Shen, Shan Wang.
      Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in various cancers, making it essential to profile m6A modifications at a transcriptome-wide scale in colorectal cancer (CRC). In the present study, we performed high-throughput sequencing to determine the m6A methylome in CRC. We obtained 6 pairs of CRC samples and tumor-adjacent normal tissues from Peking University People's Hospital. We used MeRIP-seq to determine that compared to the tumor-adjacent normal tissues, the CRC samples had 1343 dysregulated m6A peaks, and 625 m6A peaks were significantly upregulated and 718 m6A peaks were significantly downregulated. Genes with altered m6A peaks play critical roles in regulating glucose metabolism, RNA metabolism and cancer stem cells. Furthermore, we identified 297 hypermethylated m6A peaks and 328 hypomethylated m6A peaks in mRNAs through conjoint analyses of MeRIP-seq and RNA-seq data. After analyzing these genes with differentially methylated m6A peaks and synchronously differential expression, we identified four genes (WDR72, SPTBN2, MORC2 and PARM1) that were associated with prognosis of colorectal cancer patients by searching The Cancer Genome Atlas (TCGA). Our study suggests that m6A modifications play important roles in tumor progression and survival of CRC patients. The results also indicate that modulating m6A modifications may represent an alternative strategy to predict the survival of cancer patients and interfere with tumor progression in the future.
    Keywords:  MeRIP sequencing; colorectal cancer; m6A
    DOI:  https://doi.org/10.1080/15592294.2020.1805684
  7. Genes Dev. 2020 Aug 01. 34(15-16): 1003-1004
    FoxA factors: the chromatin key and doorstop essential for liver development and function.
    James A Heslop, Stephen A Duncan.
      Pioneer factors are transcriptional regulators with the capacity to bind inactive regions of chromatin and induce changes in accessibility that underpin cell fate decisions. The FOXA family of transcription factors is well understood to have pioneer capacity. Indeed, researchers have uncovered numerous examples of FOXA-dependent epigenomic modulation in developmental and disease processes. Despite the presence of FOXA being essential for correct epigenetic patterning, the need for continued FOXA presence postchromatin modulation has been debated. In a recent study in this issue of Genes & Development, Reizel and colleagues (pp. 1039-1050) show that the tissue-specific ablation of FOXA1/2/3 in the adult mouse liver results in the collapse of the epigenetic profile that maintains the hepatic gene expression profile. Thus, FOXA functions as a key, opening regions of chromatin during development, and as a doorstep, maintaining the established euchromatic structure in adult tissue.
    Keywords:  pioneer factor; transcriptional network; winged helix protein
    DOI:  https://doi.org/10.1101/gad.340570.120
  8. Elife. 2020 Aug 03. pii: e54993. [Epub ahead of print]9
    NuRD subunit CHD4 regulates super-enhancer accessibility in Rhabdomyosarcoma and represents a general tumor dependency.
    Joana G Marques, Berkley E Gryder, Blaz Pavlovic, Yeonjoo Chung, Quy A Ngo, Fabian Frommelt, Matthias Gstaiger, Young Song, Katharina Benischke, Dominik Laubscher, Marco Wachtel, Javed Khan, Beat W Schäfer.
      The NuRD complex subunit CHD4 is essential for fusion-positive rhabdomyosarcoma (FP-RMS) survival, but the mechanisms underlying this dependency are not understood. Here, a NuRD-specific CRISPR screen demonstrates that FP-RMS is particularly sensitive to CHD4 amongst the NuRD members. Mechanistically, NuRD complex containing CHD4 localizes to super-enhancers where CHD4 generates a chromatin architecture permissive for the binding of the tumor driver and fusion protein PAX3-FOXO1, allowing downstream transcription of its oncogenic program. Moreover, CHD4 depletion removes HDAC2 from the chromatin, leading to an increase and spread of histone acetylation, and prevents the positioning of RNA Polymerase 2 at promoters impeding transcription initiation. Strikingly, analysis of genome-wide cancer dependency databases identifies CHD4 as a general cancer vulnerability. Our findings describe CHD4, a classically defined repressor, as positive regulator of transcription and super-enhancer accessibility as well as establish this remodeler as an unexpected broad tumor susceptibility and promising drug target for cancer therapy.
    Keywords:  cancer biology; human
    DOI:  https://doi.org/10.7554/eLife.54993
  9. Proc Natl Acad Sci U S A. 2020 Aug 03. pii: 202010506. [Epub ahead of print]
    Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome.
    Ayako Furukawa, Masatoshi Wakamori, Yasuhiro Arimura, Hideaki Ohtomo, Yasuo Tsunaka, Hitoshi Kurumizaka, Takashi Umehara, Yoshifumi Nishimura.
      The structural unit of eukaryotic chromatin is a nucleosome, comprising two histone H2A-H2B heterodimers and one histone (H3-H4)2 tetramer, wrapped around by ∼146 bp of DNA. The N-terminal flexible histone tails stick out from the histone core and have extensive posttranslational modifications, causing epigenetic changes of chromatin. Although crystal and cryogenic electron microscopy structures of nucleosomes are available, the flexible tail structures remain elusive. Using NMR, we have examined the dynamics of histone H3 tails in nucleosomes containing unmodified and tetra-acetylated H4 tails. In unmodified nucleosome, the H3 tail adopts a dynamic equilibrium structure between DNA-contact and reduced-contact states. In acetylated H4 nucleosome, however, the H3 tail equilibrium shifts to a mainly DNA-contact state with a minor reduced-contact state. The acetylated H4 tail is dynamically released from its own DNA-contact state to a reduced-contact state, while the H3 tail DNA-contact state becomes major. Notably, H3 K14 in the acetylated H4 nucleosome is much more accessible to acetyltransferase Gcn5 relative to unmodified nucleosome, possibly due to the formation of a favorable H3 tail conformation for Gcn5. In summary, each histone tail adopts a characteristic dynamic state but regulates one other, probably creating a histone tail network even on a nucleosome.
    Keywords:  NMR; epigenetics; histone tail; nucleosome; structural biology
    DOI:  https://doi.org/10.1073/pnas.2010506117
  10. Epigenetics. 2020 Aug 02. 1-14
    Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation.
    Matt J Barter, Kathleen Cheung, Julia Falk, Andreas C Panagiotopoulos, Caitlin Cosimini, Siobhan O'Brien, Karina Teja-Putri, Graham Neill, David J Deehan, David A Young.
      Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding. Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA, in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed. Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model. Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.
    Keywords:  ATAC-seq; chromatin; genome-editing; inflammation; interleukin-1
    DOI:  https://doi.org/10.1080/15592294.2020.1789266
  11. Mol Cancer Ther. 2020 Aug 03. pii: molcanther.1013.2019. [Epub ahead of print]
    The discovery of SWI/SNF chromatin remodeling activity as a novel and targetable dependency in uveal melanoma.
    Florencia Rago, GiNell Elliott, Ailing Li, Kathleen Sprouffske, Grainne Kerr, Aurore Desplat, Dorothee Abramowski, Julie T Chen, Ali Farsidjani, Kay X Xiang, Geoffrey Bushold, Yun Feng, Matthew D Shirley, Anka Bric, Anthony Vattay, Henrik Moebitz, Katsumasa Nakajima, Christopher D Adair, Simon Mathieu, Rukundo Ntaganda, Troy Smith, Julien P N Papillon, Audrey Kauffmann, David A Ruddy, Hyo-Eun C Bhang, Deborah Castelletti, Zainab Jagani.
      Uveal melanoma is a rare and aggressive cancer that originates in the eye. Currently, there are no approved targeted therapies and very few effective treatments for this cancer. While activating mutations in the G protein alpha subunits, GNAQ and GNA11, are key genetic drivers of the disease, few additional drug targets have been identified. Recently, studies have identified context specific roles for the mammalian SWI/SNF chromatin remodeling complexes (also known as BAF/PBAF) in various cancer lineages. Here we find evidence that the SWI/SNF complex is essential through analysis of functional genomics screens and further validation in a panel of uveal melanoma cell lines using both genetic tools and small molecule inhibitors of SWI/SNF. In addition, we describe a functional relationship between the SWI/SNF complex and the melanocyte lineage specific transcription factor MITF, suggesting that these two factors cooperate to drive a transcriptional program essential for uveal melanoma cell survival. These studies highlight a critical role for SWI/SNF in uveal melanoma, and demonstrate a novel path toward the treatment of this cancer.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-19-1013
  12. PLoS Genet. 2020 Aug 04. 16(8): e1008962
    Haspin kinase modulates nuclear architecture and Polycomb-dependent gene silencing.
    Ujué Fresán, Maria A Rodríguez-Sánchez, Oscar Reina, Victor G Corces, M Lluisa Espinàs.
      Haspin, a highly conserved kinase in eukaryotes, has been shown to be responsible for phosphorylation of histone H3 at threonine 3 (H3T3ph) during mitosis, in mammals and yeast. Here we report that haspin is the kinase that phosphorylates H3T3 in Drosophila melanogaster and it is involved in sister chromatid cohesion during mitosis. Our data reveal that haspin also phosphorylates H3T3 in interphase. H3T3ph localizes in broad silenced domains at heterochromatin and lamin-enriched euchromatic regions. Loss of haspin compromises insulator activity in enhancer-blocking assays and triggers a decrease in nuclear size that is accompanied by changes in nuclear envelope morphology. We show that haspin is a suppressor of position-effect variegation involved in heterochromatin organization. Our results also demonstrate that haspin is necessary for pairing-sensitive silencing and it is required for robust Polycomb-dependent homeotic gene silencing. Haspin associates with the cohesin complex in interphase, mediates Pds5 binding to chromatin and cooperates with Pds5-cohesin to modify Polycomb-dependent homeotic transformations. Therefore, this study uncovers an unanticipated role for haspin kinase in genome organization of interphase cells and demonstrates that haspin is required for homeotic gene regulation.
    DOI:  https://doi.org/10.1371/journal.pgen.1008962
  13. Nucleic Acids Res. 2020 Aug 07. pii: gkaa663. [Epub ahead of print]
    Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility.
    Yihang Jing, Dongbo Ding, Gaofei Tian, Ka Chun Jonathan Kwan, Zheng Liu, Toyotaka Ishibashi, Xiang David Li.
      Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and function in chromatin remain poorly understood. Here, we utilized an expressed protein ligation (EPL) strategy to synthesize histone H4 with site-specific succinylation at K77 residue (H4K77succ), an evolutionarily conserved succinylation site at the nucleosomal DNA-histone interface. We then assembled mononucleosomes with the semisynthetic H4K77succ in vitro. We demonstrated that this succinylation impacts nucleosome dynamics and promotes DNA unwrapping from the histone surface, which allows proteins such as transcription factors to rapidly access buried regions of the nucleosomal DNA. In budding yeast, a lysine-to-glutamic acid mutation, which mimics Ksucc, at the H4K77 site reduced nucleosome stability and led to defects in DNA damage repair and telomere silencing in vivo. Our findings revealed this uncharacterized histone modification has important roles in nucleosome and chromatin dynamics.
    DOI:  https://doi.org/10.1093/nar/gkaa663
  14. Nat Commun. 2020 Aug 06. 11(1): 3920
    Dynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disorders.
    Dave T Gerrard, Andrew A Berry, Rachel E Jennings, Matthew J Birket, Peyman Zarrineh, Myles G Garstang, Sarah L Withey, Patrick Short, Sandra Jiménez-Gancedo, Panos N Firbas, Ian Donaldson, Andrew D Sharrocks, Karen Piper Hanley, Matthew E Hurles, José Luis Gomez-Skarmeta, Nicoletta Bobola, Neil A Hanley.
      How the genome activates or silences transcriptional programmes governs organ formation. Little is known in human embryos undermining our ability to benchmark the fidelity of stem cell differentiation or cell programming, or interpret the pathogenicity of noncoding variation. Here, we study histone modifications across thirteen tissues during human organogenesis. We integrate the data with transcription to build an overview of how the human genome differentially regulates alternative organ fates including by repression. Promoters from nearly 20,000 genes partition into discrete states. Key developmental gene sets are actively repressed outside of the appropriate organ without obvious bivalency. Candidate enhancers, functional in zebrafish, allow imputation of tissue-specific and shared patterns of transcription factor binding. Overlaying more than 700 noncoding mutations from patients with developmental disorders allows correlation to unanticipated target genes. Taken together, the data provide a comprehensive genomic framework for investigating normal and abnormal human development.
    DOI:  https://doi.org/10.1038/s41467-020-17305-2
  15. Cell Rep. 2020 Aug 04. pii: S2211-1247(20)30978-5. [Epub ahead of print]32(5): 107993
    ATF4 Regulates MYB to Increase γ-Globin in Response to Loss of β-Globin.
    Mandy Y Boontanrart, Markus S Schröder, Gautier M Stehli, Marija Banović, Stacia K Wyman, Rachel J Lew, Matteo Bordi, Benjamin G Gowen, Mark A DeWitt, Jacob E Corn.
      β-Hemoglobinopathies can trigger rapid production of red blood cells in a process known as stress erythropoiesis. Cellular stress prompts differentiating erythroid precursors to express high levels of fetal γ-globin. However, the mechanisms underlying γ-globin production during cellular stress are still poorly defined. Here, we use CRISPR-Cas genome editing to model the stress caused by reduced levels of adult β-globin. We find that decreased β-globin is sufficient to induce robust re-expression of γ-globin, and RNA sequencing (RNA-seq) of differentiating isogenic erythroid precursors implicates ATF4 as a causal regulator of this response. ATF4 binds within the HBS1L-MYB intergenic enhancer and regulates expression of MYB, a known γ-globin regulator. Overall, the reduction of ATF4 upon β-globin knockout decreases the levels of MYB and BCL11A. Identification of ATF4 as a key regulator of globin compensation adds mechanistic insight to the poorly understood phenomenon of stress-induced globin compensation and could inform strategies to treat hemoglobinopathies.
    Keywords:  BCL11A; CRISPR/Cas9; Fetal hemoglobin; HBS1L-MYB; adult hemoglobin; gene editing; hemoglobinopathies; stress erythropoiesis
    DOI:  https://doi.org/10.1016/j.celrep.2020.107993
  16. Stem Cell Reports. 2020 Jul 23. pii: S2213-6711(20)30284-8. [Epub ahead of print]
    Two Functional Axes of Feedback-Enforced PRC2 Recruitment in Mouse Embryonic Stem Cells.
    Matteo Perino, Guido van Mierlo, Chet Loh, Sandra M T Wardle, Dick W Zijlmans, Hendrik Marks, Gert Jan C Veenstra.
      Polycomb Repressive Complex 2 (PRC2) plays an essential role in gene repression during development, catalyzing H3 lysine 27 trimethylation (H3K27me3). MTF2 in the PRC2.1 sub-complex, and JARID2 in PRC2.2, are central in core PRC2 recruitment to target genes in mouse embryonic stem cells (mESCs). To investigate how PRC2.1 and PRC2.2 cooperate, we combined Polycomb mutant mESCs with chemical inhibition of binding to H3K27me3. We find that PRC2.1 and PRC2.2 mediate two distinct paths for recruitment, which are mutually reinforced. Whereas PRC2.1 recruitment is mediated by MTF2 binding to DNA, JARID2-containing PRC2.2 recruitment is more dependent on PRC1. Both recruitment axes are supported by core subunit EED binding to H3K27me3, but EED inhibition exhibits a more pronounced effect in Jarid2 null cells. Finally, we show that PRC1 and PRC2 enhance reciprocal binding. Together, these data disentangle the interdependent interactions that are important for PRC2 recruitment.
    Keywords:  Polycomb; chromatin; embryonic stem cells; epigenomics
    DOI:  https://doi.org/10.1016/j.stemcr.2020.07.007
  17. Hum Mol Genet. 2020 Aug 03. pii: ddaa168. [Epub ahead of print]
    Metabolic stress regulates genome-wide transcription in a PTEN-dependent manner.
    Ata Abbas, Roshan Padmanabhan, Charis Eng.
      PTEN is implicated in a wide variety of pathophysiological conditions and traditionally studied in the context of the PIK3-AKT-mTOR axis. Recent studies from our group and others have reported a novel role of PTEN in the regulation of transcription at the genome-wide scale. This emerging role of PTEN on global transcriptional regulation is providing a better understanding of various diseases, including cancer. Since cancer progression is an energy-demanding process and PTEN is known to regulate metabolic processes, we sought to understand the role of PTEN in transcriptional regulation under metabolic stress, a condition often developing in the tumor microenvironment. In the present study, we demonstrate that PTEN modulates genome-wide RNA Polymerase II (Pol II) occupancy in cells undergoing glucose deprivation. The glucose-deprived PTEN null cells were found to continue global gene transcription, which may activate a survival mode. However, cells with constitutive PTEN expression slow transcription, an evolutionary mechanism that may save cellular energy and activate programmed cell death pathways, in the absence of glucose. Interestingly, alternative exon usage by PTEN null cells is increased under metabolic stress compared to PTEN expressing cells. Overall, our study demonstrates distinct mechanisms involved in PTEN-dependent genome-wide transcriptional control under metabolic stress. Our findings provide a new insight in understanding tumor pathology and how PTEN loss of function, whether by genetic or non-genetic mechanisms, can contribute to a favorable transcriptional program employed by tumor cells to escape apoptosis, hence developing more aggressive and metastatic phenotypes.
    DOI:  https://doi.org/10.1093/hmg/ddaa168
  18. Mol Cell. 2020 Jul 28. pii: S1097-2765(20)30472-X. [Epub ahead of print]
    XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing.
    Jared T Winkelman, Chirangini Pukhrambam, Irina O Vvedenskaya, Yuanchao Zhang, Deanne M Taylor, Premal Shah, Richard H Ebright, Bryce E Nickels.
      Pausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a "stepping" mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a "scrunching" mechanism, has not. We report a method that directly defines the RNAP-active-center position relative to DNA with single-nucleotide resolution (XACT-seq; "crosslink-between-active-center-and-template sequencing"). We apply this method to detect and quantify pausing in initial transcription at 411 (∼4,000,000) promoter sequences in vivo in Escherichia coli. The results show initial-transcription pausing can occur in each nucleotide addition during initial transcription, particularly the first 4 to 5 nucleotide additions. The results further show initial-transcription pausing occurs at sequences that resemble the consensus sequence element for transcription-elongation pausing. Our findings define the positional and sequence determinants for initial-transcription pausing and establish initial-transcription pausing is hard coded by sequence elements similar to those for transcription-elongation pausing.
    Keywords:  RNA polymerase; initial transcription; massively parallel reporter assay; photocrosslinking; promoter; sigma factor; transcription; transcription elongation; transcription pausing
    DOI:  https://doi.org/10.1016/j.molcel.2020.07.006
  19. Oncogene. 2020 Aug 04.
    TET1 downregulates epithelial-mesenchymal transition and chemoresistance in PDAC by demethylating CHL1 to inhibit the Hedgehog signaling pathway.
    Hao Li, Wang Jiang, Xue-Ni Liu, Li-Yun Yuan, Tian-Jiao Li, Shuo Li, Shuai-Shuai Xu, Wu-Hu Zhang, He-Li Gao, Xuan Han, Wen-Quan Wang, Chun-Tao Wu, Xian-Jun Yu, Hua-Xiang Xu, Liang Liu.
      Chemoresistance is a major obstacle to prolonging pancreatic ductal adenocarcinoma (PDAC) patient survival. TET1 is identified as the most important epigenetic modification enzyme that facilitates chemoresistance in cancers. However, the chemoresistance mechanism of TET1 in PDAC is unknown. This study aimed to determine the role of TET1 in the chemoresistance of PDAC. TET1-associated chemoresistance in PDAC was investigated in vitro and in vivo. The clinical significance of TET1 was analyzed in 228 PDAC patients by tissue microarray profiling. We identified that TET1 downregulation is caused by its promoter hypermethylation and correlates with poor survival in PDAC patients. In vitro and in vivo functional studies performed by silencing or overexpressing TET1 suggested that TET1 is able to suppress epithelial-mesenchymal transition (EMT) and sensitize PDAC cells to 5FU and gemcitabine. Then RNA-seq, whole genome bisulfite sequencing (WGBS) and ChIP-seq were used to explore the TET1-associated pathway, and showed that TET1 promotes the transcription of CHL1 by binding and demethylating the CHL1 promoter, which consequently inhibits the Hedgehog pathway. Additionally, inhibiting Hedgehog signaling by CHL1 overexpression or the Hedgehog pathway inhibitor, GDC-0449, reversed the chemoresistance induced by TET1 silencing. Regarding clinical significance, we found that high TET1 and high CHL1 expression predicted a better prognosis in resectable PDAC patients. In summary, we demonstrated that TET1 reverses chemoresistance in PDAC by downregulating the CHL1-associated Hedgehog signaling pathway. PDAC patients with a high expression levels of TET1 and CHL1 have a better prognosis.
    DOI:  https://doi.org/10.1038/s41388-020-01407-8
  20. Genome Res. 2020 Jul;30(7): 1047-1059
    A limited set of transcriptional programs define major cell types.
    Alessandra Breschi, Manuel Muñoz-Aguirre, Valentin Wucher, Carrie A Davis, Diego Garrido-Martín, Sarah Djebali, Jesse Gillis, Dmitri D Pervouchine, Anna Vlasova, Alexander Dobin, Chris Zaleski, Jorg Drenkow, Cassidy Danyko, Alexandra Scavelli, Ferran Reverter, Michael P Snyder, Thomas R Gingeras, Roderic Guigó.
      We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the contribution of the major cell types to the composition of human tissues. We found this cellular composition to be a characteristic signature of tissues and to reflect tissue morphological heterogeneity and histology. We identified changes in cellular composition in different tissues associated with age and sex, and found that departures from the normal cellular composition correlate with histological phenotypes associated with disease.
    DOI:  https://doi.org/10.1101/gr.263186.120
  21. Elife. 2020 Aug 07. pii: e58215. [Epub ahead of print]9
    Stem cell regionalization during olfactory bulb neurogenesis depends on regulatory interactions between Vax1 and Pax6.
    Nathalie Coré, Andrea Erni, Hanne M Hoffmann, Pamela L Mellon, Andrew J Saurin, Christophe Béclin, Harold Cremer.
      Different subtypes of interneurons, destined for the olfactory bulb, are continuously generated by neural stem cells located in the ventricular and subventricular zones along the lateral forebrain ventricles of mice. Neuronal identity in the olfactory bulb depends on the existence of defined microdomains of pre-determined neural stem cells along the ventricle walls. The molecular mechanisms underlying positional identity of these neural stem cells are poorly understood. Here we show that the transcription factor Vax1 controls the production of two specific neuronal sub-types. First, it is directly necessary to generate Calbindin expressing interneurons from ventro-lateral progenitors. Second, it represses the generation of dopaminergic neurons by dorsolateral progenitors through inhibition of Pax6 expression. We present data indicating that this repression occurs, at least in part, via activation of microRNA miR-7.
    Keywords:  developmental biology; mouse; neuroscience
    DOI:  https://doi.org/10.7554/eLife.58215
  22. Sci Rep. 2020 Aug 04. 10(1): 13130
    Systematized reporter assays reveal ZIC protein regulatory abilities are Subclass-specific and dependent upon transcription factor binding site context.
    Jehangir N Ahmed, Koula E M Diamand, Helen M Bellchambers, Ruth M Arkell.
      The ZIC proteins are a family of transcription regulators with a well-defined zinc finger DNA-binding domain and there is evidence that they elicit functional DNA binding at a ZIC DNA binding site. Little is known, however, regarding domains within ZIC proteins that confer trans-activation or -repression. To address this question, a new cell-based trans-activation assay system suitable for ZIC proteins in HEK293T cells was constructed. This identified two previously unannotated evolutionarily conserved regions of ZIC3 that are necessary for trans-activation. These domains are found in all Subclass A ZIC proteins, but not in the Subclass B proteins. Additionally, the Subclass B proteins fail to elicit functional binding at a multimerised ZIC DNA binding site. All ZIC proteins, however, exhibit functional binding when the ZIC DNA binding site is embedded in a multiple transcription factor locus derived from ZIC target genes in the mouse genome. This ability is due to several domains, some of which are found in all ZIC proteins, that exhibit context dependent trans-activation or -repression activity. This knowledge is valuable for assessing the likely pathogenicity of variant ZIC proteins associated with human disorders and for determining factors that influence functional transcription factor binding.
    DOI:  https://doi.org/10.1038/s41598-020-69917-9
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