bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020–09–27
twenty-two papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors.
  2. Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization.
  3. Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay.
  4. Zeb2 regulates the balance between retinal interneurons and muller glia by inhibition of BMP-Smad signaling.
  5. Single-gene imaging links genome topology, promoter-enhancer communication and transcription control.
  6. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.
  7. Transcription imparts architecture, function and logic to enhancer units.
  8. BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation.
  9. A modified protocol of Capture-C allows affordable and flexible high-resolution promoter interactome analysis.
  10. TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation.
  11. A theoretical model of Polycomb/Trithorax action unites stable epigenetic memory and dynamic regulation.
  12. Telomere dysfunction activates YAP1 to drive tissue inflammation.
  13. Detect differentially methylated regions using non-homogeneous hidden Markov model for bisulfite sequencing data.
  14. SWI/SNF complexes act through CBP-1 histone acetyltransferase to regulate acute functional tolerance to alcohol.
  15. Discovery of a Functional Covalent Ligand Targeting an Intrinsically Disordered Cysteine within MYC.
  16. Detecting chromatin interactions between and along sister chromatids with SisterC.
  17. Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism.
  18. Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B.
  19. Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination.
  20. Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes.
  21. The transcription factor NRF2 enhances melanoma malignancy by blocking differentiation and inducing COX2 expression.
  22. methylclock: a Bioconductor package to estimate DNA methylation age.
  1. Genome Res. 2020 Sep 22.
    Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors.
    Martin Cusack, Hamish W King, Paolo Spingardi, Benedikt M Kessler, Robert J Klose, Skirmantas Kriaucionis.
      Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are integrated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. We observe widespread increases in chromatin accessibility at retrotransposons when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements has elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation-deficient cells demonstrates that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression.
    DOI:  https://doi.org/10.1101/gr.257576.119
  2. Nucleic Acids Res. 2020 Sep 22. pii: gkaa736. [Epub ahead of print]
    Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization.
    Xiang Guo, Jennifer Plank-Bazinet, Ivan Krivega, Ryan K Dale, Ann Dean.
      The underlying mechanism of transcriptional co-repressor ETO2 during early erythropoiesis and hemoglobin switching is unclear. We find that absence of ETO2 in mice interferes with down-regulation of PU.1 and GATA2 in the fetal liver, impeding a key step required for commitment to erythroid maturation. In human β-globin transgenic Eto2 null mice and in human CD34+ erythroid progenitor cells with reduced ETO2, loss of ETO2 results in ineffective silencing of embryonic/fetal globin gene expression, impeding hemoglobin switching during erythroid differentiation. ETO2 occupancy genome-wide occurs virtually exclusively at LDB1-complex binding sites in enhancers and ETO2 loss leads to increased enhancer activity and expression of target genes. ETO2 recruits the NuRD nucleosome remodeling and deacetylation complex to regulate histone acetylation and nucleosome occupancy in the β-globin locus control region and γ-globin gene. Loss of ETO2 elevates LDB1, MED1 and Pol II in the locus and facilitates fetal γ-globin/LCR looping and γ-globin transcription. Absence of the ETO2 hydrophobic heptad repeat region impairs ETO2-NuRD interaction and function in antagonizing γ-globin/LCR looping. Our results reveal a pivotal role for ETO2 in erythropoiesis and globin gene switching through its repressive role in the LDB1 complex, affecting the transcription factor and epigenetic environment and ultimately restructuring chromatin organization.
    DOI:  https://doi.org/10.1093/nar/gkaa736
  3. Genome Res. 2020 Sep 24.
    Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay.
    Jennifer Hammelman, Konstantin Krismer, Budhaditya Banerjee, David K Gifford, Richard I Sherwood.
      A key mechanism in cellular regulation is the ability of the transcriptional machinery to physically access DNA. Transcription factors interact with DNA to alter the accessibility of chromatin, which enables changes to gene expression during development or disease or as a response to environmental stimuli. However, the regulation of DNA accessibility via the recruitment of transcription factors is difficult to study in the context of the native genome because every genomic site is distinct in multiple ways. Here we introduce the multiplexed integrated accessibility assay (MIAA), an assay that measures chromatin accessibility of synthetic oligonucleotide sequence libraries integrated into a controlled genomic context with low native accessibility. We apply MIAA to measure the effects of sequence motifs on cell type-specific accessibility between mouse embryonic stem cells and embryonic stem cell-derived definitive endoderm cells, screening 7905 distinct DNA sequences. MIAA recapitulates differential accessibility patterns of 100-nt sequences derived from natively differential genomic regions, identifying E-box motifs common to epithelial-mesenchymal transition driver transcription factors in stem cell-specific accessible regions that become repressed in endoderm. We show that a single binding motif for a key regulatory transcription factor is sufficient to open chromatin, and classify sets of stem cell-specific, endoderm-specific, and shared accessibility-modifying transcription factor motifs. We also show that overexpression of two definitive endoderm transcription factors, T and Foxa2, results in changes to accessibility in DNA sequences containing their respective DNA-binding motifs and identify preferential motif arrangements that influence accessibility.
    DOI:  https://doi.org/10.1101/gr.263228.120
  4. Dev Biol. 2020 Sep 17. pii: S0012-1606(20)30255-4. [Epub ahead of print]
    Zeb2 regulates the balance between retinal interneurons and muller glia by inhibition of BMP-Smad signaling.
    Yotam Menuchin-Lasowski, Bar Dagan, Andrea Conidi, Mazal Cohen-Gulkar, Ahuvit David, Marcelo Ehrlich, Pazit Oren Giladi, Brian S Clark, Seth Blackshaw, Keren Shapira, Danny Huylebroeck, Yoav Henis, Ruth Ashery-Padan.
      The interplay between signaling molecules and transcription factors during retinal development is key to controlling the correct number of retinal cell types. Zeb2 (Sip1) is a zinc-finger multidomain transcription factor that plays multiple roles in central and peripheral nervous system development. Haploinsufficiency of ZEB2 causes Mowat-Wilson syndrome, a congenital disease characterized by intellectual disability, epilepsy and Hirschsprung disease. In the developing retina, Zeb2 is required for generation of horizontal cells and the correct number of interneurons; however, its potential function in controlling gliogenic versus neurogenic decisions remains unresolved. Here we present cellular and molecular evidence of the inhibition of Muller glia cell fate by Zeb2 in late stages of retinogenesis. Unbiased transcriptomic profiling of control and Zeb2-deficient early-postnatal retina revealed that Zeb2 functions in inhibiting Id1/2/4 and Hes1 gene expression. These neural progenitor factors normally inhibit neural differentiation and promote Muller glia cell fate. Chromatin immunoprecipitation (ChIP) supported direct regulation of Id1 by Zeb2 in the postnatal retina. Reporter assays and ChIP analyses in differentiating neural progenitors provided further evidence that Zeb2 inhibits Id1 through inhibition of Smad-mediated activation of Id1 transcription. Together, the results suggest that Zeb2 promotes the timely differentiation of retinal interneurons at least in part by repressing BMP-Smad/Notch target genes that inhibit neurogenesis. These findings show that Zeb2 integrates extrinsic cues to regulate the balance between neuronal and glial cell types in the developing murine retina.
    Keywords:  BMP; Muller glia; Retinal progenitor cell; Retinogenesis; Zeb2
    DOI:  https://doi.org/10.1016/j.ydbio.2020.09.006
  5. Nat Struct Mol Biol. 2020 Sep 21.
    Single-gene imaging links genome topology, promoter-enhancer communication and transcription control.
    Jieru Li, Angela Hsu, Yujing Hua, Guanshi Wang, Lingling Cheng, Hiroshi Ochiai, Takashi Yamamoto, Alexandros Pertsinidis.
      Transcription activation by distal enhancers is essential for cell-fate specification and maintenance of cellular identities. How long-range gene regulation is physically achieved, especially within complex regulatory landscapes of non-binary enhancer-promoter configurations, remains elusive. Recent nanoscopy advances have quantitatively linked promoter kinetics and ~100- to 200-nm-sized clusters of enhancer-associated regulatory factors (RFs) at important developmental genes. Here, we further dissect mechanisms of RF clustering and transcription activation in mouse embryonic stem cells. RF recruitment into clusters involves specific molecular recognition of cognate DNA and chromatin-binding sites, suggesting underlying cis-element clustering. Strikingly, imaging of tagged genomic loci, with ≤1 kilobase and ~20-nanometer precision, in live cells, reveals distal enhancer clusters over the extended locus in frequent close proximity to target genes-within RF-clustering distances. These high-interaction-frequency enhancer-cluster 'superclusters' create nano-environments wherein clustered RFs activate target genes, providing a structural framework for relating genome organization, focal RF accumulation and transcription activation.
    DOI:  https://doi.org/10.1038/s41594-020-0493-6
  6. Sci Adv. 2020 Sep;pii: eaba8811. [Epub ahead of print]6(39):
    Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.
    Ezequiel Miron, Roel Oldenkamp, Jill M Brown, David M S Pinto, C Shan Xu, Ana R Faria, Haitham A Shaban, James D P Rhodes, Cassandravictoria Innocent, Sara de Ornellas, Harald F Hess, Veronica Buckle, Lothar Schermelleh.
      Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function; however, many of its physical features at the single-cell level remain underexplored. Here, we use live- and fixed-cell 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify chains of interlinked ~200- to 300-nm-wide chromatin domains (CDs) composed of aggregated nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin compartment. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications toward the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.
    DOI:  https://doi.org/10.1126/sciadv.aba8811
  7. Nat Genet. 2020 Sep 21.
    Transcription imparts architecture, function and logic to enhancer units.
    Nathaniel D Tippens, Jin Liang, Alden King-Yung Leung, Shayne D Wierbowski, Abdullah Ozer, James G Booth, John T Lis, Haiyuan Yu.
      Distal enhancers play pivotal roles in development and disease yet remain one of the least understood regulatory elements. We used massively parallel reporter assays to perform functional comparisons of two leading enhancer models and find that gene-distal transcription start sites are robust predictors of active enhancers with higher resolution than histone modifications. We show that active enhancer units are precisely delineated by active transcription start sites, validate that these boundaries are sufficient for capturing enhancer function, and confirm that core promoter sequences are necessary for this activity. We assay adjacent enhancers and find that their joint activity is often driven by the stronger unit within the cluster. Finally, we validate these results through functional dissection of a distal enhancer cluster using CRISPR-Cas9 deletions. In summary, definition of high-resolution enhancer boundaries enables deconvolution of complex regulatory loci into modular units.
    DOI:  https://doi.org/10.1038/s41588-020-0686-2
  8. Cell Rep. 2020 Sep 22. pii: S2211-1247(20)31155-4. [Epub ahead of print]32(12): 108166
    BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation.
    Drake S Edwards, Rohin Maganti, Jarred P Tanksley, Jie Luo, James J H Park, Elena Balkanska-Sinclair, Jinjie Ling, Scott R Floyd.
      Effective spatio-temporal control of transcription and replication during S-phase is paramount to maintaining genomic integrity and cell survival. Dysregulation of these systems can lead to conflicts between the transcription and replication machinery, causing DNA damage and cell death. BRD4 allows efficient transcriptional elongation by stimulating phosphorylation of RNA polymerase II (RNAPII). We report that bromodomain and extra-terminal domain (BET) protein loss of function (LOF) causes RNAPII pausing on the chromatin and DNA damage affecting cells in S-phase. This persistent RNAPII-dependent pausing leads to an accumulation of RNA:DNA hybrids (R-loops) at sites of BRD4 occupancy, leading to transcription-replication conflicts (TRCs), DNA damage, and cell death. Finally, our data show that the BRD4 C-terminal domain, which interacts with P-TEFb, is required to prevent R-loop formation and DNA damage caused by BET protein LOF.
    Keywords:  BET bromodomain; BRD4; DNA damage; JQ1; P-TEFb; R-loop; RNApol II; gH2AX; replication stress; replication-transcription conflict
    DOI:  https://doi.org/10.1016/j.celrep.2020.108166
  9. Sci Rep. 2020 Sep 23. 10(1): 15491
    A modified protocol of Capture-C allows affordable and flexible high-resolution promoter interactome analysis.
    Arkadiy K Golov, Dmitrii A Abashkin, Nikolay V Kondratyev, Sergey V Razin, Alexey A Gavrilov, Vera E Golimbet.
      Large-scale epigenomic projects have mapped hundreds of thousands of potential regulatory sites in the human genome, but only a small proportion of these elements are proximal to transcription start sites. It is believed that the majority of these sequences are remote promoter-activating genomic sites scattered within several hundreds of kilobases from their cognate promoters and referred to as enhancers. It is still unclear what principles, aside from relative closeness in the linear genome, determine which promoter(s) is controlled by a given enhancer; however, this understanding is of great fundamental and clinical relevance. In recent years, C-methods (chromosome conformation capture-based methods) have become a powerful tool for the identification of enhancer-promoter spatial contacts that, in most cases, reflect their functional link. Here, we describe a new hybridisation-based promoter Capture-C protocol that makes use of biotinylated dsDNA probes generated by PCR from a custom pool of long oligonucleotides. The described protocol allows high-resolution promoter interactome description, providing a flexible and cost-effective alternative to the existing promoter Capture-C modifications. Based on the obtained data, we propose several tips on probe design that could potentially improve the results of future experiments.
    DOI:  https://doi.org/10.1038/s41598-020-72496-4
  10. Nucleic Acids Res. 2020 Sep 25. pii: gkaa722. [Epub ahead of print]
    TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation.
    Federico Marini, Denise Scherzinger, Sven Danckwardt.
      Alternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3' end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3' end maturation is closely linked to transcription, RNA processing and even epigenetic (histone/DNA/RNA) modifications. Here, we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and post-transcriptional gene regulation, epigenetic modifications and further processes. TREND-DB visualizes the dynamics of transcriptome 3' end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA-binding sites and RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps identify their diagnostic and therapeutic potential.
    DOI:  https://doi.org/10.1093/nar/gkaa722
  11. Nat Commun. 2020 09 22. 11(1): 4782
    A theoretical model of Polycomb/Trithorax action unites stable epigenetic memory and dynamic regulation.
    Jeannette Reinig, Frank Ruge, Martin Howard, Leonie Ringrose.
      Polycomb and Trithorax group proteins maintain stable epigenetic memory of gene expression states for some genes, but many targets show highly dynamic regulation. Here we combine experiment and theory to examine the mechanistic basis of these different modes of regulation. We present a mathematical model comprising a Polycomb/Trithorax response element (PRE/TRE) coupled to a promoter and including Drosophila developmental timing. The model accurately recapitulates published studies of PRE/TRE mediated epigenetic memory of both silencing and activation. With minimal parameter changes, the same model can also recapitulate experimental data for a different PRE/TRE that allows dynamic regulation of its target gene. The model predicts that both cell cycle length and PRE/TRE identity are critical for determining whether the system gives stable memory or dynamic regulation. Our work provides a simple unifying framework for a rich repertoire of PRE/TRE functions, and thus provides insights into  genome-wide Polycomb/Trithorax regulation.
    DOI:  https://doi.org/10.1038/s41467-020-18507-4
  12. Nat Commun. 2020 09 21. 11(1): 4766
    Telomere dysfunction activates YAP1 to drive tissue inflammation.
    Deepavali Chakravarti, Baoli Hu, Xizeng Mao, Asif Rashid, Jiexi Li, Jun Li, Wen-Ting Liao, Elizabeth M Whitley, Prasenjit Dey, Pingping Hou, Kyle A LaBella, Andrew Chang, Guocan Wang, Denise J Spring, Pingna Deng, Di Zhao, Xin Liang, Zhengdao Lan, Yiyun Lin, Sharmistha Sarkar, Christopher Terranova, Yonathan Lissanu Deribe, Sarah E Blutt, Pablo Okhuysen, Jianhua Zhang, Eduardo Vilar, Ole Haagen Nielsen, Andrew Dupont, Mamoun Younes, Kalyani R Patel, Noah F Shroyer, Kunal Rai, Mary K Estes, Y Alan Wang, Alison A Bertuch, Ronald A DePinho.
      Germline telomere maintenance defects are associated with an increased incidence of inflammatory diseases in humans, yet whether and how telomere dysfunction causes inflammation are not known. Here, we show that telomere dysfunction drives pATM/c-ABL-mediated activation of the YAP1 transcription factor, up-regulating the major pro-inflammatory factor, pro-IL-18. The colonic microbiome stimulates cytosolic receptors activating caspase-1 which cleaves pro-IL-18 into mature IL-18, leading to recruitment of interferon (IFN)-γ-secreting T cells and intestinal inflammation. Correspondingly, patients with germline telomere maintenance defects exhibit DNA damage (γH2AX) signaling together with elevated YAP1 and IL-18 expression. In mice with telomere dysfunction, telomerase reactivation in the intestinal epithelium or pharmacological inhibition of ATM, YAP1, or caspase-1 as well as antibiotic treatment, dramatically reduces IL-18 and intestinal inflammation. Thus, telomere dysfunction-induced activation of the ATM-YAP1-pro-IL-18 pathway in epithelium is a key instigator of tissue inflammation.
    DOI:  https://doi.org/10.1038/s41467-020-18420-w
  13. Methods. 2020 Sep 16. pii: S1046-2023(20)30204-8. [Epub ahead of print]
    Detect differentially methylated regions using non-homogeneous hidden Markov model for bisulfite sequencing data.
    Yingyu Chen, Chin Kiu Kwok, Hangjin Jiang, Xiaodan Fan.
      DNA methylation plays an important role in many biological processes and diseases. With the rise of the whole genome bisulfite sequencing technique, aberrant methylation patterns can now be detected by comparing paired normal and disease samples at the single nucleotide level. We develop a novel Bayesian method for detecting differentially methylated regions from paired bisulfite sequencing data, and implement it as a R package called BSDMR. Based on a non-homogeneous hidden Markov model, BSDMR provides a better modeling strategy for the spatial correlation between CpG sites and takes into consideration the relationship between methylation signals from normal and disease samples. Simulations show that BSDMR performs well even under low read depth and has a smaller false discovery rates than existing methods. We also apply BSDMR to the colon cancer data from Gene Expression Omnibus. The detected DMRs are well supported by existing biomedical literatures.
    Keywords:  Bayesian inference; Bisulfite sequencing; DNA methylation; Differentially methylated region; Non-homogeneous hidden Markov model
    DOI:  https://doi.org/10.1016/j.ymeth.2020.09.009
  14. BMC Genomics. 2020 Sep 21. 21(1): 646
    SWI/SNF complexes act through CBP-1 histone acetyltransferase to regulate acute functional tolerance to alcohol.
    Laura D Mathies, Jonathan H Lindsay, Amal P Handal, GinaMari G Blackwell, Andrew G Davies, Jill C Bettinger.
       BACKGROUND: SWI/SNF chromatin remodeling genes are required for normal acute responses to alcohol in C. elegans and are associated with alcohol use disorder in two human populations. In an effort to discover the downstream genes that are mediating this effect, we identified SWI/SNF-regulated genes in C. elegans.
    RESULTS: To identify SWI/SNF-regulated genes in adults, we compared mRNA expression in wild type and swsn-1(os22ts) worms under conditions that produce inactive swsn-1 in mature cells. To identify SWI/SNF-regulated genes in neurons, we compared gene expression in swsn-9(ok1354) null mutant worms that harbor a neuronal rescue or a control construct. RNA sequencing was performed to an average depth of 25 million reads per sample using 50-base, paired-end reads. We found that 6813 transcripts were significantly differentially expressed between swsn-1(os22ts) mutants and wild-type worms and 2412 transcripts were significantly differentially expressed between swsn-9(ok1354) mutants and swsn-9(ok1354) mutants with neuronal rescue. We examined the intersection between these two datasets and identified 603 genes that were differentially expressed in the same direction in both comparisons; we defined these as SWI/SNF-regulated genes in neurons and in adults. Among the differentially expressed genes was cbp-1, a C. elegans homolog of the mammalian CBP/p300 family of histone acetyltransferases. CBP has been implicated in the epigenetic regulation in response to alcohol in animal models and a polymorphism in the human CBP gene, CREBBP, has been associated with alcohol-related phenotypes. We found that cbp-1 is required for the development of acute functional tolerance to alcohol in C. elegans.
    CONCLUSIONS: We identified 603 transcripts that were regulated by two different SWI/SNF complex subunits in adults and in neurons. The SWI/SNF-regulated genes were highly enriched for genes involved in membrane rafts, suggesting an important role for this membrane microdomain in the acute alcohol response. Among the differentially expressed genes was cbp-1; CBP-1 homologs have been implicated in alcohol responses across phyla and we found that C. elegans cbp-1 was required for the acute alcohol response in worms.
    Keywords:  Alcohol; C. elegans; Differential gene expression; Ethanol; Histone acetyltransferase; SWI/SNF chromatin remodeling; Transcriptome; cbp-1
    DOI:  https://doi.org/10.1186/s12864-020-07059-y
  15. Cell Chem Biol. 2020 Sep 16. pii: S2451-9456(20)30342-1. [Epub ahead of print]
    Discovery of a Functional Covalent Ligand Targeting an Intrinsically Disordered Cysteine within MYC.
    Lydia Boike, Alexander G Cioffi, Felix C Majewski, Jennifer Co, Nathaniel J Henning, Michael D Jones, Gang Liu, Jeffrey M McKenna, John A Tallarico, Markus Schirle, Daniel K Nomura.
      MYC is a major oncogenic transcriptional driver of most human cancers that has remained intractable to direct targeting because much of MYC is intrinsically disordered. Here, we have performed a cysteine-reactive covalent ligand screen to identify compounds that could disrupt the binding of MYC to its DNA consensus sequence in vitro and also impair MYC transcriptional activity in situ in cells. We have identified a covalent ligand, EN4, that targets cysteine 171 of MYC within a predicted intrinsically disordered region of the protein. We show that EN4 directly targets MYC in cells, reduces MYC and MAX thermal stability, inhibits MYC transcriptional activity, downregulates multiple MYC transcriptional targets, and impairs tumorigenesis. We also show initial structure-activity relationships of EN4 and identify compounds that show improved potency. Overall, we identify a unique ligandable site within an intrinsically disordered region of MYC that leads to inhibition of MYC transcriptional activity.
    Keywords:  MYC; activity-based protein profiling; chemoproteomics; covalent ligand; cysteine; intrinsically disordered; transcription factor; undruggable
    DOI:  https://doi.org/10.1016/j.chembiol.2020.09.001
  16. Nat Methods. 2020 Sep 23.
    Detecting chromatin interactions between and along sister chromatids with SisterC.
    Marlies E Oomen, Adam K Hedger, Jonathan K Watts, Job Dekker.
      Chromosome segregation requires both compaction and disentanglement of sister chromatids. We describe SisterC, a chromosome conformation capture assay that distinguishes interactions between and along identical sister chromatids. SisterC employs 5-bromo-2'-deoxyuridine (BrdU) incorporation during S-phase to label newly replicated strands, followed by Hi-C and then the destruction of 5-bromodeoxyuridine-containing strands via Hoechst/ultraviolet treatment. After sequencing of the remaining intact strands, this allows assignment of Hi-C products as inter- and intra-sister interactions based on the strands that reads are mapped to. We performed SisterC on mitotic Saccharomyces cerevisiae cells. We find precise alignment of sister chromatids at centromeres. Along arms, sister chromatids are less precisely aligned, with inter-sister connections every ~35 kilobase (kb). Inter-sister interactions occur between cohesin binding sites that are often offset by 5 to 25 kb. Along sister chromatids, cohesin results in the formation of loops of up to 50 kb. SisterC allows study of the complex interplay between sister chromatid compaction and their segregation during mitosis.
    DOI:  https://doi.org/10.1038/s41592-020-0930-9
  17. Nat Commun. 2020 Sep 25. 11(1): 4873
    Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism.
    Gokul Ramaswami, Hyejung Won, Michael J Gandal, Jillian Haney, Jerry C Wang, Chloe C Y Wong, Wenjie Sun, Shyam Prabhakar, Jonathan Mill, Daniel H Geschwind.
      Autism spectrum disorder (ASD) is a phenotypically and genetically heterogeneous neurodevelopmental disorder. Despite this heterogeneity, previous studies have shown patterns of molecular convergence in post-mortem brain tissue from autistic subjects. Here, we integrate genome-wide measures of mRNA expression, miRNA expression, DNA methylation, and histone acetylation from ASD and control brains to identify a convergent molecular subtype of ASD with shared dysregulation across both the epigenome and transcriptome. Focusing on this convergent subtype, we substantially expand the repertoire of differentially expressed genes in ASD and identify a component of upregulated immune processes that are associated with hypomethylation. We utilize eQTL and chromosome conformation datasets to link differentially acetylated regions with their cognate genes and identify an enrichment of ASD genetic risk variants in hyperacetylated noncoding regulatory regions linked to neuronal genes. These findings help elucidate how diverse genetic risk factors converge onto specific molecular processes in ASD.
    DOI:  https://doi.org/10.1038/s41467-020-18526-1
  18. Nature. 2020 Sep 23.
    Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B.
    Ting-Hai Xu, Minmin Liu, X Edward Zhou, Gangning Liang, Gongpu Zhao, H Eric Xu, Karsten Melcher, Peter A Jones.
      CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer1. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core2, and they favour the methylation of linker DNA at positioned nucleosomes3,4. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.
    DOI:  https://doi.org/10.1038/s41586-020-2747-1
  19. Mol Cell. 2020 Sep 16. pii: S1097-2765(20)30579-7. [Epub ahead of print]
    Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination.
    Kai-Lieh Huang, David Jee, Chad B Stein, Nathan D Elrod, Telmo Henriques, Lauren G Mascibroda, David Baillat, William K Russell, Karen Adelman, Eric J Wagner.
      Efficient release of promoter-proximally paused RNA Pol II into productive elongation is essential for gene expression. Recently, we reported that the Integrator complex can bind paused RNA Pol II and drive premature transcription termination, potently attenuating the activity of target genes. Premature termination requires RNA cleavage by the endonuclease subunit of Integrator, but the roles of other Integrator subunits in gene regulation have yet to be elucidated. Here we report that Integrator subunit 8 (IntS8) is critical for transcription repression and required for association with protein phosphatase 2A (PP2A). We find that Integrator-bound PP2A dephosphorylates the RNA Pol II C-terminal domain and Spt5, preventing the transition to productive elongation. Thus, blocking PP2A association with Integrator stimulates pause release and gene activity. These results reveal a second catalytic function associated with Integrator-mediated transcription termination and indicate that control of productive elongation involves active competition between transcriptional kinases and phosphatases.
    Keywords:  Integrator; paused RNA Pol II; phosphatase; transcription regulation; transcription termination
    DOI:  https://doi.org/10.1016/j.molcel.2020.08.016
  20. Genome Res. 2020 Sep 22.
    Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes.
    Andrea Halaburkova, Vincent Cahais, Alexei Novoloaca, Mariana Gomes da Silva Araujo, Rita Khoueiry, Akram Ghantous, Zdenko Herceg.
      The recent identification of recurrently mutated epigenetic regulator genes (ERGs) supports their critical role in tumorigenesis. We conducted a pan-cancer analysis integrating (epi)genome, transcriptome, and DNA methylome alterations in a curated list of 426 ERGs across 33 cancer types, comprising 10,845 tumor and 730 normal tissues. We found that, in addition to mutations, copy number alterations in ERGs were more frequent than previously anticipated and tightly linked to expression aberrations. Novel bioinformatics approaches, integrating the strengths of various driver prediction and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far; it is also the first experimental effort to specifically identify ERG drivers (epidrivers) and characterize their deregulation and functional impact in oncogenic processes.
    DOI:  https://doi.org/10.1101/gr.268292.120
  21. Oncogene. 2020 Sep 25.
    The transcription factor NRF2 enhances melanoma malignancy by blocking differentiation and inducing COX2 expression.
    Christina Jessen, Julia K C Kreß, Apoorva Baluapuri, Anita Hufnagel, Werner Schmitz, Susanne Kneitz, Sabine Roth, André Marquardt, Silke Appenzeller, Carsten P Ade, Valerie Glutsch, Marion Wobser, José Pedro Friedmann-Angeli, Laura Mosteo, Colin R Goding, Bastian Schilling, Eva Geissinger, Elmar Wolf, Svenja Meierjohann.
      The transcription factor NRF2 is the major mediator of oxidative stress responses and is closely connected to therapy resistance in tumors harboring activating mutations in the NRF2 pathway. In melanoma, such mutations are rare, and it is unclear to what extent melanomas rely on NRF2. Here we show that NRF2 suppresses the activity of the melanocyte lineage marker MITF in melanoma, thereby reducing the expression of pigmentation markers. Intriguingly, we furthermore identified NRF2 as key regulator of immune-modulating genes, linking oxidative stress with the induction of cyclooxygenase 2 (COX2) in an ATF4-dependent manner. COX2 is critical for the secretion of prostaglandin E2 and was strongly induced by H2O2 or TNFα only in presence of NRF2. Induction of MITF and depletion of COX2 and PGE2 were also observed in NRF2-deleted melanoma cells in vivo. Furthermore, genes corresponding to the innate immune response such as RSAD2 and IFIH1 were strongly elevated in absence of NRF2 and coincided with immune evasion parameters in human melanoma datasets. Even in vitro, NRF2 activation or prostaglandin E2 supplementation blunted the induction of the innate immune response in melanoma cells. Transcriptome analyses from lung adenocarcinomas indicate that the observed link between NRF2 and the innate immune response is not restricted to melanoma.
    DOI:  https://doi.org/10.1038/s41388-020-01477-8
  22. Bioinformatics. 2020 Sep 22. pii: btaa825. [Epub ahead of print]
    methylclock: a Bioconductor package to estimate DNA methylation age.
    Dolors Pelegí-Sisó, Paula de Prado, Justiina Ronkainen, Mariona Bustamante, Juan R González.
       MOTIVATION: Ageing is a biological and psychosocial process related to diseases and mortality. It correlates with changes in DNA methylation (DNAm) in all human tissues. Therefore, epigenetic markers can be used to estimate biological age using DNA methylation profiling across tissues.
    RESULTS: We developed a Bioconductor package that allows computation of several existing DNAm adult/childhood and gestational age clocks. Functions to visualize the DNAm age prediction versus chronological age and the correlation between DNAm clocks are also available as well as other features such as missing data imputation of cell types estimates that are required for DNAm age clocks.
    AVAILABILITY: https://github.com/isglobal-brge/methylclock.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa825
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