bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2021‒07‒11
twenty-four papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit
  1. BANP opens chromatin and activates CpG-island-regulated genes.
  2. M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity.
  3. Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver.
  4. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes.
  5. EZH2-induced lysine K362 methylation enhances TMPRSS2-ERG oncogenic activity in prostate cancer.
  6. Local states of chromatin compaction at transcription start sites control transcription levels.
  7. TAD cliques predict key features of chromatin organization.
  8. How subtle changes in 3D structure can create large changes in transcription.
  9. Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness.
  10. Enhanced regulation of prokaryotic gene expression by a eukaryotic transcriptional activator.
  11. LSH catalyzes ATP-driven exchange of histone variants macroH2A1 and macroH2A2.
  12. Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.
  13. Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer's disease.
  14. Differential ATAC-seq and ChIP-seq peak detection using ROTS.
  15. Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication.
  16. Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility.
  17. ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors.
  18. Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast.
  19. Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci.
  20. Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma.
  21. SoxD transcription factor deficiency in Schwann cells delays myelination in the developing peripheral nervous system.
  22. Distinct nuclear compartment-associated genome architecture in the developing mammalian brain.
  23. Dynamic chromatin association of IκBα is regulated by acetylation and cleavage of histone H4.
  24. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination.
  1. Nature. 2021 Jul 07.
    BANP opens chromatin and activates CpG-island-regulated genes.
    Ralph S Grand, Lukas Burger, Cathrin Gräwe, Alicia K Michael, Luke Isbel, Daniel Hess, Leslie Hoerner, Vytautas Iesmantavicius, Sevi Durdu, Marco Pregnolato, Arnaud R Krebs, Sébastien A Smallwood, Nicolas Thomä, Michiel Vermeulen, Dirk Schübeler.
      The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3-5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6-8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening.
    DOI:  https://doi.org/10.1038/s41586-021-03689-8
  2. Nat Commun. 2021 Jul 07. 12(1): 4170
    M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity.
    Indira Bag, Shue Chen, Leah F Rosin, Yang Chen, Chen-Yu Liu, Guo-Yun Yu, Elissa P Lei.
      Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP facilitates CP190 chromatin binding at many shared sites and vice versa. Both factors promote Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP reduces chromatin accessibility and increases both inter- and intra-TAD local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.
    DOI:  https://doi.org/10.1038/s41467-021-24407-y
  3. Nat Commun. 2021 07 05. 12(1): 4110
    Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver.
    Chi Zhang, Filippo Macchi, Elena Magnani, Kirsten C Sadler.
      We hypothesized that the highly controlled pattern of gene expression that is essential for liver regeneration is encoded by an epigenetic code set in quiescent hepatocytes. Here we report that epigenetic and transcriptomic profiling of quiescent and regenerating mouse livers define chromatin states that dictate gene expression and transposon repression. We integrate ATACseq and DNA methylation profiling with ChIPseq for the histone marks H3K4me3, H3K27me3 and H3K9me3 and the histone variant H2AZ to identify 6 chromatin states with distinct functional characteristics. We show that genes involved in proliferation reside in active states, but are marked with H3K27me3 and silenced in quiescent livers. We find that during regeneration, H3K27me3 is depleted from their promoters, facilitating their dynamic expression. These findings demonstrate that hepatic chromatin states in quiescent livers predict gene expression and that pro-regenerative genes are maintained in active chromatin states, but are restrained by H3K27me3, permitting a rapid and synchronized response during regeneration.
    DOI:  https://doi.org/10.1038/s41467-021-24466-1
  4. Clin Epigenetics. 2021 Jul 08. 13(1): 138
    The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes.
    Tasnim H Beacon, Geneviève P Delcuve, Camila López, Gino Nardocci, Igor Kovalchuk, Andre J van Wijnen, James R Davie.
      Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain which extensively covers the coding region. Although most studies focus on the H3K4me3 mark, the broad H3K4me3 domain is associated with a plethora of histone modifications (e.g., H3 acetylated at K27) and is therein termed broad epigenetic domain. Genes marked with the broad epigenetic domain are involved in cell identity and essential cell functions and have clinical potential as biomarkers for patient stratification. Reducing expression of genes with the broad epigenetic domain may increase the metastatic potential of cancer cells. Enhancers and super-enhancers interact with the broad epigenetic domain marked genes forming a hub of interactions involving nucleosome-depleted regions. Together, the regulatory elements coalesce with transcription factors, chromatin modifying/remodeling enzymes, coactivators, and the Mediator and/or Integrator complex into a transcription factory which may be analogous to a liquid-liquid phase-separated condensate. The broad epigenetic domain has a dynamic chromatin structure which supports frequent transcription bursts. In this review, we present the current knowledge of broad epigenetic domains.
    Keywords:  Broad H3K4me3 domains; Cell identity genes; Enhancers; Epigenetics; Histone modifications; Tumor suppressor genes
    DOI:  https://doi.org/10.1186/s13148-021-01126-1
  5. Nat Commun. 2021 07 06. 12(1): 4147
    EZH2-induced lysine K362 methylation enhances TMPRSS2-ERG oncogenic activity in prostate cancer.
    Marita Zoma, Laura Curti, Dheeraj Shinde, Domenico Albino, Abhishek Mitra, Jacopo Sgrignani, Sarah N Mapelli, Giada Sandrini, Gianluca Civenni, Jessica Merulla, Giovanna Chiorino, Paolo Kunderfranco, Alessia Cacciatore, Aleksandra Kokanovic, Andrea Rinaldi, Andrea Cavalli, Carlo V Catapano, Giuseppina M Carbone.
      The TMPRSS2-ERG gene fusion is the most frequent alteration observed in human prostate cancer. However, its role in disease progression is still unclear. In this study, we uncover an important mechanism promoting ERG oncogenic activity. We show that ERG is methylated by Enhancer of zest homolog 2 (EZH2) at a specific lysine residue (K362) located within the internal auto-inhibitory domain. Mechanistically, K362 methylation modifies intra-domain interactions, favors DNA binding and enhances ERG transcriptional activity. In a genetically engineered mouse model of ERG fusion-positive prostate cancer (Pb-Cre4 Pten flox/flox Rosa26-ERG, ERG/PTEN), ERG K362 methylation is associated with PTEN loss and progression to invasive adenocarcinomas. In both ERG positive VCaP cells and ERG/PTEN mice, PTEN loss results in AKT activation and EZH2 phosphorylation at serine 21 that favors ERG methylation. We find that ERG and EZH2 interact and co-occupy several sites in the genome forming trans-activating complexes. Consistently, ERG/EZH2 co-regulated target genes are deregulated preferentially in tumors with concomitant ERG gain and PTEN loss and in castration-resistant prostate cancers. Collectively, these findings identify ERG methylation as a post-translational modification sustaining disease progression in ERG-positive prostate cancers.
    DOI:  https://doi.org/10.1038/s41467-021-24380-6
  6. Nucleic Acids Res. 2021 Jul 07. pii: gkab587. [Epub ahead of print]
    Local states of chromatin compaction at transcription start sites control transcription levels.
    Satoru Ishihara, Yohei Sasagawa, Takeru Kameda, Hayato Yamashita, Mana Umeda, Naoe Kotomura, Masayuki Abe, Yohei Shimono, Itoshi Nikaido.
      The 'open' and 'compact' regions of chromatin are considered to be regions of active and silent transcription, respectively. However, individual genes produce transcripts at different levels, suggesting that transcription output does not depend on the simple open-compact conversion of chromatin, but on structural variations in chromatin itself, which so far have remained elusive. In this study, weakly crosslinked chromatin was subjected to sedimentation velocity centrifugation, which fractionated the chromatin according to its degree of compaction. Open chromatin remained in upper fractions, while compact chromatin sedimented to lower fractions depending on the level of nucleosome assembly. Although nucleosomes were evenly detected in all fractions, histone H1 was more highly enriched in the lower fractions. H1 was found to self-associate and crosslinked to histone H3, suggesting that H1 bound to H3 interacts with another H1 in an adjacent nucleosome to form compact chromatin. Genome-wide analyses revealed that nearly the entire genome consists of compact chromatin without differences in compaction between repeat and non-repeat sequences; however, active transcription start sites (TSSs) were rarely found in compact chromatin. Considering the inverse correlation between chromatin compaction and RNA polymerase binding at TSSs, it appears that local states of chromatin compaction determine transcription levels.
    DOI:  https://doi.org/10.1093/nar/gkab587
  7. BMC Genomics. 2021 Jul 03. 22(1): 499
    TAD cliques predict key features of chromatin organization.
    Tharvesh M Liyakat Ali, Annaël Brunet, Philippe Collas, Jonas Paulsen.
      BACKGROUND: Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and interactions with the nuclear lamina dynamically act on chromatin at multiple levels. Here, we explore long-range interaction patterns between topologically associated domains (TADs) in several cell types.RESULTS: We find that TAD long-range interactions are connected to many key features of chromatin organization, including open and closed compartments, compaction and loop extrusion processes. Domains that form large TAD cliques tend to be repressive across cell types, when comparing gene expression, LINE/SINE repeat content and chromatin subcompartments. Further, TADs in large cliques are larger in genomic size, less dense and depleted of convergent CTCF motifs, in contrast to smaller and denser TADs formed by a loop extrusion process.
    CONCLUSIONS: Our results shed light on the organizational principles that govern repressive and active domains in the human genome.
    Keywords:  3D genome; Hi-C, TAD, CTCF motif; chromatin conformation
    DOI:  https://doi.org/10.1186/s12864-021-07815-8
  8. Elife. 2021 Jul 09. pii: e64320. [Epub ahead of print]10
    How subtle changes in 3D structure can create large changes in transcription.
    Jordan Yupeng Xiao, Antonina Hafner, Alistair N Boettiger.
      Animal genomes are organized into topologically associated domains (TADs). TADs are thought to contribute to gene regulation by facilitating enhancer-promoter (E-P) contacts within a TAD preventing these contacts across TAD borders. However, the absolute difference in contact frequency across TAD boundaries is usually less than two-fold, even though disruptions of TAD borders can change gene expression by ten-fold. Existing models fail to explain this hypersensitive response. Here, we propose a futile cycle model of enhancer-mediated regulation that can exhibit hypersensitivity through bistability and hysteresis. Consistent with recent experiments, this regulation does not exhibit strong correlation between enhancer-promoter contact and promoter activity, even though regulation occurs through contact. Through mathematical analysis and stochastic simulation, we show that this system can create an illusion of enhancer-promoter biochemical specificity and explain the importance of weak TAD boundaries. It also offers a mechanism to reconcile apparently contradictory results from recent global TAD disruption with local TAD boundary deletion experiments. Together, these analyses advance our understanding of cis-regulatory contacts in controlling gene expression, and suggest new experimental directions.
    Keywords:  D. melanogaster; chromosomes; computational biology; gene expression; human; mouse; systems biology
    DOI:  https://doi.org/10.7554/eLife.64320
  9. Elife. 2021 Jul 08. pii: e64212. [Epub ahead of print]10
    Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness.
    Haritha Mathsyaraja, Jonathen Catchpole, Brian Freie, Emily Eastwood, Ekaterina Babaeva, Michael Geuenich, Pei Feng Cheng, Jessica Ayers, Ming Yu, Nan Wu, Sitapriya Moorthi, Kumud R Poudel, Amanda Koehne, William Grady, A McGarry Houghton, Alice H Berger, Yuzuru Shiio, David MacPherson, Robert N Eisenman.
      MGA, a transcription factor and member of the MYC network, is mutated or deleted in a broad spectrum of malignancies. As a critical test of a tumor suppressive role, we inactivated Mga in two mouse models of non-small cell lung cancer using a CRISPR-based approach. MGA loss significantly accelerated tumor growth in both models and led to de-repression of non-canonical Polycomb ncPRC1.6 targets, including genes involved in metastasis and meiosis. Moreover, MGA deletion in human lung adenocarcinoma lines augmented invasive capabilities. We further show that MGA-MAX, E2F6, and L3MBTL2 co-occupy thousands of promoters and that MGA stabilizes these ncPRC1.6 subunits. Lastly, we report that MGA loss also induces a pro-growth effect in human colon organoids. Our studies establish MGA as a bona fide tumor suppressor in vivo and suggest a tumor suppressive mechanism in adenocarcinomas resulting from widespread transcriptional attenuation of MYC and E2F target genes mediated by MGA-MAX associated with a non-canonical Polycomb complex.
    Keywords:  MAX; MGA; cancer biology; colon organoids; lung adenocarcinoma; mouse; non-canonical polycomb; tumor suppressor
    DOI:  https://doi.org/10.7554/eLife.64212
  10. Nat Commun. 2021 07 05. 12(1): 4109
    Enhanced regulation of prokaryotic gene expression by a eukaryotic transcriptional activator.
    I Cody MacDonald, Travis R Seamons, Jonathan C Emmons, Shwan B Javdan, Tara L Deans.
      Expanding the genetic toolbox for prokaryotic synthetic biology is a promising strategy for enhancing the dynamic range of gene expression and enabling new engineered applications for research and biomedicine. Here, we reverse the current trend of moving genetic parts from prokaryotes to eukaryotes and demonstrate that the activating eukaryotic transcription factor QF and its corresponding DNA-binding sequence can be moved to E. coli to introduce transcriptional activation, in addition to tight off states. We further demonstrate that the QF transcription factor can be used in genetic devices that respond to low input levels with robust and sustained output signals. Collectively, we show that eukaryotic gene regulator elements are functional in prokaryotes and establish a versatile and broadly applicable approach for constructing genetic circuits with complex functions. These genetic tools hold the potential to improve biotechnology applications for medical science and research.
    DOI:  https://doi.org/10.1038/s41467-021-24434-9
  11. Nucleic Acids Res. 2021 Jul 05. pii: gkab588. [Epub ahead of print]
    LSH catalyzes ATP-driven exchange of histone variants macroH2A1 and macroH2A2.
    Kai Ni, Kathrin Muegge.
      LSH, a homologue of the ISWI/SNF2 family of chromatin remodelers, is required in vivo for deposition of the histone variants macroH2A1 and macroH2A2 at specific genomic locations. However, it remains unknown whether LSH is directly involved in this process or promotes other factors. Here we show that recombinant LSH interacts in vitro with macroH2A1-H2B and macroH2A2-H2B dimers, but not with H2A.Z-H2B dimers. Moreover, LSH catalyzes the transfer of macroH2A into mono-nucleosomes reconstituted with canonical core histones in an ATP dependent manner. LSH requires the ATP binding site and the replacement process is unidirectional leading to heterotypic and homotypic nucleosomes. Both variants macroH2A1 and macroH2A2 are equally well incorporated into the nucleosome. The histone exchange reaction is specific for histone variant macroH2A, since LSH is not capable to incorporate H2A.Z. These findings define a previously unknown role for LSH in chromatin remodeling and identify a novel molecular mechanism for deposition of the histone variant macroH2A.
    DOI:  https://doi.org/10.1093/nar/gkab588
  12. Mol Cell. 2021 Jun 29. pii: S1097-2765(21)00493-7. [Epub ahead of print]
    Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.
    Jaclyn M Einstein, Mark Perelis, Isaac A Chaim, Jitendra K Meena, Julia K Nussbacher, Alexandra T Tankka, Brian A Yee, Heyuan Li, Assael A Madrigal, Nicholas J Neill, Archana Shankar, Siddhartha Tyagi, Thomas F Westbrook, Gene W Yeo.
      RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, and aberrant RBP-RNA interactions can promote cancer progression. Here, we interrogate the function of RBPs in cancer using pooled CRISPR-Cas9 screening and identify 57 RBP candidates with distinct roles in supporting MYC-driven oncogenic pathways. We find that disrupting YTHDF2-dependent mRNA degradation triggers apoptosis in triple-negative breast cancer (TNBC) cells and tumors. eCLIP and m6A sequencing reveal that YTHDF2 interacts with mRNAs encoding proteins in the MAPK pathway that, when stabilized, induce epithelial-to-mesenchymal transition and increase global translation rates. scRibo-STAMP profiling of translating mRNAs reveals unique alterations in the translatome of single cells within YTHDF2-depleted solid tumors, which selectively contribute to endoplasmic reticulum stress-induced apoptosis in TNBC cells. Thus, our work highlights the therapeutic potential of RBPs by uncovering a critical role for YTHDF2 in counteracting the global increase of mRNA synthesis in MYC-driven breast cancers.
    Keywords:  CRISPR screening; MYC-driven cancer; N6-methyladenosine; RNA-binding protein; STAMP; YTHDF2; scRNA-seq
    DOI:  https://doi.org/10.1016/j.molcel.2021.06.014
  13. Nat Genet. 2021 Jul 08.
    Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer's disease.
    Samuel Morabito, Emily Miyoshi, Neethu Michael, Saba Shahin, Alessandra Cadete Martini, Elizabeth Head, Justine Silva, Kelsey Leavy, Mari Perez-Rosendahl, Vivek Swarup.
      The gene-regulatory landscape of the brain is highly dynamic in health and disease, coordinating a menagerie of biological processes across distinct cell types. Here, we present a multi-omic single-nucleus study of 191,890 nuclei in late-stage Alzheimer's disease (AD), accessible through our web portal, profiling chromatin accessibility and gene expression in the same biological samples and uncovering vast cellular heterogeneity. We identified cell-type-specific, disease-associated candidate cis-regulatory elements and their candidate target genes, including an oligodendrocyte-associated regulatory module containing links to APOE and CLU. We describe cis-regulatory relationships in specific cell types at a subset of AD risk loci defined by genome-wide association studies, demonstrating the utility of this multi-omic single-nucleus approach. Trajectory analysis of glial populations identified disease-relevant transcription factors, such as SREBF1, and their regulatory targets. Finally, we introduce single-nucleus consensus weighted gene coexpression analysis, a coexpression network analysis strategy robust to sparse single-cell data, and perform a systems-level analysis of the AD transcriptome.
    DOI:  https://doi.org/10.1038/s41588-021-00894-z
  14. NAR Genom Bioinform. 2021 Sep;3(3): lqab059
    Differential ATAC-seq and ChIP-seq peak detection using ROTS.
    Thomas Faux, Kalle T Rytkönen, Mehrad Mahmoudian, Niklas Paulin, Sini Junttila, Asta Laiho, Laura L Elo.
      Changes in cellular chromatin states fine-tune transcriptional output and ultimately lead to phenotypic changes. Here we propose a novel application of our reproducibility-optimized test statistics (ROTS) to detect differential chromatin states (ATAC-seq) or differential chromatin modification states (ChIP-seq) between conditions. We compare the performance of ROTS to existing and widely used methods for ATAC-seq and ChIP-seq data using both synthetic and real datasets. Our results show that ROTS outperformed other commonly used methods when analyzing ATAC-seq data. ROTS also displayed the most accurate detection of small differences when modeling with synthetic data. We observed that two-step methods that require the use of a separate peak caller often more accurately called enrichment borders, whereas one-step methods without a separate peak calling step were more versatile in calling sub-peaks. The top ranked differential regions detected by the methods had marked correlation with transcriptional differences of the closest genes. Overall, our study provides evidence that ROTS is a useful addition to the available differential peak detection methods to study chromatin and performs especially well when applied to study differential chromatin states in ATAC-seq data.
    DOI:  https://doi.org/10.1093/nargab/lqab059
  15. Cell Metab. 2021 Jul 02. pii: S1550-4131(21)00275-8. [Epub ahead of print]
    Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication.
    Anne Loft, Ana Jimena Alfaro, Søren Fisker Schmidt, Felix Boel Pedersen, Mike Krogh Terkelsen, Michele Puglia, Kan Kau Chow, Annette Feuchtinger, Maria Troullinaki, Adriano Maida, Gretchen Wolff, Minako Sakurai, Riccardo Berutti, Bilgen Ekim Üstünel, Peter Nawroth, Kim Ravnskjaer, Mauricio Berriel Diaz, Blagoy Blagoev, Stephan Herzig.
      Liver fibrosis is a strong predictor of long-term mortality in individuals with metabolic-associated fatty liver disease; yet, the mechanisms underlying the progression from the comparatively benign fatty liver state to advanced non-alcoholic steatohepatitis (NASH) and liver fibrosis are incompletely understood. Using cell-type-resolved genomics, we show that comprehensive alterations in hepatocyte genomic and transcriptional settings during NASH progression, led to a loss of hepatocyte identity. The hepatocyte reprogramming was under tight cooperative control of a network of fibrosis-activated transcription factors, as exemplified by the transcription factor Elf-3 (ELF3) and zinc finger protein GLIS2 (GLIS2). Indeed, ELF3- and GLIS2-controlled fibrosis-dependent hepatokine genes targeting disease-associated hepatic stellate cell gene programs. Thus, interconnected transcription factor networks not only promoted hepatocyte dysfunction but also directed the intra-hepatic crosstalk necessary for NASH and fibrosis progression, implying that molecular "hub-centered" targeting strategies are superior to existing mono-target approaches as currently used in NASH therapy.
    Keywords:  Cell type-specific profiling; ELF3; GLIS2; genomic reprogramming; hepatocytes; liver fibrosis; metabolic-associated fatty liver disease; nonalcoholic steatohepatitis; transcription factor networks
    DOI:  https://doi.org/10.1016/j.cmet.2021.06.005
  16. Nat Cell Biol. 2021 Jul 08.
    Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility.
    Janis Koester, Yekaterina A Miroshnikova, Sushmita Ghatak, Carlos Andrés Chacón-Martínez, Jessica Morgner, Xinping Li, Ilian Atanassov, Janine Altmüller, David E Birk, Manuel Koch, Wilhelm Bloch, Michaela Bartusel, Carien M Niessen, Alvaro Rada-Iglesias, Sara A Wickström.
      Tissue turnover requires activation and lineage commitment of tissue-resident stem cells (SCs). These processes are impacted by ageing, but the mechanisms remain unclear. Here, we addressed the mechanisms of ageing in murine hair follicle SCs (HFSCs) and observed a widespread reduction in chromatin accessibility in aged HFSCs, particularly at key self-renewal and differentiation genes, characterized by bivalent promoters occupied by active and repressive chromatin marks. Consistent with this, aged HFSCs showed reduced ability to activate bivalent genes for efficient self-renewal and differentiation. These defects were niche dependent as the transplantation of aged HFSCs into young recipients or synthetic niches restored SC functions. Mechanistically, the aged HFSC niche displayed widespread alterations in extracellular matrix composition and mechanics, resulting in mechanical stress and concomitant transcriptional repression to silence promoters. As a consequence, increasing basement membrane stiffness recapitulated age-related SC changes. These data identify niche mechanics as a central regulator of chromatin state, which, when altered, leads to age-dependent SC exhaustion.
    DOI:  https://doi.org/10.1038/s41556-021-00705-x
  17. Elife. 2021 Jul 05. pii: e57376. [Epub ahead of print]10
    ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors.
    Brian D Alford, Eduardo Tassoni-Tsuchida, Danish Khan, Jeremy J Work, Gregory Valiant, Onn Brandman.
      Understanding cellular stress response pathways is challenging because of the complexity of regulatory mechanisms and response dynamics, which can vary with both time and the type of stress. We developed a reverse genetic method called ReporterSeq to comprehensively identify genes regulating a stress-induced transcription factor under multiple conditions in a time-resolved manner. ReporterSeq links RNA-encoded barcode levels to pathway-specific output under genetic perturbations, allowing pooled pathway activity measurements via DNA sequencing alone and without cell enrichment or single-cell isolation. We used ReporterSeq to identify regulators of the heat shock response (HSR), a conserved, poorly understood transcriptional program that protects cells from proteotoxicity and is misregulated in disease. Genome-wide HSR regulation in budding yeast was assessed across 15 stress conditions, uncovering novel stress-specific, time-specific, and constitutive regulators. ReporterSeq can assess the genetic regulators of any transcriptional pathway with the scale of pooled genetic screens and the precision of pathway-specific readouts.
    Keywords:  CRISPR; HSF1; S. cerevisiae; cell biology; chaperones; genetic screens; genetics; genomics; heat shock response; protein quality control
    DOI:  https://doi.org/10.7554/eLife.57376
  18. Elife. 2021 Jul 07. pii: e65331. [Epub ahead of print]10
    Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast.
    Rachael Emily Turner, Paul F Harrison, Angavai Swaminathan, Calvin A Kraupner-Taylor, Belinda J Goldie, Michael See, Amanda L Peterson, Ralf B Schittenhelm, David R Powell, Darren J Creek, Bernhard Dichtl, Traude H Beilharz.
      Most eukaryotic mRNAs accommodate alternative sites of poly(A) addition in the 3' untranslated region in order to regulate mRNA function. Here, we present a systematic analysis of 3' end formation factors, which revealed 3'UTR lengthening in response to a loss of the core machinery, whereas a loss of the Sen1 helicase resulted in shorter 3'UTRs. We show that the anti-cancer drug cordycepin, 3' deoxyadenosine, caused nucleotide accumulation and the usage of distal poly(A) sites. Mycophenolic acid, a drug which reduces GTP levels and impairs RNA polymerase II (RNAP II) transcription elongation, promoted the usage of proximal sites and reversed the effects of cordycepin on alternative polyadenylation. Moreover, cordycepin-mediated usage of distal sites was associated with a permissive chromatin template and was suppressed in the presence of an rpb1 mutation, which slows RNAP II elongation rate. We propose that alternative polyadenylation is governed by temporal coordination of RNAP II transcription and 3' end processing and controlled by the availability of 3' end factors, nucleotide levels and chromatin landscape.
    Keywords:  S. cerevisiae; Sen1; alternative polyadenylation; chromosomes; cleavage; cordycepin; gene expression; genetics; genomics; mycophenolic acid; polyadenylation; transcription elongation
    DOI:  https://doi.org/10.7554/eLife.65331
  19. Elife. 2021 Jul 06. pii: e64932. [Epub ahead of print]10
    Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci.
    Victoria J Sugrue, Joseph Alan Zoller, Pritika Narayan, Ake T Lu, Oscar J Ortega-Recalde, Matthew J Grant, C Simon Bawden, Skye R Rudiger, Amin Haghani, Donna M Bond, Reuben R Hore, Michael Garratt, Karen E Sears, Nan Wang, Xiangdong William Yang, Russell G Snell, Timothy A Hore, Steve Horvath.
      In mammals, females generally live longer than males. Nevertheless, the mechanisms underpinning sex-dependent longevity are currently unclear. Epigenetic clocks are powerful biological biomarkers capable of precisely estimating chronological age and identifying novel factors influencing the aging rate using only DNA methylation data. In this study, we developed the first epigenetic clock for domesticated sheep (Ovis aries), which can predict chronological age with a median absolute error of 5.1 months. We have discovered that castrated male sheep have a decelerated aging rate compared to intact males, mediated at least in part by the removal of androgens. Furthermore, we identified several androgen-sensitive CpG dinucleotides that become progressively hypomethylated with age in intact males, but remain stable in castrated males and females. Comparable sex-specific methylation differences in MKLN1 also exist in bat skin and a range of mouse tissues that have high androgen receptor expression, indicating that it may drive androgen-dependent hypomethylation in divergent mammalian species. In characterizing these sites, we identify biologically plausible mechanisms explaining how androgens drive male-accelerated aging.
    Keywords:  DNA methylation; aging; androgens; castration; developmental biology; epigenetic clock; genetics; genomics; human; mouse; sheep
    DOI:  https://doi.org/10.7554/eLife.64932
  20. Cancer Discov. 2021 Jul;2(4): 370-387
    Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma.
    Hiroto Ohguchi, Paul M C Park, Tingjian Wang, Berkley E Gryder, Daisuke Ogiya, Keiji Kurata, Xiaofeng Zhang, Deyao Li, Chengkui Pei, Takeshi Masuda, Catrine Johansson, Virangika K Wimalasena, Yong Kim, Shinjiro Hino, Shingo Usuki, Yawara Kawano, Mehmet K Samur, Yu-Tzu Tai, Nikhil C Munshi, Masao Matsuoka, Sumio Ohtsuki, Mitsuyoshi Nakao, Takashi Minami, Shannon Lauberth, Javed Khan, Udo Oppermann, Adam D Durbin, Kenneth C Anderson, Teru Hideshima, Jun Qi.
      Lysine demethylase 5A (KDM5A) is a negative regulator of histone H3 lysine 4 trimethy-lation (H3K4me3), a histone mark associated with activate gene transcription. We identify that KDM5A interacts with the P-TEFb complex and cooperates with MYC to control MYC-targeted genes in multiple myeloma cells. We develop a cell-permeable and selective KDM5 inhibitor, JQKD82, that increases H3K4me3 but paradoxically inhibits downstream MYC-driven transcriptional output in vitro and in vivo. Using genetic ablation together with our inhibitor, we establish that KDM5A supports MYC target gene transcription independent of MYC itself by supporting TFIIH (CDK7)- and P-TEFb (CDK9)-mediated phosphorylation of RNAPII. These data identify KDM5A as a unique vulnerability in multiple myeloma functioning through regulation of MYC target gene transcription and establish JQKD82 as a tool compound to block KDM5A function as a potential therapeutic strategy for multiple myeloma. SIGNIFICANCE: We delineate the function of KDM5A in activating the MYC-driven transcriptional landscape. We develop a cell-permeable KDM5 inhibitor to define the activating role of KDM5A on MYC target gene expression and implicate the therapeutic potential of this compound in mouse models and multiple myeloma patient samples.See related video from the AACR Annual Meeting 2021: https://vimeo.com/554896826.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-20-0108
  21. Sci Rep. 2021 Jul 07. 11(1): 14044
    SoxD transcription factor deficiency in Schwann cells delays myelination in the developing peripheral nervous system.
    Ella Ittner, Anna C Hartwig, Olga Elsesser, Hannah M Wüst, Franziska Fröb, Miriam Wedel, Margit Schimmel, Ernst R Tamm, Michael Wegner, Elisabeth Sock.
      The three SoxD proteins, Sox5, Sox6 and Sox13, represent closely related transcription factors with important roles during development. In the developing nervous system, SoxD proteins have so far been primarily studied in oligodendroglial cells and in interneurons of brain and spinal cord. In oligodendroglial cells, Sox5 and Sox6 jointly maintain the precursor state, interfere with terminal differentiation, and thereby ensure the proper timing of myelination in the central nervous system. Here we studied the role of SoxD proteins in Schwann cells, the functional counterpart of oligodendrocytes in the peripheral nervous system. We show that Schwann cells express Sox5 and Sox13 but not Sox6. Expression was transient and ceased with the onset of terminal differentiation. In mice with early Schwann cell-specific deletion of both Sox5 and Sox13, embryonic Schwann cell development was not substantially affected and progressed normally into the promyelinating stage. However, there was a mild and transient delay in the myelination of the peripheral nervous system of these mice. We therefore conclude that SoxD proteins-in stark contrast to their action in oligodendrocytes-promote differentiation and myelination in Schwann cells.
    DOI:  https://doi.org/10.1038/s41598-021-93437-9
  22. Nat Neurosci. 2021 Jul 08.
    Distinct nuclear compartment-associated genome architecture in the developing mammalian brain.
    Sajad Hamid Ahanger, Ryan N Delgado, Eugene Gil, Mitchel A Cole, Jingjing Zhao, Sung Jun Hong, Arnold R Kriegstein, Tomasz J Nowakowski, Alex A Pollen, Daniel A Lim.
      Nuclear compartments are thought to play a role in three-dimensional genome organization and gene expression. In mammalian brain, the architecture and dynamics of nuclear compartment-associated genome organization is not known. In this study, we developed Genome Organization using CUT and RUN Technology (GO-CaRT) to map genomic interactions with two nuclear compartments-the nuclear lamina and nuclear speckles-from different regions of the developing mouse, macaque and human brain. Lamina-associated domain (LAD) architecture in cells in vivo is distinct from that of cultured cells, including major differences in LADs previously considered to be cell type invariant. In the mouse and human forebrain, dorsal and ventral neural precursor cells have differences in LAD architecture that correspond to their regional identity. LADs in the human and mouse cortex contain transcriptionally highly active sub-domains characterized by broad depletion of histone-3-lysine-9 dimethylation. Evolutionarily conserved LADs in human, macaque and mouse brain are enriched for transcriptionally active neural genes associated with synapse function. By integrating GO-CaRT maps with genome-wide association study data, we found speckle-associated domains to be enriched for schizophrenia risk loci, indicating a physical relationship between these disease-associated genetic variants and a specific nuclear structure. Our work provides a framework for understanding the relationship between distinct nuclear compartments and genome function in brain development and disease.
    DOI:  https://doi.org/10.1038/s41593-021-00879-5
  23. EMBO Rep. 2021 Jul 05. e52649
    Dynamic chromatin association of IκBα is regulated by acetylation and cleavage of histone H4.
    Laura Marruecos, Joan Bertran, Daniel Álvarez-Villanueva, María Carmen Mulero, Yolanda Guillén, Luis G Palma, Martin Floor, Anna Vert, Sara Arce-Gallego, Irene Pecharroman, Laura Batlle, Jordi Villà-Freixa, Gourisankar Ghosh, Anna Bigas, Lluís Espinosa.
      IκBs exert principal functions as cytoplasmic inhibitors of NF-kB transcription factors. Additional roles for IκB homologues have been described, including chromatin association and transcriptional regulation. Phosphorylated and SUMOylated IκBα (pS-IκBα) binds to histones H2A and H4 in the stem cell and progenitor cell compartment of skin and intestine, but the mechanisms controlling its recruitment to chromatin are largely unknown. Here, we show that serine 32-36 phosphorylation of IκBα favors its binding to nucleosomes and demonstrate that p-IκBα association with H4 depends on the acetylation of specific H4 lysine residues. The N-terminal tail of H4 is removed during intestinal cell differentiation by proteolytic cleavage by trypsin or chymotrypsin at residues 17-19, which reduces p-IκBα binding. Inhibition of trypsin and chymotrypsin activity in HT29 cells increases p-IκBα chromatin binding but, paradoxically, impaired goblet cell differentiation, comparable to IκBα deletion. Taken together, our results indicate that dynamic binding of IκBα to chromatin is a requirement for intestinal cell differentiation and provide a molecular basis for the understanding of the restricted nuclear distribution of p-IκBα in specific stem cell compartments.
    Keywords:  differentiation; histone H4; histone cleavage; intestine; nuclear IkappaB
    DOI:  https://doi.org/10.15252/embr.202152649
  24. Mol Cell. 2021 Jun 30. pii: S1097-2765(21)00496-2. [Epub ahead of print]
    Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination.
    Ashwin Narain, Pranjali Bhandare, Bikash Adhikari, Simone Backes, Martin Eilers, Lars Dölken, Andreas Schlosser, Florian Erhard, Apoorva Baluapuri, Elmar Wolf.
      SPT6 is a histone chaperone that tightly binds RNA polymerase II (RNAPII) during transcription elongation. However, its primary role in transcription is uncertain. We used targeted protein degradation to rapidly deplete SPT6 in human cells and analyzed defects in RNAPII behavior by a multi-omics approach and mathematical modeling. Our data indicate that SPT6 is a crucial factor for RNAPII processivity and is therefore required for the productive transcription of protein-coding genes. Unexpectedly, SPT6 also has a vital role in RNAPII termination, as acute depletion induced readthrough transcription for thousands of genes. Long-term depletion of SPT6 induced cryptic intragenic transcription, as observed earlier in yeast. However, this phenotype was not observed upon acute SPT6 depletion and therefore can be attributed to accumulated epigenetic perturbations in the prolonged absence of SPT6. In conclusion, targeted degradation of SPT6 allowed the temporal discrimination of its function as an epigenetic safeguard and RNAPII elongation factor.
    Keywords:  RNA polymerase II; SPT6; SUPT6H; auxin; elongation; histone chaperone; mathematical modeling; targeted protein degradation; termination; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2021.06.016
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