bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2024–02–25
fourteen papers selected by
Connor Rogerson, University of Cambridge
  1. Transcription factor exchange enables prolonged transcriptional bursts.
  2. Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays.
  3. Complex regulatory networks influence pluripotent cell state transitions in human iPSCs.
  4. Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease.
  5. The landscape of transcription factor promoter activity during vegetative development in Marchantia.
  6. Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy in a CTCF-dependent manner.
  7. Targeting nuclear receptor corepressors for reversible male contraception.
  8. Serine/arginine-rich splicing factor 7 promotes the type I interferon response by activating Irf7 transcription.
  9. The BTB transcription factor, Abrupt, acts cooperatively with Chronologically inappropriate morphogenesis (Chinmo) to repress metamorphosis and promotes leg regeneration.
  10. SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data.
  11. Mechanisms of action and resistance in histone methylation-targeted therapy.
  12. Hyperacetylated histone H4 is a source of carbon contributing to lipid synthesis.
  13. scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data.
  14. Nr5a2 ensures inner cell mass formation in mouse blastocyst.
  1. Mol Cell. 2024 Feb 09. pii: S1097-2765(24)00056-X. [Epub ahead of print]
    Transcription factor exchange enables prolonged transcriptional bursts.
    Wim Pomp, Joseph V W Meeussen, Tineke L Lenstra.
      Single-molecule imaging inside living cells has revealed that transcription factors (TFs) bind to DNA transiently, but a long-standing question is how this transient binding is related to transcription activation. Here, we devised a microscopy method to simultaneously measure transient TF binding at a single locus and the effect of these binding events on transcription. We show that DNA binding of the yeast TF Gal4 activates transcription of a target gene within a few seconds, with at least ∼20% efficiency and with a high initiation rate of ∼1 RNA/s. Gal4 DNA dissociation decreases transcription rapidly. Moreover, at a gene with multiple binding sites, individual Gal4 molecules only rarely stay bound throughout the entire burst but instead frequently exchange during a burst to increase the transcriptional burst duration. Our results suggest a mechanism for enhancer regulation in more complex eukaryotes, where TF cooperativity and exchange enable robust and responsive transcription regulation.
    Keywords:  DNA binding kinetics; cooperativity; single-molecule imaging; transcription factor; transcriptional bursting
    DOI:  https://doi.org/10.1016/j.molcel.2024.01.020
  2. Nat Commun. 2024 Feb 22. 15(1): 1620
    Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays.
    Fabian Blombach, Michal Sýkora, Jo Case, Xu Feng, Diana P Baquero, Thomas Fouqueau, Duy Khanh Phung, Declan Barker, Mart Krupovic, Qunxin She, Finn Werner.
      CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbour extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposons. Cbp1 recruits Cren7 forming together 'chimeric' chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third helix-turn-helix domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.
    DOI:  https://doi.org/10.1038/s41467-024-45728-8
  3. Nat Commun. 2024 Feb 23. 15(1): 1664
    Complex regulatory networks influence pluripotent cell state transitions in human iPSCs.
    iPSCORE Consortium
      Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines.
    DOI:  https://doi.org/10.1038/s41467-024-45506-6
  4. Nat Genet. 2024 Feb 20.
    Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease.
    Feng Xiao, Xiaoran Zhang, Sarah U Morton, Seong Won Kim, Youfei Fan, Joshua M Gorham, Huan Zhang, Paul J Berkson, Neil Mazumdar, Yangpo Cao, Jian Chen, Jacob Hagen, Xujie Liu, Pingzhu Zhou, Felix Richter, Yufeng Shen, Tarsha Ward, Bruce D Gelb, Jonathan G Seidman, Christine E Seidman, William T Pu.
      Rare coding mutations cause ∼45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity, often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context, four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing, we used the MPRA data to develop a regression model, EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together, we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD.
    DOI:  https://doi.org/10.1038/s41588-024-01669-y
  5. Plant Cell. 2024 Feb 23. pii: koae053. [Epub ahead of print]
    The landscape of transcription factor promoter activity during vegetative development in Marchantia.
    Facundo Romani, Susanna Sauret-Güeto, Marius Rebmann, Davide Annese, Ignacy Bonter, Marta Tomaselli, Tom Dierschke, Mihails Delmans, Eftychios Frangedakis, Linda Silvestri, Jenna Rever, John L Bowman, Ignacio Romani, Jim Haseloff.
      Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterising the transcriptional activity of TF genes in space and time is a critical step towards understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analysed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.
    Keywords:  Bryophytes; evo-devo; meristem; stem cell; synthetic biology; transcription factors
    DOI:  https://doi.org/10.1093/plcell/koae053
  6. Nat Commun. 2024 Feb 21. 15(1): 1579
    Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy in a CTCF-dependent manner.
    Silvia Peripolli, Leticia Meneguello, Chiara Perrod, Tanya Singh, Harshil Patel, Sazia T Rahman, Koshiro Kiso, Peter Thorpe, Vincenzo Calvanese, Cosetta Bertoli, Robertus A M de Bruin.
      Oncogene-induced replication stress is a crucial driver of genomic instability and one of the key events contributing to the onset and evolution of cancer. Despite its critical role in cancer, the mechanisms that generate oncogene-induced replication stress remain not fully understood. Here, we report that an oncogenic c-Myc-dependent increase in cohesins on DNA contributes to the induction of replication stress. Accumulation of cohesins on chromatin is not sufficient to cause replication stress, but also requires cohesins to accumulate at specific sites in a CTCF-dependent manner. We propose that the increased accumulation of cohesins at CTCF site interferes with the progression of replication forks, contributing to oncogene-induced replication stress. This is different from, and independent of, previously suggested mechanisms of oncogene-induced replication stress. This, together with the reported protective role of cohesins in preventing replication stress-induced DNA damage, supports a double-edge involvement of cohesins in causing and tolerating oncogene-induced replication stress.
    DOI:  https://doi.org/10.1038/s41467-024-45955-z
  7. Proc Natl Acad Sci U S A. 2024 Feb 27. 121(9): e2320129121
    Targeting nuclear receptor corepressors for reversible male contraception.
    Suk-Hyun Hong, Glenda Castro, Dan Wang, Russell Nofsinger, Maureen Kane, Alexandra Folias, Annette R Atkins, Ruth T Yu, Joseph L Napoli, Paolo Sassone-Corsi, Dirk G de Rooij, Christopher Liddle, Michael Downes, Ronald M Evans.
      Despite numerous female contraceptive options, nearly half of all pregnancies are unintended. Family planning choices for men are currently limited to unreliable condoms and invasive vasectomies with questionable reversibility. Here, we report the development of an oral contraceptive approach based on transcriptional disruption of cyclical gene expression patterns during spermatogenesis. Spermatogenesis involves a continuous series of self-renewal and differentiation programs of spermatogonial stem cells (SSCs) that is regulated by retinoic acid (RA)-dependent activation of receptors (RARs), which control target gene expression through association with corepressor proteins. We have found that the interaction between RAR and the corepressor silencing mediator of retinoid and thyroid hormone receptors (SMRT) is essential for spermatogenesis. In a genetically engineered mouse model that negates SMRT-RAR binding (SMRTmRID mice), the synchronized, cyclic expression of RAR-dependent genes along the seminiferous tubules is disrupted. Notably, the presence of an RA-resistant SSC population that survives RAR de-repression suggests that the infertility attributed to the loss of SMRT-mediated repression is reversible. Supporting this notion, we show that inhibiting the action of the SMRT complex with chronic, low-dose oral administration of a histone deacetylase inhibitor reversibly blocks spermatogenesis and fertility without affecting libido. This demonstration validates pharmacologic targeting of the SMRT repressor complex for non-hormonal male contraception.
    Keywords:  retinoic acid signaling; spermatogenesis; transcriptional corepression
    DOI:  https://doi.org/10.1073/pnas.2320129121
  8. Cell Rep. 2024 Feb 22. pii: S2211-1247(24)00144-X. [Epub ahead of print]43(3): 113816
    Serine/arginine-rich splicing factor 7 promotes the type I interferon response by activating Irf7 transcription.
    Haley M Scott, Mackenzie H Smith, Aja K Coleman, Kaitlyn S Armijo, Morgan J Chapman, Summer L Apostalo, Allison R Wagner, Robert O Watson, Kristin L Patrick.
      Tight regulation of macrophage immune gene expression is required to fight infection without risking harmful inflammation. The contribution of RNA-binding proteins (RBPs) to shaping the macrophage response to pathogens remains poorly understood. Transcriptomic analysis reveals that a member of the serine/arginine-rich (SR) family of mRNA processing factors, SRSF7, is required for optimal expression of a cohort of interferon-stimulated genes in macrophages. Using genetic and biochemical assays, we discover that in addition to its canonical role in regulating alternative splicing, SRSF7 drives transcription of interferon regulatory transcription factor 7 (IRF7) to promote antiviral immunity. At the Irf7 promoter, SRSF7 maximizes STAT1 transcription factor binding and RNA polymerase II elongation via cooperation with the H4K20me1 histone methyltransferase KMT5a (SET8). These studies define a role for an SR protein in activating transcription and reveal an RBP-chromatin network that orchestrates macrophage antiviral gene expression.
    Keywords:  CP: Cell biology; CP: Molecular biology; RNA binding proteins; antiviral immunity; chromatin; co-transcriptional splicing; histone methylation; innate immunity; pre-mRNA splicing
    DOI:  https://doi.org/10.1016/j.celrep.2024.113816
  9. Dev Biol. 2024 Feb 17. pii: S0012-1606(24)00026-5. [Epub ahead of print]
    The BTB transcription factor, Abrupt, acts cooperatively with Chronologically inappropriate morphogenesis (Chinmo) to repress metamorphosis and promotes leg regeneration.
    Hesper Khong, Kayli Hattley, Yuichiro Suzuki.
      Many insects undergo the process of metamorphosis when larval precursor cells begin to differentiate to create the adult body. The larval precursor cells retain stem cell-like properties and contribute to the regenerative ability of larval appendages. Here we demonstrate that two Broad-complex/Tramtrack/Bric-à-brac Zinc-finger (BTB) domain transcription factors, Chronologically inappropriate morphogenesis (Chinmo) and Abrupt (Ab), act cooperatively to repress metamorphosis in the flour beetle, Tribolium castaneum. Knockdown of chinmo led to precocious development of pupal legs and antennae. We show that although topical application of juvenile hormone (JH) prevents the decrease in chinmo expression in the final instar, chinmo and JH act in distinct pathways. We demonstrate that another gene encoding the BTB domain transcription factor, Ab, is also necessary for the suppression of broad (br) expression in T. castaneum in a chinmo RNAi background and that simultaneous knockdown of ab and chinmo leads to the precocious onset of metamorphosis. Furthermore, we demonstrate that knockdown of ab leads to the loss of regenerative potential of larval legs independently of br. In contrast, chinmo knockdown larvae exhibit pupal leg regeneration when a larval leg is ablated. Taken together, our results show that both ab and chinmo are necessary for the maintenance of the larval tissue identity and, apart from its role in repressing br, ab acts as a crucial regulator of larval leg regeneration. Our findings indicate that BTB domain proteins interact in a complex manner to regulate larval and pupal tissue homeostasis.
    Keywords:  Abrupt; Chinmo; Juvenile hormone; Limb regeneration; Metamorphosis; Tribolium castaneum
    DOI:  https://doi.org/10.1016/j.ydbio.2024.02.006
  10. Genome Biol. 2024 Feb 23. 25(1): 55
    SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data.
    Nour El Kazwini, Guido Sanguinetti.
      Multi-omic single-cell technologies, which simultaneously measure the transcriptional and epigenomic state of the same cell, enable understanding epigenetic mechanisms of gene regulation. However, noisy and sparse data pose fundamental statistical challenges to extract biological knowledge from complex datasets. SHARE-Topic, a Bayesian generative model of multi-omic single cell data using topic models, aims to address these challenges. SHARE-Topic identifies common patterns of co-variation between different omic layers, providing interpretable explanations for the data complexity. Tested on data from different technological platforms, SHARE-Topic provides low dimensional representations recapitulating known biology and defines associations between genes and distal regulators in individual cells.
    Keywords:  Bayesian modeling; Gene regulation; Gene regulator in cancer; Interpretability; Lymphoma; Single-cell multi-omics
    DOI:  https://doi.org/10.1186/s13059-024-03180-3
  11. Nature. 2024 Feb 21.
    Mechanisms of action and resistance in histone methylation-targeted therapy.
    Makoto Yamagishi, Yuta Kuze, Seiichiro Kobayashi, Makoto Nakashima, Satoko Morishima, Toyotaka Kawamata, Junya Makiyama, Kako Suzuki, Masahide Seki, Kazumi Abe, Kiyomi Imamura, Eri Watanabe, Kazumi Tsuchiya, Isao Yasumatsu, Gensuke Takayama, Yoshiyuki Hizukuri, Kazumi Ito, Yukihiro Taira, Yasuhito Nannya, Arinobu Tojo, Toshiki Watanabe, Shinji Tsutsumi, Yutaka Suzuki, Kaoru Uchimaru.
      Epigenomes enable the rectification of disordered cancer gene expression, thereby providing new targets for pharmacological interventions. The clinical utility of targeting histone H3 lysine trimethylation (H3K27me3) as an epigenetic hallmark has been demonstrated1-7. However, in actual therapeutic settings, the mechanism by which H3K27me3-targeting therapies exert their effects and the response of tumour cells remain unclear. Here we show the potency and mechanisms of action and resistance of the EZH1-EZH2 dual inhibitor valemetostat in clinical trials of patients with adult T cell leukaemia/lymphoma. Administration of valemetostat reduced tumour size and demonstrated durable clinical response in aggressive lymphomas with multiple genetic mutations. Integrative single-cell analyses showed that valemetostat abolishes the highly condensed chromatin structure formed by the plastic H3K27me3 and neutralizes multiple gene loci, including tumour suppressor genes. Nevertheless, subsequent long-term treatment encounters the emergence of resistant clones with reconstructed aggregate chromatin that closely resemble the pre-dose state. Acquired mutations at the PRC2-compound interface result in the propagation of clones with increased H3K27me3 expression. In patients free of PRC2 mutations, TET2 mutation or elevated DNMT3A expression causes similar chromatin recondensation through de novo DNA methylation in the H3K27me3-associated regions. We identified subpopulations with distinct metabolic and gene translation characteristics implicated in primary susceptibility until the acquisition of the heritable (epi)mutations. Targeting epigenetic drivers and chromatin homeostasis may provide opportunities for further sustained epigenetic cancer therapies.
    DOI:  https://doi.org/10.1038/s41586-024-07103-x
  12. EMBO J. 2024 Feb 21.
    Hyperacetylated histone H4 is a source of carbon contributing to lipid synthesis.
    Evelina Charidemou, Roberta Noberini, Chiara Ghirardi, Polymnia Georgiou, Panayiota Marcou, Andria Theophanous, Katerina Strati, Hector Keun, Volker Behrends, Tiziana Bonaldi, Antonis Kirmizis.
      Histone modifications commonly integrate environmental cues with cellular metabolic outputs by affecting gene expression. However, chromatin modifications such as acetylation do not always correlate with transcription, pointing towards an alternative role of histone modifications in cellular metabolism. Using an approach that integrates mass spectrometry-based histone modification mapping and metabolomics with stable isotope tracers, we demonstrate that elevated lipids in acetyltransferase-depleted hepatocytes result from carbon atoms derived from deacetylation of hyperacetylated histone H4 flowing towards fatty acids. Consistently, enhanced lipid synthesis in acetyltransferase-depleted hepatocytes is dependent on histone deacetylases and acetyl-CoA synthetase ACSS2, but not on the substrate specificity of the acetyltransferases. Furthermore, we show that during diet-induced lipid synthesis the levels of hyperacetylated histone H4 decrease in hepatocytes and in mouse liver. In addition, overexpression of acetyltransferases can reverse diet-induced lipogenesis by blocking lipid droplet accumulation and maintaining the levels of hyperacetylated histone H4. Overall, these findings highlight hyperacetylated histones as a metabolite reservoir that can directly contribute carbon to lipid synthesis, constituting a novel function of chromatin in cellular metabolism.
    Keywords:  Acetylation; Epigenetics; Histone Reservoirs; Lipid Metabolism
    DOI:  https://doi.org/10.1038/s44318-024-00053-0
  13. Nat Commun. 2024 Feb 22. 15(1): 1629
    scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data.
    Songming Tang, Xuejian Cui, Rongxiang Wang, Sijie Li, Siyu Li, Xin Huang, Shengquan Chen.
      Single-cell chromatin accessibility sequencing (scCAS) has emerged as a valuable tool for interrogating and elucidating epigenomic heterogeneity and gene regulation. However, scCAS data inherently suffers from limitations such as high sparsity and dimensionality, which pose significant challenges for downstream analyses. Although several methods are proposed to enhance scCAS data, there are still challenges and limitations that hinder the effectiveness of these methods. Here, we propose scCASE, a scCAS data enhancement method based on non-negative matrix factorization which incorporates an iteratively updating cell-to-cell similarity matrix. Through comprehensive experiments on multiple datasets, we demonstrate the advantages of scCASE over existing methods for scCAS data enhancement. The interpretable cell type-specific peaks identified by scCASE can provide valuable biological insights into cell subpopulations. Moreover, to leverage the large compendia of available omics data as a reference, we further expand scCASE to scCASER, which enables the incorporation of external reference data to improve enhancement performance.
    DOI:  https://doi.org/10.1038/s41467-024-46045-w
  14. Cell Rep. 2024 Feb 21. pii: S2211-1247(24)00168-2. [Epub ahead of print]43(3): 113840
    Nr5a2 ensures inner cell mass formation in mouse blastocyst.
    Yanhua Zhao, Meiting Zhang, Jiqiang Liu, Xinglin Hu, Yuchen Sun, Xingwei Huang, Jingyu Li, Lei Lei.
      Recent studies have elucidated Nr5a2's role in activating zygotic genes during early mouse embryonic development. Subsequent research, however, reveals that Nr5a2 is not critical for zygotic genome activation but is vital for the gene program between the 4- and 8-cell stages. A significant gap exists in experimental evidence regarding its function during the first lineage differentiation's pivotal period. In this study, we observed that approximately 20% of embryos developed to the blastocyst stage following Nr5a2 ablation. However, these blastocysts lacked inner cell mass (ICM), highlighting Nr5a2's importance in first lineage differentiation. Mechanistically, using RNA sequencing and CUT&Tag, we found that Nr5a2 transcriptionally regulates ICM-specific genes, such as Oct4, to establish the pluripotent network. Interference with or overexpression of Nr5a2 in single blastomeres of 2-cell embryos can alter the fate of daughter cells. Our results indicate that Nr5a2 works as a doorkeeper to ensure ICM formation in mouse blastocyst.
    Keywords:  CP: Developmental biology; CP: Stem cell research; ICM; Nr5a2; Oct4; ZGA; inner cell mass; the first lineage differentiation; zygotic genome activation
    DOI:  https://doi.org/10.1016/j.celrep.2024.113840
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