bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022‒05‒22
27 papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit
  1. Transcription elongation is finely tuned by dozens of regulatory factors.
  2. Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer.
  3. TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes.
  4. Enhancers regulate 3' end processing activity to control expression of alternative 3'UTR isoforms.
  5. Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction.
  6. Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences.
  7. H3-K27M-mutant nucleosomes interact with MLL1 to shape the glioma epigenetic landscape.
  8. Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory.
  9. Gibbin mesodermal regulation patterns epithelial development.
  10. Compatibility rules of human enhancer and promoter sequences.
  11. Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells.
  12. Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.
  13. Esrrb is a cell-cycle-dependent associated factor balancing pluripotency and XEN differentiation.
  14. The transcription factor Atf1 lowers the transition barrier for nucleosome-mediated establishment of heterochromatin.
  15. Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG.
  16. MCM complexes are barriers that restrict cohesin-mediated loop extrusion.
  17. Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction.
  18. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk.
  19. Acute lymphoblastic leukemia displays a distinct highly methylated genome.
  20. The lysine deacetylase activity of HDAC1/2 is required to safeguard zygotic genome activation in mice and cattle.
  21. Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1-3 in mesendoderm cell differentiation.
  22. Twist2-driven chromatin remodeling governs the postnatal maturation of dermal fibroblasts.
  23. Chromatin structure predicts survival in glioma patients.
  24. BMP4 drives primed to naïve transition through PGC-like state.
  25. Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.
  26. Transcriptional repression by FoxM1 suppresses tumor differentiation and promotes metastasis of breast cancer.
  27. Identifying common transcriptome signatures of cancer by interpreting deep learning models.
  1. Elife. 2022 May 16. pii: e78944. [Epub ahead of print]11
    Transcription elongation is finely tuned by dozens of regulatory factors.
    Mary Couvillion, Kevin M Harlen, Kate C Lachance, Kristine L Trotta, Erin Smith, Christian Brion, Brendan M Smalec, L Stirling Churchman.
      Understanding the complex network that regulates transcription elongation requires the quantitative analysis of RNA polymerase II (Pol II) activity in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 41 strains of S. cerevisiae lacking known elongation regulators, including RNA processing factors, transcription elongation factors, chromatin modifiers, and remodelers. We found that the opposing effects of these factors balance transcription elongation and antisense transcription. Different sets of factors tightly regulate Pol II progression across gene bodies so that Pol II density peaks at key points of RNA processing. These regulators control where Pol II pauses with each obscuring large numbers of potential pause sites that are primarily determined by DNA sequence and shape. Antisense transcription varies highly across the regulatory landscapes analyzed, but antisense transcription in itself does not affect sense transcription at the same locus. Our findings collectively show that a diverse array of factors regulate transcription elongation by precisely balancing Pol II activity.
    Keywords:  S. cerevisiae; chromosomes; gene expression; genetics; genomics
    DOI:  https://doi.org/10.7554/eLife.78944
  2. Cancer Res. 2022 May 18. pii: canres.CAN-21-2072-E.2021. [Epub ahead of print]
    Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer.
    Amrita M Nargund, Chang Xu, Amit Mandoli, Atsushi Okabe, Gao Bin Chen, Kie Kyon Huang, Taotao Sheng, Xiaosai Yao, Jia Ming Nickolas Teo, Raghav Sundar, Yee Jiun Kok, Yi Xiang See, Manjie Xing, Zhimei Li, Chern Han Yong, Aparna Anand, Zul Fazreen A I, Lai Fong Poon, Michelle Shu Wen Ng, Javier Yu Peng Koh, Wen Fong Ooi, Su Ting Tay, Xuewen Ong, Angie Lay Keng Tan, Heike I Grabsch, Melissa Jane Fullwood, Tean Bin Teh, Xuezhi Bi, Atsushi Kaneda, Shang Li, Patrick Tan.
      Mutations in the DNA mismatch repair gene MSH2 are causative of microsatellite instability (MSI) in multiple cancers. Here, we discovered that besides its well-established role in DNA repair, MSH2 exerts a novel epigenomic function in gastric cancer (GC). Unbiased CRISPR-based mass spectrometry combined with genome-wide CRISPR functional screening revealed that in early-stage GC MSH2 genomic binding is not randomly distributed but rather is associated specifically with tumor-associated super-enhancers controlling the expression of cell adhesion genes. At these loci, MSH2 genomic binding was required for chromatin rewiring, de novo enhancer-promoter interactions, maintenance of histone acetylation levels, and regulation of cell adhesion pathway expression. The chromatin function of MSH2 was independent of its DNA repair catalytic activity but required MSH6, another DNA repair gene, and recruitment to gene loci by the SWI/SNF chromatin remodeler SMARCA4/BRG1. Loss of MSH2 in advanced GCs was accompanied by deficient cell adhesion pathway expression, epithelial-mesenchymal transition, and enhanced tumorigenesis in vitro and in vivo. However, MSH2-deficient GCs also displayed addiction to BAZ1B, a bromodomain-containing family member, and consequent synthetic lethality to bromodomain and extra-terminal motif (BET) inhibition. Our results reveal a role for MSH2 in GC epigenomic regulation and identify BET inhibition as a potential therapy in MSH2-deficient gastric malignancies.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-2072
  3. PLoS Genet. 2022 May 17. 18(5): e1010207
    TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes.
    Colin Kenny, Ramile Dilshat, Hannah E Seberg, Eric Van Otterloo, Gregory Bonde, Annika Helverson, Christopher M Franke, Eiríkur Steingrímsson, Robert A Cornell.
      In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that Tfap2 facilitates MITF's ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa-expressing cells that also express Tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the latter necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.
    DOI:  https://doi.org/10.1371/journal.pgen.1010207
  4. Nat Commun. 2022 May 17. 13(1): 2709
    Enhancers regulate 3' end processing activity to control expression of alternative 3'UTR isoforms.
    Buki Kwon, Mervin M Fansler, Neil D Patel, Jihye Lee, Weirui Ma, Christine Mayr.
      Multi-UTR genes are widely transcribed and express their alternative 3'UTR isoforms in a cell type-specific manner. As transcriptional enhancers regulate mRNA expression, we investigated if they also regulate 3'UTR isoform expression. Endogenous enhancer deletion of the multi-UTR gene PTEN did not impair transcript production but prevented 3'UTR isoform switching which was recapitulated by silencing of an enhancer-bound transcription factor. In reporter assays, enhancers increase transcript production when paired with single-UTR gene promoters. However, when combined with multi-UTR gene promoters, they change 3'UTR isoform expression by increasing 3' end processing activity of polyadenylation sites. Processing activity of polyadenylation sites is affected by transcription factors, including NF-κB and MYC, transcription elongation factors, chromatin remodelers, and histone acetyltransferases. As endogenous cell type-specific enhancers are associated with genes that increase their short 3'UTRs in a cell type-specific manner, our data suggest that transcriptional enhancers integrate cellular signals to regulate cell type-and condition-specific 3'UTR isoform expression.
    DOI:  https://doi.org/10.1038/s41467-022-30525-y
  5. PLoS Genet. 2022 May 18. 18(5): e1010201
    Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction.
    R A Greenstein, Henry Ng, Ramon R Barrales, Catherine Tan, Sigurd Braun, Bassem Al-Sady.
      Heterochromatin spreading, the expansion of repressive chromatin structure from sequence-specific nucleation sites, is critical for stable gene silencing. Spreading re-establishes gene-poor constitutive heterochromatin across cell cycles but can also invade gene-rich euchromatin de novo to steer cell fate decisions. How chromatin context (i.e. euchromatic, heterochromatic) or different nucleation pathways influence heterochromatin spreading remains poorly understood. Previously, we developed a single-cell sensor in fission yeast that can separately record heterochromatic gene silencing at nucleation sequences and distal sites. Here we couple our quantitative assay to a genetic screen to identify genes encoding nuclear factors linked to the regulation of heterochromatin nucleation and the distal spreading of gene silencing. We find that mechanisms underlying gene silencing distal to a nucleation site differ by chromatin context. For example, Clr6 histone deacetylase complexes containing the Fkh2 transcription factor are specifically required for heterochromatin spreading at constitutive sites. Fkh2 recruits Clr6 to nucleation-distal chromatin sites in such contexts. In addition, we find that a number of chromatin remodeling complexes antagonize nucleation-distal gene silencing. Our results separate the regulation of heterochromatic gene silencing at nucleation versus distal sites and show that it is controlled by context-dependent mechanisms. The results of our genetic analysis constitute a broad community resource that will support further analysis of the mechanisms underlying the spread of epigenetic silencing along chromatin.
    DOI:  https://doi.org/10.1371/journal.pgen.1010201
  6. Nat Commun. 2022 May 17. 13(1): 2720
    Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences.
    Zhiyuan Luo, Jiacheng Zhang, Jingyi Fei, Shengdong Ke.
      The N6-methyladenosine (m6A) modification is deposited to nascent transcripts on chromatin, but its site-specificity mechanism is mostly unknown. Here we model the m6A deposition to pre-mRNA by iM6A (intelligent m6A), a deep learning method, demonstrating that the site-specific m6A methylation is primarily determined by the flanking nucleotide sequences. iM6A accurately models the m6A deposition (AUROC = 0.99) and uncovers surprisingly that the cis-elements regulating the m6A deposition preferentially reside within the 50 nt downstream of the m6A sites. The m6A enhancers mostly include part of the RRACH motif and the m6A silencers generally contain CG/GT/CT motifs. Our finding is supported by both independent experimental validations and evolutionary conservation. Moreover, our work provides evidences that mutations resulting in synonymous codons can affect the m6A deposition and the TGA stop codon favors m6A deposition nearby. Our iM6A deep learning modeling enables fast paced biological discovery which would be cost-prohibitive and unpractical with traditional experimental approaches, and uncovers a key cis-regulatory mechanism for m6A site-specific deposition.
    DOI:  https://doi.org/10.1038/s41467-022-30209-7
  7. Cell Rep. 2022 May 17. pii: S2211-1247(22)00609-X. [Epub ahead of print]39(7): 110836
    H3-K27M-mutant nucleosomes interact with MLL1 to shape the glioma epigenetic landscape.
    Noa Furth, Danielle Algranati, Bareket Dassa, Olga Beresh, Vadim Fedyuk, Natasha Morris, Lawryn H Kasper, Dan Jones, Michelle Monje, Suzanne J Baker, Efrat Shema.
      Cancer-associated mutations in genes encoding histones dramatically reshape chromatin and support tumorigenesis. Lysine to methionine substitution of residue 27 on histone H3 (K27M) is a driver mutation in high-grade pediatric gliomas, known to abrogate polycomb repressive complex 2 (PRC2) activity. We applied single-molecule systems to image individual nucleosomes and delineate the combinatorial epigenetic patterns associated with H3-K27M expression. We found that chromatin marks on H3-K27M-mutant nucleosomes are dictated both by their incorporation preferences and by intrinsic properties of the mutation. Mutant nucleosomes not only preferentially bind PRC2 but also directly interact with MLL1, leading to genome-wide redistribution of H3K4me3. H3-K27M-mediated deregulation of repressive and active chromatin marks leads to unbalanced "bivalent" chromatin, which may support a poorly differentiated cellular state. This study provides evidence for a direct effect of H3-K27M oncohistone on the MLL1-H3K4me3 pathway and highlights the capability of single-molecule tools to reveal mechanisms of chromatin deregulation in cancer.
    Keywords:  CP: Cancer; CP: Molecular biology; DIPG; H3-K27M; chromatin; histone modifications; oncohistone; single molecule
    DOI:  https://doi.org/10.1016/j.celrep.2022.110836
  8. Elife. 2022 May 17. pii: e77646. [Epub ahead of print]11
    Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory.
    Bethany Sump, Donna G Brickner, Agustina D'Urso, Seo Hyun Kim, Jason H Brickner.
      For some inducible genes, the rate and molecular mechanism of transcriptional activation depends on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation and requires both changes in chromatin structure and recruitment of poised RNA Polymerase II (RNAPII) to the promoter. Memory of inositol starvation in budding yeast involves a positive feedback loop between transcription factor-dependent interaction with the nuclear pore complex and histone H3 lysine 4 dimethylation (H3K4me2). While H3K4me2 is essential for recruitment of RNAPII and faster reactivation, RNAPII is not required for H3K4me2. Unlike RNAPII-dependent H3K4me2 associated with transcription, RNAPII-independent H3K4me2 requires Nup100, SET3C, the Leo1 subunit of the Paf1 complex and, upon degradation of an essential transcription factor, is inherited through multiple cell cycles. The writer of this mark (COMPASS) physically interacts with the potential reader (SET3C), suggesting a molecular mechanism for the spreading and re-incorporation of H3K4me2 following DNA replication.
    Keywords:  S. cerevisiae; chromosomes; gene expression; genetics; genomics
    DOI:  https://doi.org/10.7554/eLife.77646
  9. Nature. 2022 May 18.
    Gibbin mesodermal regulation patterns epithelial development.
    Ann Collier, Angela Liu, Jessica Torkelson, Jillian Pattison, Sadhana Gaddam, Hanson Zhen, Tiffany Patel, Kelly McCarthy, Hana Ghanim, Anthony E Oro.
      Proper ectodermal patterning during human development requires previously identified transcription factors such as GATA3 and p63, as well as positional signalling from regional mesoderm1-6. However, the mechanism by which ectoderm and mesoderm factors act to stably pattern gene expression and lineage commitment remains unclear. Here we identify the protein Gibbin, encoded by the Xia-Gibbs AT-hook DNA-binding-motif-containing 1 (AHDC1) disease gene7-9, as a key regulator of early epithelial morphogenesis. We find that enhancer- or promoter-bound Gibbin interacts with dozens of sequence-specific zinc-finger transcription factors and methyl-CpG-binding proteins to regulate the expression of mesoderm genes. The loss of Gibbin causes an increase in DNA methylation at GATA3-dependent mesodermal genes, resulting in a loss of signalling between developing dermal and epidermal cell types. Notably, Gibbin-mutant human embryonic stem-cell-derived skin organoids lack dermal maturation, resulting in p63-expressing basal cells that possess defective keratinocyte stratification. In vivo chimeric CRISPR mouse mutants reveal a spectrum of Gibbin-dependent developmental patterning defects affecting craniofacial structure, abdominal wall closure and epidermal stratification that mirror patient phenotypes. Our results indicate that the patterning phenotypes seen in Xia-Gibbs and related syndromes derive from abnormal mesoderm maturation as a result of gene-specific DNA methylation decisions.
    DOI:  https://doi.org/10.1038/s41586-022-04727-9
  10. Nature. 2022 May 20.
    Compatibility rules of human enhancer and promoter sequences.
    Drew T Bergman, Thouis R Jones, Vincent Liu, Judhajeet Ray, Evelyn Jagoda, Layla Siraj, Helen Y Kang, Joseph Nasser, Michael Kane, Antonio Rios, Tung H Nguyen, Sharon R Grossman, Charles P Fulco, Eric S Lander, Jesse M Engreitz.
      Gene regulation in the human genome is controlled by distal enhancers that activate specific nearby promoters1. One model for this specificity is that promoters might have sequence-encoded preferences for certain enhancers, for example mediated by interacting sets of transcription factors or cofactors2. This "biochemical compatibility" model has been supported by observations at individual human promoters and by genome-wide measurements in Drosophila3-9. However, the degree to which human enhancers and promoters are intrinsically compatible has not been systematically measured, and how their activities combine to control RNA expression remains unclear. Here we designed a high-throughput reporter assay called ExP STARR-seq (enhancer x promoter self-transcribing active regulatory region sequencing) and applied it to examine the combinatorial compatibilities of 1,000 enhancer and 1,000 promoter sequences in human K562 cells. We identify simple rules for enhancer-promoter compatibility: most enhancers activated all promoters by similar amounts, and intrinsic enhancer and promoter activities combine multiplicatively to determine RNA output (R2=0.82). In addition, two classes of enhancers and promoters showed subtle preferential effects. Promoters of housekeeping genes contained built-in activating motifs for factors such as GABPA and YY1, which decreased the responsiveness of promoters to distal enhancers. Promoters of variably expressed genes lacked these motifs and showed stronger responsiveness to enhancers. Together, this systematic assessment of enhancer-promoter compatibility suggests a multiplicative model tuned by enhancer and promoter class to control gene transcription in the human genome.
    DOI:  https://doi.org/10.1038/s41586-022-04877-w
  11. Nat Commun. 2022 May 16. 13(1): 2691
    Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells.
    Naoki Itokawa, Motohiko Oshima, Shuhei Koide, Naoya Takayama, Wakako Kuribayashi, Yaeko Nakajima-Takagi, Kazumasa Aoyama, Satoshi Yamazaki, Kiyoshi Yamaguchi, Yoichi Furukawa, Koji Eto, Atsushi Iwama.
      Hematopoietic stem cells (HSCs) exhibit considerable cell-intrinsic changes with age. Here, we present an integrated analysis of transcriptome and chromatin accessibility of aged HSCs and downstream progenitors. Alterations in chromatin accessibility preferentially take place in HSCs with aging, which gradually resolve with differentiation. Differentially open accessible regions (open DARs) in aged HSCs are enriched for enhancers and show enrichment of binding motifs of the STAT, ATF, and CNC family transcription factors that are activated in response to external stresses. Genes linked to open DARs show significantly higher levels of basal expression and their expression reaches significantly higher peaks after cytokine stimulation in aged HSCs than in young HSCs, suggesting that open DARs contribute to augmented transcriptional responses under stress conditions. However, a short-term stress challenge that mimics infection is not sufficient to induce persistent chromatin accessibility changes in young HSCs. These results indicate that the ongoing and/or history of exposure to external stresses may be epigenetically inscribed in HSCs to augment their responses to external stimuli.
    DOI:  https://doi.org/10.1038/s41467-022-30440-2
  12. Nat Struct Mol Biol. 2022 May;29(5): 493-501
    Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.
    Marco Dombrowski, Maik Engeholm, Christian Dienemann, Svetlana Dodonova, Patrick Cramer.
      Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions.
    DOI:  https://doi.org/10.1038/s41594-022-00768-w
  13. Stem Cell Reports. 2022 May 10. pii: S2213-6711(22)00205-3. [Epub ahead of print]
    Esrrb is a cell-cycle-dependent associated factor balancing pluripotency and XEN differentiation.
    Sapir Herchcovici Levy, Sharon Feldman Cohen, Lee Arnon, Shlomtzion Lahav, Muhammad Awawdy, Adi Alajem, Danny Bavli, Xue Sun, Yosef Buganim, Oren Ram.
      Cell cycle and differentiation decisions are linked; however, the underlying principles that drive these decisions are unclear. Here, we combined cell-cycle reporter system and single-cell RNA sequencing (scRNA-seq) profiling to study the transcriptomes of embryonic stem cells (ESCs) in the context of cell-cycle states and differentiation. By applying retinoic acid, to G1 and G2/M ESCs, we show that, while both populations can differentiate toward epiblast stem cells (EpiSCs), only G2/M ESCs could differentiate into extraembryonic endoderm cells. We identified Esrrb, a pluripotency factor that is upregulated during G2/M, as a driver of extraembryonic endoderm stem cell (XEN) differentiation. Furthermore, enhancer chromatin states based on wild-type (WT) and ESRRB knockout (KO) ESCs show association of ESRRB with XEN poised enhancers. G1 cells overexpressing Esrrb allow ESCs to produce XENs, while ESRRB-KO ESCs lost their potential to differentiate into XEN. Overall, this study reveals a vital link between Esrrb and cell-cycle states during the exit from pluripotency.
    Keywords:  ChIP-seq and single-cell RNA-seq (scRNA-seq); Esrrb transcription factor; Exit from pluripotency; cell cycle; cellular differentiation and lineage specification; embryonic stem cells; epiblast stem cells (EpiSC); extraembryonic endoderm stem cells(XEN)
    DOI:  https://doi.org/10.1016/j.stemcr.2022.04.016
  14. Cell Rep. 2022 May 17. pii: S2211-1247(22)00599-X. [Epub ahead of print]39(7): 110828
    The transcription factor Atf1 lowers the transition barrier for nucleosome-mediated establishment of heterochromatin.
    Jan Fabio Nickels, Maria Eduarda Della-Rosa, Iñigo Miguelez Goyeneche, Sebastian Jespersen Charlton, Kim Sneppen, Genevieve Thon.
      Transcription factors can exert opposite effects depending on the chromosomal context. The fission yeast transcription factor Atf1 both activates numerous genes in response to stresses and mediates heterochromatic gene silencing in the mating-type region. Investigating this context dependency, we report here that the establishment of silent heterochromatin in the mating-type region occurs at a reduced rate in the absence of Atf1 binding. Quantitative modeling accounts for the observed establishment profiles by a combinatorial recruitment of histone-modifying enzymes: locally by Atf1 at two binding sites and over the whole region by dynamically appearing heterochromatic nucleosomes, a source of which is the RNAi-dependent cenH element. In the absence of Atf1 binding, the synergy is lost, resulting in a slow rate of heterochromatin formation. The system shows how DNA-binding proteins can influence local nucleosome states and thereby potentiate long-range positive feedback on histone-modification reactions to enable heterochromatin formation over large regions in a context-dependent manner.
    Keywords:  CP: Molecular biology; epigenetics; fission yeast; gene silencing; heterochromatin; histone modifications; mathematical modeling; position effects; positive feedback; single-cell studies; transcription factors
    DOI:  https://doi.org/10.1016/j.celrep.2022.110828
  15. Genome Biol. 2022 May 16. 23(1): 114
    Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG.
    Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong.
      Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pearson correlation-based method and the 27-fold enrichment of GWAS variants for inflammatory bowel disease in the cis-regulatory elements. The R package scREG provides comprehensive functions for single cell multiome data analysis.
    Keywords:  Dimension reduction; Single cell multiome; cis-Regulatory networks; cis-Regulatory potential
    DOI:  https://doi.org/10.1186/s13059-022-02682-2
  16. Nature. 2022 May 18.
    MCM complexes are barriers that restrict cohesin-mediated loop extrusion.
    Bart J H Dequeker, Matthias J Scherr, Hugo B Brandão, Johanna Gassler, Sean Powell, Imre Gaspar, Ilya M Flyamer, Aleksandar Lalic, Wen Tang, Roman Stocsits, Iain F Davidson, Jan-Michael Peters, Karl E Duderstadt, Leonid A Mirny, Kikuë Tachibana.
      Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)1-3, which contribute to transcription, recombination and genomic stability4,5. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered6-12. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are 'active' barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.
    DOI:  https://doi.org/10.1038/s41586-022-04730-0
  17. Nat Commun. 2022 May 17. 13(1): 2714
    Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction.
    Jingyao Wang, Shihe Zhang, Hongfang Lu, Heng Xu.
      Many eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the kinetic mechanisms of complex eukaryotic gene regulation.
    DOI:  https://doi.org/10.1038/s41467-022-30315-6
  18. Nat Genet. 2022 May 19.
    Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk.
    Adam W Turner, Shengen Shawn Hu, Jose Verdezoto Mosquera, Wei Feng Ma, Chani J Hodonsky, Doris Wong, Gaëlle Auguste, Yipei Song, Katia Sol-Church, Emily Farber, Soumya Kundu, Anshul Kundaje, Nicolas G Lopez, Lijiang Ma, Saikat Kumar B Ghosh, Suna Onengut-Gumuscu, Euan A Ashley, Thomas Quertermous, Aloke V Finn, Nicholas J Leeper, Jason C Kovacic, Johan L M Björkgren, Chongzhi Zang, Clint L Miller.
      Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements. Here, we applied single-nucleus assay for transposase-accessible chromatin with sequencing to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell-type-specific elements and transcription factors, and prioritized functional CAD risk variants. We identified elements in smooth muscle cell transition states (for example, fibromyocytes) and functional variants predicted to alter smooth muscle cell- and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single-nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.
    DOI:  https://doi.org/10.1038/s41588-022-01069-0
  19. Nat Cancer. 2022 May 19.
    Acute lymphoblastic leukemia displays a distinct highly methylated genome.
    Sara Hetzel, Alexandra L Mattei, Helene Kretzmer, Chunxu Qu, Xiang Chen, Yiping Fan, Gang Wu, Kathryn G Roberts, Selina Luger, Mark Litzow, Jacob Rowe, Elisabeth Paietta, Wendy Stock, Elaine R Mardis, Richard K Wilson, James R Downing, Charles G Mullighan, Alexander Meissner.
      DNA methylation is tightly regulated during development and is stably maintained in healthy cells. In contrast, cancer cells are commonly characterized by a global loss of DNA methylation co-occurring with CpG island hypermethylation. In acute lymphoblastic leukemia (ALL), the commonest childhood cancer, perturbations of CpG methylation have been reported to be associated with genetic disease subtype and outcome, but data from large cohorts at a genome-wide scale are lacking. Here, we performed whole-genome bisulfite sequencing across ALL subtypes, leukemia cell lines and healthy hematopoietic cells, and show that unlike most cancers, ALL samples exhibit CpG island hypermethylation but minimal global loss of methylation. This was most pronounced in T cell ALL and accompanied by an exceptionally broad range of hypermethylation of CpG islands between patients, which is influenced by TET2 and DNMT3B. These findings demonstrate that ALL is characterized by an unusually highly methylated genome and provide further insights into the non-canonical regulation of methylation in cancer.
    DOI:  https://doi.org/10.1038/s43018-022-00370-5
  20. Development. 2022 May 16. pii: dev.200854. [Epub ahead of print]
    The lysine deacetylase activity of HDAC1/2 is required to safeguard zygotic genome activation in mice and cattle.
    Yanna Dang, Shuang Li, Panpan Zhao, Lieying Xiao, Lefeng Wang, Yan Shi, Lei Luo, Shaohua Wang, Huanan Wang, Kun Zhang.
      The genome is transcriptionally inert at fertilization and must be activated through a remarkable developmental process called zygotic genome activation (ZGA). Epigenetic reprogramming contributes significantly to the dynamic gene expression during ZGA, however the mechanism has yet to be resolved. Here, we find histone deacetylase 1 and 2 (HDAC1/2) can regulate ZGA through the lysine deacetylase activity. Notably, in mouse embryos, overexpression of HDAC1/2 dominant negative mutant leads to a developmental arrest at 2-cell stage. RNA-seq reveals that 64% of down-regulated genes are ZGA genes and 49% of up-regulated genes are developmental genes. Inhibition of the deacetylase activity of HDAC1/2 causes a failure of histone deacetylation at multiple sites including H4K5, H4K16, H3K14, H3K18, and H3K27. ChIP-seq analysis exhibits an increase and decrease of H3K27ac enrichment at promoters of up- and down-regulated genes, respectively. Moreover, HDAC1 mutants prohibited the removal of H3K4me3 via impeding KDM5s. Importantly, the developmental block can be greatly rescued through Kdm5b injection and expression of the majority of dysregulated genes partially corrected. Similar functional significance of HDAC1/2 is conserved in cattle embryos. Overall, we propose that HDAC1/2 is indispensable for ZGA via creating correct transcriptional repressive and active states in mouse and bovine embryos.
    Keywords:  Chromatin; Embryo; HDAC1/2; Preimplantation; Reprogramming; ZGA
    DOI:  https://doi.org/10.1242/dev.200854
  21. Cell Rep. 2022 May 17. pii: S2211-1247(22)00589-7. [Epub ahead of print]39(7): 110818
    Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1-3 in mesendoderm cell differentiation.
    Enakshi Sinniah, Zhixuan Wu, Sophie Shen, Marina Naval-Sanchez, Xiaoli Chen, Junxian Lim, Abbigail Helfer, Abishek Iyer, Jiahui Tng, Andrew J Lucke, Robert C Reid, Meredith A Redd, Christian M Nefzger, David P Fairlie, Nathan J Palpant.
      Histone deacetylases (HDACs) are a class of enzymes that control chromatin state and influence cell fate. We evaluated the chromatin accessibility and transcriptome dynamics of zinc-containing HDACs during cell differentiation in vitro coupled with chemical perturbation to identify the role of HDACs in mesendoderm cell fate specification. Single-cell RNA sequencing analyses of HDAC expression during human pluripotent stem cell (hPSC) differentiation in vitro and mouse gastrulation in vivo reveal a unique association of HDAC1 and -3 with mesendoderm gene programs during exit from pluripotency. Functional perturbation with small molecules reveals that inhibition of HDAC1 and -3, but not HDAC2, induces mesoderm while impeding endoderm and early cardiac progenitor specification. These data identify unique biological functions of the structurally homologous enzymes HDAC1-3 in influencing hPSC differentiation from pluripotency toward mesendodermal and cardiac progenitor populations.
    Keywords:  CP: Molecular biology; CP: Stem cell research; HDAC inhibitors; HDACs; cardiac development; cardiac differentiation; cardiac progenitor specification; cell fate; embryonic development; endoderm differentiation; epigenetics; genomics; hPSCs; histone deacetylases; mesendoderm specification; mesoderm differentiation; scRNA-seq; single-cell RNA sequencing; stem cell differentiation; transcriptomics
    DOI:  https://doi.org/10.1016/j.celrep.2022.110818
  22. Cell Rep. 2022 May 17. pii: S2211-1247(22)00592-7. [Epub ahead of print]39(7): 110821
    Twist2-driven chromatin remodeling governs the postnatal maturation of dermal fibroblasts.
    Jin Yong Kim, Minji Park, Jungyoon Ohn, Rho Hyun Seong, Jin Ho Chung, Kyu Han Kim, Seong Jin Jo, Ohsang Kwon.
      Dermal fibroblasts lose stem cell potency after birth, which prevents regenerative healing. However, the underlying intracellular mechanisms are largely unknown. We uncover the postnatal maturation of papillary fibroblasts (PFs) driven by the extensive Twist2-mediated remodeling of chromatin accessibility. A loss of the regenerative ability of postnatal PFs occurs with decreased H3K27ac levels. Single-cell transcriptomics, assay for transposase-accessible chromatin sequencing (ATAC-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) reveal the postnatal maturation trajectory associated with the loss of the regenerative trajectory in PFs, which is characterized by a marked decrease in chromatin accessibility and H3K27ac modifications. Histone deacetylase inhibition delays spontaneous chromatin remodeling, thus maintaining the regenerative ability of postnatal PFs. Genomic analysis identifies Twist2 as a major regulator within chromatin regions with decreased accessibility during the postnatal period. When Twist2 is genetically deleted in dermal fibroblasts, the intracellular cascade of postnatal maturation is significantly delayed. Our findings reveal the comprehensive intracellular mechanisms underlying intrinsic postnatal changes in dermal fibroblasts.
    Keywords:  CP: Developmental biology; CP: Molecular biology; H3K27ac modifications; Twist2; chromatin accessibility; dermal fibroblast; hair follicle; papillary fibroblast; postnatal maturation
    DOI:  https://doi.org/10.1016/j.celrep.2022.110821
  23. Sci Rep. 2022 May 17. 12(1): 8221
    Chromatin structure predicts survival in glioma patients.
    Matthew C Garrett, Rebecca Albano, Troy Carnwath, Sanjit Shah, Daniel Woo, Michael Lamba, David R Plas, Aditi Paranjpe, Krishna Roskin, Chuntao Zhao, Richard Lu.
      The pathological changes in epigenetics and gene regulation that accompany the progression of low-grade to high-grade gliomas are under-studied. The authors use a large set of paired atac-seq and RNA-seq data from surgically resected glioma specimens to infer gene regulatory relationships in glioma. Thirty-eight glioma patient samples underwent atac-seq sequencing and 16 samples underwent additional RNA-seq analysis. Using an atac-seq/RNA-seq correlation matrix, atac-seq peaks were paired with genes based on high correlation values (|r2| > 0.6). Samples clustered by IDH1 status but not by grade. Surprisingly there was a trend for IDH1 mutant samples to have more peaks. The majority of peaks are positively correlated with survival and positively correlated with gene expression. Constructing a model of the top six atac-seq peaks created a highly accurate survival prediction model (r2 = 0.68). Four of these peaks were still significant after controlling for age, grade, pathology, IDH1 status and gender. Grade II, III, and IV (primary) samples have similar transcription factors and gene modules. However, grade IV (recurrent) samples have strikingly few peaks. Patient-derived glioma cultures showed decreased peak counts following radiation indicating that this may be radiation-induced. This study supports the notion that IDH1 mutant and IDH1 wildtype gliomas have different epigenetic landscapes and that accessible chromatin sites mapped by atac-seq peaks tend to be positively correlated with expression. The data in this study leads to a new model of treatment response wherein glioma cells respond to radiation therapy by closing open regions of DNA.
    DOI:  https://doi.org/10.1038/s41598-022-11019-9
  24. Nat Commun. 2022 May 19. 13(1): 2756
    BMP4 drives primed to naïve transition through PGC-like state.
    Shengyong Yu, Chunhua Zhou, Jiangping He, Zhaokai Yao, Xingnan Huang, Bowen Rong, Hong Zhu, Shijie Wang, Shuyan Chen, Xialian Wang, Baomei Cai, Guoqing Zhao, Yuhan Chen, Lizhan Xiao, He Liu, Yue Qin, Jing Guo, Haokaifeng Wu, Zhen Zhang, Man Zhang, Xiaoyang Zhao, Fei Lan, Yixuan Wang, Jiekai Chen, Shangtao Cao, Duanqing Pei, Jing Liu.
      Multiple pluripotent states have been described in mouse and human stem cells. Here, we apply single-cell RNA-seq to a newly established BMP4 induced mouse primed to naïve transition (BiPNT) system and show that the reset is not a direct reversal of cell fate but goes through a primordial germ cell-like cells (PGCLCs) state. We first show that epiblast stem cells bifurcate into c-Kit+ naïve and c-Kit- trophoblast-like cells, among which, the naïve branch undergoes further transition through a PGCLCs intermediate capable of spermatogenesis in vivo. Mechanistically, we show that DOT1L inhibition permits the transition from primed pluripotency to PGCLCs in part by facilitating the loss of H3K79me2 from Gata3/6. In addition, Prdm1/Blimp1 is required for PGCLCs and naïve cells, while Gata2 inhibits PGC-like state by promoting trophoblast-like fate. Our work not only reveals an alternative route for primed to naïve transition, but also gains insight into germ cell development.
    DOI:  https://doi.org/10.1038/s41467-022-30325-4
  25. Mol Cell. 2022 Apr 23. pii: S1097-2765(22)00320-3. [Epub ahead of print]
    Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.
    Miguel Martinez-Ara, Federico Comoglio, Joris van Arensbergen, Bas van Steensel.
      Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter need to be biochemically compatible for promoter regulation to occur, but this compatibility has remained poorly characterized in mammalian cells. We used high-throughput combinatorial reporter assays to test thousands of CRE-promoter pairs from three Mb-sized genomic regions in mouse cells. This revealed that CREs vary substantially in their promoter compatibility, ranging from striking specificity to broad promiscuity. More than half of the tested CREs exhibit significant promoter selectivity. Housekeeping promoters tend to have similar CRE preferences, but other promoters exhibit a wide diversity of compatibilities. Higher-order transcription factors (TF) motif combinations may account for compatibility. CRE-promoter selectivity does not correlate with looping interactions in the native genomic context, suggesting that chromatin folding and compatibility are two orthogonal mechanisms that confer specificity to gene regulation.
    Keywords:  MPRA; cis-regulatory element; combinatorial; compatibility; enhancer; promoter; specificity; systematic; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2022.04.009
  26. Cancer Res. 2022 May 18. pii: canres.0410.2022. [Epub ahead of print]
    Transcriptional repression by FoxM1 suppresses tumor differentiation and promotes metastasis of breast cancer.
    Dragana Kopanja, Vaibhav Chand, Eilidh Mills O'Brien, Nishit K Mukhopadhyay, Maria Paula Zappia, Abul B M M K Islam, Maxim Frolov, Bradley J Merrill, Pradip Raychaudhuri.
      The transcription factor Forkhead box M1 (FoxM1) is overexpressed in breast cancers and correlates with poor prognosis. Mechanistically, FoxM1 associates with CBP to activate transcription and with Rb to repress transcription. While the activating function of FoxM1 in breast cancer has been well documented, the significance of its repressive activity is poorly understood. Using CRISPR-Cas9 engineering, we generated a mouse model that expresses FoxM1 harboring point mutations that block binding to Rb while retaining its ability to bind CBP. Unlike FoxM1-null mice, mice harboring Rb-binding mutant FoxM1 did not exhibit significant developmental defects. The mutant mouse line developed PyMT-driven mammary tumors that were deficient in lung metastasis, which was tumor cell-intrinsic. Single-cell RNA-seq of the tumors revealed a deficiency in pro-metastatic tumor cells and an expansion of differentiated alveolar-type tumor cells, and further investigation identified that loss of the FoxM1/Rb interaction caused enhancement of the mammary alveolar differentiation program. The FoxM1 mutant tumors also showed increased Pten expression, and FoxM1/Rb was found to activate Akt signaling by repressing Pten. In human breast cancers, expression of FoxM1 negatively correlated with Pten mRNA. Furthermore, the lack of tumor-infiltrating cells in FoxM1 mutant tumors appeared related to decreases in pro-metastatic tumor cells that express factors required for infiltration. These observations demonstrate that the FoxM1/Rb-regulated transcriptome is critical for the plasticity of breast cancer cells that drive metastasis, identifying a pro-metastatic role of Rb when bound to FoxM1.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0410
  27. Genome Biol. 2022 May 17. 23(1): 117
    Identifying common transcriptome signatures of cancer by interpreting deep learning models.
    Anupama Jha, Mathieu Quesnel-Vallières, David Wang, Andrei Thomas-Tikhonenko, Kristen W Lynch, Yoseph Barash.
      BACKGROUND: Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute to oncogenesis vary widely between tumor types, but common gene signatures that relate to core cancer pathways have also been identified. It is not clear, however, whether there exist additional sets of genes or transcriptomic features that are less well known in cancer biology but that are also commonly deregulated across several cancer types.RESULTS: Here, we agnostically identify transcriptomic features that are commonly shared between cancer types using 13,461 RNA-seq samples from 19 normal tissue types and 18 solid tumor types to train three feed-forward neural networks, based either on protein-coding gene expression, lncRNA expression, or splice junction use, to distinguish between normal and tumor samples. All three models recognize transcriptome signatures that are consistent across tumors. Analysis of attribution values extracted from our models reveals that genes that are commonly altered in cancer by expression or splicing variations are under strong evolutionary and selective constraints. Importantly, we find that genes composing our cancer transcriptome signatures are not frequently affected by mutations or genomic alterations and that their functions differ widely from the genes genetically associated with cancer.
    CONCLUSIONS: Our results highlighted that deregulation of RNA-processing genes and aberrant splicing are pervasive features on which core cancer pathways might converge across a large array of solid tumor types.
    Keywords:  Cancer genomics; Deep learning; Transcriptomics
    DOI:  https://doi.org/10.1186/s13059-022-02681-3
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