bims-crepig 2022-09-04 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2022–09–04
eightteen papers selected by
Connor Rogerson, University of Cambridge

Characterization of sequence determinants of enhancer function using natural genetic variation.
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions.
WhichTF is functionally important in your open chromatin data?
CTCF and cohesin promote focal detachment of DNA from the nuclear lamina.
3D chromatin remodeling potentiates transcriptional programs driving cell invasion.
SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression.
Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells.
Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation.
Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation.
Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation.
ZFP281 drives a mesenchymal-like dormancy program in early disseminated breast cancer cells that prevents metastatic outgrowth in the lung.
Differential regulation of alternate promoter regions in Sox17 during endodermal and vascular endothelial development.
Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling.
GRHL2 Enhances Phosphorylated Estrogen Receptor (ER) Chromatin Binding and Regulates ER-Mediated Transcriptional Activation and Repression.
Arid1a mutation suppresses TGF-β signaling and induces cholangiocarcinoma.
NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis.
Distinct silencer states generate epigenetic states of heterochromatin.
The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila.

Elife. 2022 Aug 31. pii: e76500. [Epub ahead of print]11

Characterization of sequence determinants of enhancer function using natural genetic variation.

Marty G Yang, Emi Ling, Christopher J Cowley, Michael E Greenberg, Thomas Vierbuchen.

  Sequence variation in enhancers that control cell type-specific gene transcription contributes significantly to phenotypic variation within human populations. However, it remains difficult to predict precisely the effect of any given sequence variant on enhancer function due to the complexity of DNA sequence motifs that determine transcription factor (TF) binding to enhancers in their native genomic context. Using F1-hybrid cells derived from crosses between distantly related inbred strains of mice, we identified thousands of enhancers with allele-specific TF binding and/or activity. We find that genetic variants located within the central region of enhancers are most likely to alter TF binding and enhancer activity. We observe that the AP-1 family of TFs (Fos/Jun) are frequently required for binding of TEAD TFs and for enhancer function. However, many sequence variants outside of core motifs for AP-1 and TEAD also impact enhancer function, including sequences flanking core TF motifs and AP-1 half sites. Taken together, these data represent one of the most comprehensive assessments of allele-specific TF binding and enhancer function to date and reveal how sequence changes at enhancers alter their function across evolutionary timescales.

Keywords:  chromosomes; gene expression; genetics; genomics; mouse

DOI:  https://doi.org/10.7554/eLife.76500
Cell Syst. 2022 Aug 29. pii: S2405-4712(22)00348-9. [Epub ahead of print]

Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions.

Yuchao Jiang, Yuriko Harigaya, Zhaojun Zhang, Hongpan Zhang, Chongzhi Zang, Nancy R Zhang.

  The epigenetic control of gene expression is highly cell-type and context specific. Yet, despite its complexity, gene regulatory logic can be broken down into modular components consisting of a transcription factor (TF) activating or repressing the target gene expression through its binding to a cis-regulatory region. We propose a nonparametric approach, TRIPOD, to detect and characterize the three-way relationships between a TF, its target gene, and the accessibility of the TF's binding site using single-cell RNA and ATAC multiomic data. We apply TRIPOD to interrogate the cell-type-specific regulatory logic in peripheral blood mononuclear cells and contrast our results to detections from enhancer databases, cis-eQTL studies, ChIP-seq experiments, and TF knockdown/knockout studies. We then apply TRIPOD to mouse embryonic brain data and identify regulatory relationships, validated by ChIP-seq and PLAC-seq. Finally, we demonstrate TRIPOD on the SHARE-seq data of differentiating mouse hair follicle cells and identify lineage-specific regulation supported by histone marks and super-enhancer annotations. A record of this paper's transparent peer review process is included in the supplemental information.

Keywords:  chromatin accessibility; gene expression; single-cell RNA and ATAC; single-cell multiomics; transcription factor; transcriptional regulation

DOI:  https://doi.org/10.1016/j.cels.2022.08.004
PLoS Comput Biol. 2022 Aug;18(8): e1010378

WhichTF is functionally important in your open chromatin data?

Yosuke Tanigawa, Ethan S Dyer, Gill Bejerano.

We present WhichTF, a computational method to identify functionally important transcription factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF applies an ontology-guided functional approach to compute novel enrichment by integrating accessibility measurements, high-confidence pre-computed conservation-aware TF binding sites, and putative gene-regulatory models. Comparison with prior sheer abundance-based methods reveals the unique ability of WhichTF to identify context-specific TFs with functional relevance, including NF-κB family members in lymphocytes and GATA factors in cardiac cells. To distinguish the transcriptional regulatory landscape in closely related samples, we apply differential analysis and demonstrate its utility in lymphocyte, mesoderm developmental, and disease cells. We find suggestive, under-characterized TFs, such as RUNX3 in mesoderm development and GLI1 in systemic lupus erythematosus. We also find TFs known for stress response, suggesting routine experimental caveats that warrant careful consideration. WhichTF yields biological insight into known and novel molecular mechanisms of TF-mediated transcriptional regulation in diverse contexts, including human and mouse cell types, cell fate trajectories, and disease-associated cells.

DOI: https://doi.org/10.1371/journal.pcbi.1010378
Genome Biol. 2022 Sep 01. 23(1): 185

CTCF and cohesin promote focal detachment of DNA from the nuclear lamina.

Tom van Schaik, Ning Qing Liu, Stefano G Manzo, Daan Peric-Hupkes, Elzo de Wit, Bas van Steensel.

   BACKGROUND: Lamina-associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina. It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator protein CTCF is enriched at LAD borders, it was postulated that CTCF binding could position some LAD boundaries, possibly through its function in stalling cohesin and hence preventing cohesin invading into the LAD. To test this, we mapped genome-nuclear lamina interactions in mouse embryonic stem cells after rapid depletion of CTCF and other perturbations of cohesin dynamics.
RESULTS: CTCF and cohesin contribute to a sharp transition in lamina interactions at LAD borders, while LADs are maintained after depletion of these proteins, also at borders marked by CTCF. CTCF and cohesin may thus reinforce LAD borders, but do not position these. CTCF binding sites within LADs are locally detached from the lamina and enriched for accessible DNA and active histone modifications. Remarkably, despite lamina positioning being strongly correlated with genome inactivity, this DNA remains accessible after the local detachment is lost following CTCF depletion. At a chromosomal scale, cohesin depletion and cohesin stabilization by depletion of the unloading factor WAPL quantitatively affect lamina interactions, indicative of perturbed chromosomal positioning in the nucleus. Finally, while H3K27me3 is locally enriched at CTCF-marked LAD borders, we find no evidence for an interplay between CTCF and H3K27me3 on lamina interactions.
CONCLUSIONS: These findings illustrate that CTCF and cohesin are not primary determinants of LAD patterns. Rather, these proteins locally modulate NL interactions.

Keywords:  Acute protein depletion; CTCF; Cohesin; Heterochromatin; Lamina-associated domains; Local detachment; Nuclear lamina; pA-DamID

DOI:  https://doi.org/10.1186/s13059-022-02754-3
Proc Natl Acad Sci U S A. 2022 Sep 06. 119(36): e2203452119

3D chromatin remodeling potentiates transcriptional programs driving cell invasion.

Benjamin Lebeau, Maïka Jangal, Tiejun Zhao, Cheng Kit Wong, Nolan Wong, Eduardo Cepeda Cañedo, Steven Hébert, Adriana Aguilar-Mahecha, Catherine Chabot, Marguerite Buchanan, Rachel Catterall, Luke McCaffrey, Geneviève Deblois, Claudia Kleinman, Morag Park, Mark Basik, Michael Witcher.

  The contribution of deregulated chromatin architecture, including topologically associated domains (TADs), to cancer progression remains ambiguous. CCCTC-binding factor (CTCF) is a central regulator of higher-order chromatin structure that undergoes copy number loss in over half of all breast cancers, but the impact of this defect on epigenetic programming and chromatin architecture remains unclear. We find that under physiological conditions, CTCF organizes subTADs to limit the expression of oncogenic pathways, including phosphatidylinositol 3-kinase (PI3K) and cell adhesion networks. Loss of a single CTCF allele potentiates cell invasion through compromised chromatin insulation and a reorganization of chromatin architecture and histone programming that facilitates de novo promoter-enhancer contacts. However, this change in the higher-order chromatin landscape leads to a vulnerability to inhibitors of mTOR. These data support a model whereby subTAD reorganization drives both modification of histones at de novo enhancer-promoter contacts and transcriptional up-regulation of oncogenic transcriptional networks.

Keywords:  CTCF; TAD; breast cancer; epigenetics; subTAD

DOI:  https://doi.org/10.1073/pnas.2203452119
Cell Rep. 2022 Aug 30. pii: S2211-1247(22)01108-1. [Epub ahead of print]40(9): 111288

SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression.

Tamara Casteels, Simon Bajew, Jiří Reiniš, Lennart Enders, Michael Schuster, Frédéric Fontaine, André C Müller, Bridget K Wagner, Christoph Bock, Stefan Kubicek.

  Insulin expression is primarily restricted to the pancreatic β cells, which are physically or functionally depleted in diabetes. Identifying targetable pathways repressing insulin in non-β cells, particularly in the developmentally related glucagon-secreting α cells, is an important aim of regenerative medicine. Here, we perform an RNA interference screen in a murine α cell line to identify silencers of insulin expression. We discover that knockdown of the splicing factor Smndc1 triggers a global repression of α cell gene-expression programs in favor of increased β cell markers. Mechanistically, Smndc1 knockdown upregulates the β cell transcription factor Pdx1 by modulating the activities of the BAF and Atrx chromatin remodeling complexes. SMNDC1's repressive role is conserved in human pancreatic islets, its loss triggering enhanced insulin secretion and PDX1 expression. Our study identifies Smndc1 as a key factor connecting splicing and chromatin remodeling to the control of insulin expression in human and mouse islet cells.

Keywords:  CP: Metabolism; CP: Molecular biology; RNAi screen; SMNDC1; alpha cells; beta cells; chromatin remodelers; insulin transcription; pancreatic islets; splicing

DOI:  https://doi.org/10.1016/j.celrep.2022.111288
PLoS Comput Biol. 2022 Sep 02. 18(9): e1010450

Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells.

Kapil Newar, Amith Zafal Abdulla, Hossein Salari, Eric Fanchon, Daniel Jost.

The Polycomb system via the methylation of the lysine 27 of histone H3 (H3K27) plays central roles in the silencing of many lineage-specific genes during development. Recent experimental evidence suggested that the recruitment of histone modifying enzymes like the Polycomb repressive complex 2 (PRC2) at specific sites and their spreading capacities from these sites are key to the establishment and maintenance of a proper epigenomic landscape around Polycomb-target genes. Here, to test whether such mechanisms, as a minimal set of qualitative rules, are quantitatively compatible with data, we developed a mathematical model that can predict the locus-specific distributions of H3K27 modifications based on previous biochemical knowledge. Within the biological context of mouse embryonic stem cells, our model showed quantitative agreement with experimental profiles of H3K27 acetylation and methylation around Polycomb-target genes in wild-type and mutants. In particular, we demonstrated the key role of the reader-writer module of PRC2 and of the competition between the binding of activating and repressing enzymes in shaping the H3K27 landscape around transcriptional start sites. The predicted dynamics of establishment and maintenance of the repressive trimethylated H3K27 state suggest a slow accumulation, in perfect agreement with experiments. Our approach represents a first step towards a quantitative description of PcG regulation in various cellular contexts and provides a generic framework to better characterize epigenetic regulation in normal or disease situations.

DOI: https://doi.org/10.1371/journal.pcbi.1010450
Nucleic Acids Res. 2022 Aug 30. pii: gkac716. [Epub ahead of print]

Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation.

Jordi Bernués, Andrea Izquierdo-Boulstridge, Oscar Reina, Lucía Castejón, Elena Fernández-Castañer, Núria Leal, Nancy Guerrero-Pepinosa, Carles Bonet-Costa, Olivera Vujatovic, Paula Climent-Cantó, Fernando Azorín.

Post-translational modifications (PTMs) of core histones are important epigenetic determinants that correlate with functional chromatin states. However, despite multiple linker histone H1s PTMs have been identified, little is known about their genomic distribution and contribution to the epigenetic regulation of chromatin. Here, we address this question in Drosophila that encodes a single somatic linker histone, dH1. We previously reported that dH1 is dimethylated at K27 (dH1K27me2). Here, we show that dH1K27me2 is a major PTM of Drosophila heterochromatin. At mitosis, dH1K27me2 accumulates at pericentromeric heterochromatin, while, in interphase, it is also detected at intercalary heterochromatin. ChIPseq experiments show that >98% of dH1K27me2 enriched regions map to heterochromatic repetitive DNA elements, including transposable elements, simple DNA repeats and satellite DNAs. Moreover, expression of a mutated dH1K27A form, which impairs dH1K27me2, alters heterochromatin organization, upregulates expression of heterochromatic transposable elements and results in the accumulation of RNA:DNA hybrids (R-loops) in heterochromatin, without affecting H3K9 methylation and HP1a binding. The pattern of dH1K27me2 is H3K9 methylation independent, as it is equally detected in flies carrying a H3K9R mutation, and is not affected by depletion of Su(var)3-9, HP1a or Su(var)4-20. Altogether these results suggest that dH1K27me2 contributes to heterochromatin organization independently of H3K9 methylation.

DOI: https://doi.org/10.1093/nar/gkac716
Nat Commun. 2022 Sep 02. 13(1): 5173

Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation.

María Arroyo, Florian D Hastert, Andreas Zhadan, Florian Schelter, Susanne Zimbelmann, Cathia Rausch, Anne K Ludwig, Thomas Carell, M Cristina Cardoso.

Oxidation of the epigenetic DNA mark 5-methylcytosine by Tet dioxygenases is an established route to diversify the epigenetic information, modulate gene expression and overall cellular (patho-)physiology. Here, we demonstrate that Tet1 and its short isoform Tet1s exhibit distinct nuclear localization during DNA replication resulting in aberrant cytosine modification levels in human and mouse cells. We show that Tet1 is tethered away from heterochromatin via its zinc finger domain, which is missing in Tet1s allowing its targeting to these regions. We find that Tet1s interacts with and is ubiquitinated by CRL4(VprBP). The ubiquitinated Tet1s is then recognized by Uhrf1 and recruited to late replicating heterochromatin. This leads to spreading of 5-methylcytosine oxidation to heterochromatin regions, LINE 1 activation and chromatin decondensation. In summary, we elucidate a dual regulation mechanism of Tet1, contributing to the understanding of how epigenetic information can be diversified by spatio-temporal directed Tet1 catalytic activity.

DOI: https://doi.org/10.1038/s41467-022-32799-8
Nat Commun. 2022 Aug 30. 13(1): 5114

Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation.

Wenqi Hu, Haitao Zeng, Yanan Shi, Chuanchuan Zhou, Jiana Huang, Lei Jia, Siqi Xu, Xiaoyu Feng, Yanyan Zeng, Tuanlin Xiong, Wenze Huang, Peng Sun, Yajie Chang, Tingting Li, Cong Fang, Keliang Wu, Lingbo Cai, Wuhua Ni, Yan Li, Zhiyong Yang, Qiangfeng Cliff Zhang, RiCheng Chian, Zijiang Chen, Xiaoyan Liang, Kehkooi Kee.

The combined use of transcriptome and translatome as indicators of gene expression profiles is usually more accurate than the use of transcriptomes alone, especially in cell types governed by translational regulation, such as mammalian oocytes. Here, we developed a dual-omics methodology that includes both transcriptome and translatome sequencing (T&T-seq) of single-cell oocyte samples, and we used it to characterize the transcriptomes and translatomes during mouse and human oocyte maturation. T&T-seq analysis revealed distinct translational expression patterns between mouse and human oocytes and delineated a sequential gene expression regulation from the cytoplasm to the nucleus during human oocyte maturation. By these means, we also identified a functional role of OOSP2 inducing factor in human oocyte maturation, as human recombinant OOSP2 induced in vitro maturation of human oocytes, which was blocked by anti-OOSP2. Single-oocyte T&T-seq analyses further elucidated that OOSP2 induces specific signaling pathways, including small GTPases, through translational regulation.

DOI: https://doi.org/10.1038/s41467-022-32791-2
Nat Cancer. 2022 Sep 01.

ZFP281 drives a mesenchymal-like dormancy program in early disseminated breast cancer cells that prevents metastatic outgrowth in the lung.

Ana Rita Nobre, Erica Dalla, Jihong Yang, Xin Huang, Lena Wullkopf, Emma Risson, Pedram Razghandi, Melisa Lopez Anton, Wei Zheng, Jose A Seoane, Christina Curtis, Ephraim Kenigsberg, Jianlong Wang, Julio A Aguirre-Ghiso.

Increasing evidence shows that cancer cells can disseminate from early evolved primary lesions much earlier than the classical metastasis models predicted. Here, we reveal at a single-cell resolution that mesenchymal-like (M-like) and pluripotency-like programs coordinate dissemination and a long-lived dormancy program of early disseminated cancer cells (DCCs). The transcription factor ZFP281 induces a permissive state for heterogeneous M-like transcriptional programs, which associate with a dormancy signature and phenotype in vivo. Downregulation of ZFP281 leads to a loss of an invasive, M-like dormancy phenotype and a switch to lung metastatic outgrowth. We also show that FGF2 and TWIST1 induce ZFP281 expression to induce the M-like state, which is linked to CDH1 downregulation and upregulation of CDH11. We found that ZFP281 not only controls the early dissemination of cancer cells but also locks early DCCs in a dormant state by preventing the acquisition of an epithelial-like proliferative program and consequent metastases outgrowth.

DOI: https://doi.org/10.1038/s43018-022-00424-8
iScience. 2022 Sep 16. 25(9): 104905

Differential regulation of alternate promoter regions in Sox17 during endodermal and vascular endothelial development.

Linh T Trinh, Anna B Osipovich, Leesa Sampson, Jonathan Wong, Chris V E Wright, Mark A Magnuson.

  Sox17 gene expression is essential for both endothelial and endodermal cell differentiation. To better understand the genetic basis for the expression of multiple Sox17 mRNA forms, we identified and performed CRISPR/Cas9 mutagenesis of two evolutionarily conserved promoter regions (CRs). The deletion of the upstream and endothelial cell-specific CR1 caused only a modest increase in lympho-vasculogenesis likely via reduced Notch signaling downstream of SOX17. In contrast, the deletion of the downstream CR2 region, which functions in both endothelial and endodermal cells, impairs both vascular and endodermal development causing death by embryonic day 12.5. Analyses of 3D chromatin looping, transcription factor binding, histone modification, and chromatin accessibility data at the Sox17 locus and surrounding region further support differential regulation of the two promoters during the development.

Keywords:  Developmental biology; Developmental genetics; Embryology; Genetics

DOI:  https://doi.org/10.1016/j.isci.2022.104905
Nat Commun. 2022 Aug 29. 13(1): 5075

Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling.

Marios G Koliopoulos, Reyhan Muhammad, Theodoros I Roumeliotis, Fabienne Beuron, Jyoti S Choudhary, Claudio Alfieri.

Genes encoding the core cell cycle machinery are transcriptionally regulated by the MuvB family of protein complexes in a cell cycle-specific manner. Complexes of MuvB with the transcription factors B-MYB and FOXM1 activate mitotic genes during cell proliferation. The mechanisms of transcriptional regulation by these complexes are still poorly characterised. Here, we combine biochemical analysis and in vitro reconstitution, with structural analysis by cryo-electron microscopy and cross-linking mass spectrometry, to functionally examine these complexes. We find that the MuvB:B-MYB complex binds and remodels nucleosomes, thereby exposing nucleosomal DNA. This remodelling activity is supported by B-MYB which directly binds the remodelled DNA. Given the remodelling activity on the nucleosome, we propose that the MuvB:B-MYB complex functions as a pioneer transcription factor complex. In this work, we rationalise prior biochemical and cellular studies and provide a molecular framework of interactions on a protein complex that is key for cell cycle regulation.

DOI: https://doi.org/10.1038/s41467-022-32798-9
Mol Cell Biol. 2022 Aug 29. e0019122

GRHL2 Enhances Phosphorylated Estrogen Receptor (ER) Chromatin Binding and Regulates ER-Mediated Transcriptional Activation and Repression.

Rebecca M Reese, Kyle T Helzer, Kaelyn O Allen, Christy Zheng, Natalia Solodin, Elaine T Alarid.

  Phosphorylation of estrogen receptor α (ER) at serine 118 (pS118-ER) is induced by estrogen and is the most abundant posttranslational mark associated with a transcriptionally active receptor. Cistromic analysis of pS118-ER from our group revealed enrichment of the GRHL2 motif near pS118-ER binding sites. In this study, we used cistromic and transcriptomic analyses to interrogate the relationship between GRHL2 and pS118-ER. We found that GRHL2 is bound to chromatin at pS118-ER/GRHL2 co-occupancy sites prior to ligand treatment, and GRHL2 binding is required for maximal pS118-ER recruitment. pS118-ER/GRHL2 co-occupancy sites were enriched at active enhancers marked by H3K27ac and H3K4me1, along with FOXA1 and p300, compared to sites where each factor binds independently. Transcriptomic analysis yielded four subsets of ER/GRHL2-coregulated genes revealing that GRHL2 can both enhance and antagonize E2-mediated ER transcriptional activity. Gene ontology analysis indicated that coregulated genes are involved in cell migration. Accordingly, knockdown of GRHL2, combined with estrogen treatment, resulted in increased cell migration but no change in proliferation. These results support a model in which GRHL2 binds to selected enhancers and facilitates pS118-ER recruitment to chromatin, which then results in differential activation and repression of genes that control estrogen-regulated ER-positive breast cancer cell migration.

Keywords:  DNA binding; GRHL2; estrogen receptor; nuclear receptor; regulation of gene expression; transcription

DOI:  https://doi.org/10.1128/mcb.00191-22
Cell Rep. 2022 Aug 30. pii: S2211-1247(22)01071-3. [Epub ahead of print]40(9): 111253

Arid1a mutation suppresses TGF-β signaling and induces cholangiocarcinoma.

Bing Guo, Scott C Friedland, William Alexander, Jacquelyn A Myers, Wenjia Wang, Michael R O'Dell, Michael Getman, Christa L Whitney-Miller, Diana Agostini-Vulaj, Aaron R Huber, Stephano S Mello, Paula M Vertino, Hartmut K Land, Laurie A Steiner, Aram F Hezel.

  Activating KRAS mutations and functional loss of members of the SWI/SNF complex, including ARID1A, are found together in the primary liver tumor cholangiocarcinoma (CC). How these mutations cooperate to promote CC has not been established. Using murine models of hepatocyte and biliary-specific lineage tracing, we show that Kras and Arid1a mutations drive the formation of CC and tumor precursors from the biliary compartment, which are accelerated by liver inflammation. Using cultured cells, we find that Arid1a loss causes cellular proliferation, escape from cell-cycle control, senescence, and widespread changes in chromatin structure. Notably, we show that the biliary proliferative response elicited by Kras/Arid1a cooperation and tissue injury in CC is caused by failed engagement of the TGF-β-Smad4 tumor suppressor pathway. We thus identify an ARID1A-TGF-β-Smad4 axis as essential in limiting the biliary epithelial response to oncogenic insults, while its loss leads to biliary pre-neoplasia and CC.

Keywords:  ARID1A; ATAC-seq; CP: Cancer; KRAS; RNA-seq; TGF-β; bile ducts; cell cycle; cholangiocarcinoma; mouse embryonic fibroblasts; transdifferentiation

DOI:  https://doi.org/10.1016/j.celrep.2022.111253
Nat Commun. 2022 Aug 27. 13(1): 5058

NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis.

Zsolt Karányi, Ágnes Mosolygó-L, Orsolya Feró, Adrienn Horváth, Beáta Boros-Oláh, Éva Nagy, Szabolcs Hetey, Imre Holb, Henrik Mihály Szaker, Márton Miskei, Tibor Csorba, Lóránt Székvölgyi.

Arabidopsis NODULIN HOMEOBOX (NDX) is a nuclear protein described as a regulator of specific euchromatic genes within transcriptionally active chromosome arms. Here we show that NDX is primarily a heterochromatin regulator that functions in pericentromeric regions to control siRNA production and non-CG methylation. Most NDX binding sites coincide with pericentromeric het-siRNA loci that mediate transposon silencing, and are antagonistic with R-loop structures that are prevalent in euchromatic chromosomal arms. Inactivation of NDX leads to differential siRNA accumulation and DNA methylation, of which CHH/CHG hypomethylation colocalizes with NDX binding sites. Hi-C analysis shows significant chromatin structural changes in the ndx mutant, with decreased intrachromosomal interactions at pericentromeres where NDX is enriched in wild-type plants, and increased interchromosomal contacts between KNOT-forming regions, similar to those observed in DNA methylation mutants. We conclude that NDX is a key regulator of heterochromatin that is functionally coupled to het-siRNA loci and non-CG DNA methylation pathways.

DOI: https://doi.org/10.1038/s41467-022-32709-y
Mol Cell. 2022 Aug 25. pii: S1097-2765(22)00755-9. [Epub ahead of print]

Distinct silencer states generate epigenetic states of heterochromatin.

Daniel S Saxton, Jasper Rine.

  Heterochromatic loci can exhibit different transcriptional states in genetically identical cells. A popular model posits that the inheritance of modified histones is sufficient for inheritance of the silenced state. However, silencing inheritance requires silencers and therefore cannot be driven by the inheritance of modified histones alone. To address these observations, we determined the chromatin architectures produced by strong and weak silencers in Saccharomyces. Strong silencers recruited Sir proteins and silenced the locus in all cells. Strikingly, weakening these silencers reduced Sir protein recruitment and stably silenced the locus in some cells; however, this silenced state could probabilistically convert to an expressed state that lacked Sir protein recruitment. Additionally, changes in the constellation of silencer-bound proteins or the concentration of a structural Sir protein modulated the probability that a locus exhibited the silenced or expressed state. These findings argued that distinct silencer states generate epigenetic states and regulate their dynamics.

Keywords:  bistability; epigenetics; heterochromatin; histones; silencing

DOI:  https://doi.org/10.1016/j.molcel.2022.08.002
PLoS Genet. 2022 Sep 01. 18(9): e1010351

The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila.

Tao Chen, Xiaolu Wei, Cécile Courret, Min Cui, Lin Cheng, Jing Wu, Kami Ahmad, Amanda M Larracuente, Yikang S Rong.

Advances in genomic technology led to a more focused pattern for the distribution of chromosomal proteins and a better understanding of their functions. The recent development of the CUT&RUN technique marks one of the important such advances. Here we develop a modified CUT&RUN technique that we termed nanoCUT&RUN, in which a high affinity nanobody to GFP is used to bring micrococcal nuclease to the binding sites of GFP-tagged chromatin proteins. Subsequent activation of the nuclease cleaves the chromatin, and sequencing of released DNA identifies binding sites. We show that nanoCUT&RUN efficiently produces high quality data for the TRL transcription factor in Drosophila embryos, and distinguishes binding sites specific between two TRL isoforms. We further show that nanoCUT&RUN dissects the distributions of the HipHop and HOAP telomere capping proteins, and uncovers unexpected binding of telomeric proteins at centromeres. nanoCUT&RUN can be readily applied to any system in which a chromatin protein of interest, or its isoforms, carries the GFP tag.

DOI: https://doi.org/10.1371/journal.pgen.1010351