bims-crepig 2022-04-10 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2022–04–10
28 papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit

DNA sequence-dependent formation of heterochromatin nanodomains.
The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma.
CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming.
H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells.
STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming.
A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters.
HIRA-dependent boundaries between H3 variants shape early replication in mammals.
Phosphorylated MED1 links transcription recycling and cancer growth.
Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments.
Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma.
Idax and Rinf facilitate expression of Tet enzymes to promote neural and suppress trophectodermal programs during differentiation of embryonic stem cells.
Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide.
FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.
H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes.
Chromatin interaction aware gene regulatory modeling with graph attention networks.
Elevated ASCL1 activity creates de novo regulatory elements associated with neuronal differentiation.
Single-cell profiling of transcriptome and histone modifications with EpiDamID.
Multivalent DNA and nucleosome acidic patch interactions specify VRK1 mitotic localization and activity.
CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus.
Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion.
SWI/SNF chromatin remodeler complex within the reward pathway is required for behavioral adaptations to stress.
Regulatory elements can be essential for maintaining broad chromatin organization and cell viability.
Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery.
Genetic loci and metabolic states associated with murine epigenetic aging.
The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17.
Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma.
Determinants of epigenetic resistance to HDAC inhibitors in dystrophic fibro-adipogenic progenitors.
Multi-omic rejuvenation of human cells by maturation phase transient reprogramming.

Nat Commun. 2022 Apr 06. 13(1): 1861

DNA sequence-dependent formation of heterochromatin nanodomains.

Graeme J Thorn, Christopher T Clarkson, Anne Rademacher, Hulkar Mamayusupova, Gunnar Schotta, Karsten Rippe, Vladimir B Teif.

The mammalian epigenome contains thousands of heterochromatin nanodomains (HNDs) marked by di- and trimethylation of histone H3 at lysine 9 (H3K9me2/3), which have a typical size of 3-10 nucleosomes. However, what governs HND location and extension is only partly understood. Here, we address this issue by introducing the chromatin hierarchical lattice framework (ChromHL) that predicts chromatin state patterns with single-nucleotide resolution. ChromHL is applied to analyse four HND types in mouse embryonic stem cells that are defined by histone methylases SUV39H1/2 or GLP, transcription factor ADNP or chromatin remodeller ATRX. We find that HND patterns can be computed from PAX3/9, ADNP and LINE1 sequence motifs as nucleation sites and boundaries that are determined by DNA sequence (e.g. CTCF binding sites), cooperative interactions between nucleosomes as well as nucleosome-HP1 interactions. Thus, ChromHL rationalizes how patterns of H3K9me2/3 are established and changed via the activity of protein factors in processes like cell differentiation.

DOI: https://doi.org/10.1038/s41467-022-29360-y
Mol Cell. 2022 Apr 04. pii: S1097-2765(22)00257-X. [Epub ahead of print]

The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma.

Hayley J Zullow, Akshay Sankar, Davis R Ingram, Daniel D Samé Guerra, Andrew R D'Avino, Clayton K Collings, Rossana Lazcano, Wei-Lien Wang, Yu Liang, Jun Qi, Alexander J Lazar, Cigall Kadoch.

  Mammalian SWI/SNF (mSWI/SNF or BAF) ATP-dependent chromatin remodeling complexes play critical roles in governing genomic architecture and gene expression and are frequently perturbed in human cancers. Transcription factors (TFs), including fusion oncoproteins, can bind to BAF complex surfaces to direct chromatin targeting and accessibility, often activating oncogenic gene loci. Here, we demonstrate that the FUS::DDIT3 fusion oncoprotein hallmark to myxoid liposarcoma (MLPS) inhibits BAF complex-mediated remodeling of adipogenic enhancer sites via sequestration of the adipogenic TF, CEBPB, from the genome. In mesenchymal stem cells, small-molecule inhibition of BAF complex ATPase activity attenuates adipogenesis via failure of BAF-mediated DNA accessibility and gene activation at CEBPB target sites. BAF chromatin occupancy and gene expression profiles of FUS::DDIT3-expressing cell lines and primary tumors exhibit similarity to SMARCB1-deficient tumor types. These data present a mechanism by which a fusion oncoprotein generates a BAF complex loss-of-function phenotype, independent of deleterious subunit mutations.

Keywords:  ATP-dependent chromatin remodeling; BAF complex; CEBPB; FUS-DDIT3; MLPS; adipogenesis; enhancers; fusion oncoprotein; mesenchymal stem cells; myxoid liposarcoma

DOI:  https://doi.org/10.1016/j.molcel.2022.03.019
Cell Rep. 2022 Apr 05. pii: S2211-1247(22)00374-6. [Epub ahead of print]39(1): 110626

CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming.

Yawei Song, Zhengyu Liang, Jie Zhang, Gongcheng Hu, Juehan Wang, Yaoyi Li, Rong Guo, Xiaotao Dong, Isaac A Babarinde, Wangfang Ping, Ying-Liang Sheng, Huanhuan Li, Zhaoming Chen, Minghui Gao, Yang Chen, Ge Shan, Michael Q Zhang, Andrew P Hutchins, Xiang-Dong Fu, Hongjie Yao.

  CTCF mediates chromatin insulation and long-distance enhancer-promoter (EP) interactions; however, little is known about how these regulatory functions are partitioned among target genes in key biological processes. Here, we show that Ctcf expression is progressively increased during induced pluripotency. In this process, CTCF first functions as a chromatin insulator responsible for direct silencing of the somatic gene expression program and, interestingly, elevated Ctcf expression next ensures chromatin accessibility and contributes to increased EP interactions for a fraction of pluripotency-associated genes. Therefore, CTCF functions in a context-specific manner to modulate the 3D genome to enable cellular reprogramming. We further discover that these context-specific CTCF functions also enlist SMARCA5, an imitation switch (ISWI) chromatin remodeler, together rewiring the epigenome to facilitate cell-fate switch. These findings reveal the dual functions of CTCF in conjunction with a key chromatin remodeler to drive reprogramming toward pluripotency.

Keywords:  CP: Molecular biology; CP: Stem cell research; CTCF; SMARCA5; chromatin accessibility; chromatin insulation; enhancer-promoter interactions; reprogramming

DOI:  https://doi.org/10.1016/j.celrep.2022.110626
Genome Res. 2022 Apr 08. pii: gr.276383.121. [Epub ahead of print]

H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells.

Haifen Chen, Bo Hu, Cynthia Horth, Eric Bareke, Phillip Rosenbaum, Sin Young Kwon, Jacinthe Sirois, Daniel Neil Weinberg, Faith M Robison, Benjamin A Garcia, Chao Lu, William Abraham Pastor, Jacek Majewski.

Epigenetic modifications on the chromatin do not occur in isolation. Chromatin associated proteins and their modification products form a highly interconnected network, and disturbing one component may rearrange the entire system. We see this increasingly clearly in epigenetically dysregulated cancers. It is important to understand the rules governing epigenetic interactions. Here, we use the mouse embryonic stem cell (mESC) model to describe in detail the relationships within the H3K27-H3K36-DNA methylation subnetwork. In particular, we focus on the major epigenetic reorganization caused by deletion of the histone 3 lysine 36 methyltransferase NSD1, which in mESCs deposits nearly all of the intergenic H3K36me2. Although disturbing the H3K27 and DNA methylation (DNAme) components also affects this network to a certain extent, the removal of H3K36me2 has the most drastic effect on the epigenetic landscape, resulting in full intergenic spread of H3K27me3 and a substantial decrease in DNAme. By profiling DNMT3A and CHH methylation (mCHH), we show that H3K36me2 loss upon Nsd1-KO leads to a massive redistribution of DNMT3A and mCHH away from intergenic regions and towards active gene bodies, suggesting that DNAme reduction is at least in part caused by redistribution of de novo methylation. Additionally, we show that pervasive acetylation of H3K27 is regulated by the interplay of H3K36 and H3K27 methylation. Our analysis highlights the importance of H3K36me2 as a major determinant of the developmental epigenome and provides a framework for further consolidating our knowledge of epigenetic networks.

DOI: https://doi.org/10.1101/gr.276383.121
Nat Commun. 2022 Apr 06. 13(1): 1859

STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming.

Zhaowei Chu, Lei Gu, Yeguang Hu, Xiaoyang Zhang, Man Li, Jiajia Chen, Da Teng, Man Huang, Che-Hung Shen, Li Cai, Toshimi Yoshida, Yifeng Qi, Zhixin Niu, Austin Feng, Songmei Geng, Dennie T Frederick, Emma Specht, Adriano Piris, Ryan J Sullivan, Keith T Flaherty, Genevieve M Boland, Katia Georgopoulos, David Liu, Yang Shi, Bin Zheng.

The cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization, especially the long-range enhancer-promoter contacts and subsequent gene expression control in cancer, remains poorly understood. Here we show that depletion of STAG2 in melanoma cells leads to expansion of topologically associating domains (TADs) and enhances the formation of acetylated histone H3 lysine 27 (H3K27ac)-associated DNA loops at sites where binding of STAG2 is switched to its paralog STAG1. We further identify Interferon Regulatory Factor 9 (IRF9) as a major direct target of STAG2 in melanoma cells via integrated RNA-seq, STAG2 ChIP-seq and H3K27ac HiChIP analyses. We demonstrate that loss of STAG2 activates IRF9 through modulating the 3D genome organization, which in turn enhances type I interferon signaling and increases the expression of PD-L1. Our findings not only establish a previously unknown role of the STAG2 to STAG1 switch in 3D genome organization, but also reveal a functional link between STAG2 and interferon signaling in cancer cells, which may enhance the immune evasion potential in STAG2-mutant cancer.

DOI: https://doi.org/10.1038/s41467-022-29541-9
Nucleic Acids Res. 2022 Apr 07. pii: gkac233. [Epub ahead of print]

A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters.

Wenmeng Wang, Shiyao Qiao, Guangyue Li, Jiahui Cheng, Cuicui Yang, Chen Zhong, Daniel B Stovall, Jinming Shi, Chunbo Teng, Dangdang Li, Guangchao Sui.

As an oncogenic transcription factor, Yin Yang 1 (YY1) regulates enhancer and promoter connection. However, gaps still exist in understanding how YY1 coordinates coactivators and chromatin enhancer elements to assemble enhancers and super-enhancers. Here, we demonstrate that a histidine cluster in YY1's transactivation domain is essential for its formation of phase separation condensates, which can be extended to additional proteins. The histidine cluster is also required for YY1-promoted cell proliferation, migration, clonogenicity and tumor growth. YY1-rich nuclear puncta contain coactivators EP300, BRD4, MED1 and active RNA polymerase II, and colocalize with histone markers of gene activation, but not that of repression. Furthermore, YY1 binds to the consensus motifs in the FOXM1 promoter to activate its expression. Wild-type YY1, but not its phase separation defective mutant, connects multiple enhancer elements and the FOXM1 promoter to form an enhancer cluster. Consistently, fluorescent in situ hybridization (FISH) assays reveal the colocalization of YY1 puncta with both the FOXM1 gene locus and its nascent RNA transcript. Overall, this study demonstrates that YY1 activates target gene expression through forming liquid-liquid phase separation condensates to compartmentalize both coactivators and enhancer elements, and the histidine cluster of YY1 plays a determinant role in this regulatory mechanism.

DOI: https://doi.org/10.1093/nar/gkac233
Mol Cell. 2022 Mar 25. pii: S1097-2765(22)00255-6. [Epub ahead of print]

HIRA-dependent boundaries between H3 variants shape early replication in mammals.

Alberto Gatto, Audrey Forest, Jean-Pierre Quivy, Geneviève Almouzni.

  The lack of a consensus DNA sequence defining replication origins in mammals has led researchers to consider chromatin as a means to specify these regions. However, to date, there is no mechanistic understanding of how this could be achieved and maintained given that nucleosome disruption occurs with each fork passage and with transcription. Here, by genome-wide mapping of the de novo deposition of the histone variants H3.1 and H3.3 in human cells during S phase, we identified how their dual deposition mode ensures a stable marking with H3.3 flanked on both sides by H3.1. These H3.1/H3.3 boundaries correspond to the initiation zones of early origins. Loss of the H3.3 chaperone HIRA leads to the concomitant disruption of H3.1/H3.3 boundaries and initiation zones. We propose that the HIRA-dependent deposition of H3.3 preserves H3.1/H3.3 boundaries by protecting them from H3.1 invasion linked to fork progression, contributing to a chromatin-based definition of early replication zones.

Keywords:  DNA replication; genome-wide chromatin mapping; histone H3 variants; histone chaperones; mammalian replication origins

DOI:  https://doi.org/10.1016/j.molcel.2022.03.017
Nucleic Acids Res. 2022 Apr 08. pii: gkac246. [Epub ahead of print]

Phosphorylated MED1 links transcription recycling and cancer growth.

Zhong Chen, Zhenqing Ye, Raymond E Soccio, Tomoyoshi Nakadai, William Hankey, Yue Zhao, Furong Huang, Fuwen Yuan, Hongyan Wang, Zhifen Cui, Benjamin Sunkel, Dayong Wu, Richard K Dzeng, Jennifer M Thomas-Ahner, Tim H M Huang, Steven K Clinton, Jiaoti Huang, Mitchell A Lazar, Victor X Jin, Robert G Roeder, Qianben Wang.

Mediator activates RNA polymerase II (Pol II) function during transcription, but it remains unclear whether Mediator is able to travel with Pol II and regulate Pol II transcription beyond the initiation and early elongation steps. By using in vitro and in vivo transcription recycling assays, we find that human Mediator 1 (MED1), when phosphorylated at the mammal-specific threonine 1032 by cyclin-dependent kinase 9 (CDK9), dynamically moves along with Pol II throughout the transcribed genes to drive Pol II recycling after the initial round of transcription. Mechanistically, MED31 mediates the recycling of phosphorylated MED1 and Pol II, enhancing mRNA output during the transcription recycling process. Importantly, MED1 phosphorylation increases during prostate cancer progression to the lethal phase, and pharmacological inhibition of CDK9 decreases prostate tumor growth by decreasing MED1 phosphorylation and Pol II recycling. Our results reveal a novel role of MED1 in Pol II transcription and identify phosphorylated MED1 as a targetable driver of dysregulated Pol II recycling in cancer.

DOI: https://doi.org/10.1093/nar/gkac246
BMC Bioinformatics. 2022 Apr 02. 23(1): 116

Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments.

Mikhail D Magnitov, Azat K Garaev, Alexander V Tyakht, Sergey V Ulianov, Sergey V Razin.

   BACKGROUND: Understanding the role of various factors in 3D genome organization is essential to determine their impact on shaping large-scale chromatin units such as euchromatin (A) and heterochromatin (B) compartments. At this level, chromatin compaction is extensively modulated when transcription and epigenetic profiles change upon cell differentiation and response to various external impacts. However, detailed analysis of chromatin contact patterns within and between compartments is complicated because of a lack of suitable computational methods.
RESULTS: We developed a tool, Pentad, to perform calculation, visualisation and quantitative analysis of the average chromatin compartment from the Hi-C matrices in cis, trans, and specified genomic distances. As we demonstrated by applying Pentad to publicly available Hi-C datasets, it helps to reliably detect redistribution of contact frequency in the chromatin compartments and assess alterations in the compartment strength.
CONCLUSIONS: Pentad is a simple tool for the analysis of changes in chromatin compartmentalization in various biological conditions. Pentad is freely available at https://github.com/magnitov/pentad .

Keywords:  3D genome; Chromosomal compartments; Chromosome conformation capture; Genomic interactions; Hi-C; Hi-C data analysis

DOI:  https://doi.org/10.1186/s12859-022-04654-6
Cell Rep. 2022 Apr 05. pii: S2211-1247(22)00389-8. [Epub ahead of print]39(1): 110637

Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma.

Saul Carcamo, Christie B Nguyen, Elena Grossi, Dan Filipescu, Aktan Alpsoy, Alisha Dhiman, Dan Sun, Sonali Narang, Jochen Imig, Tiphaine C Martin, Ramon Parsons, Iannis Aifantis, Aristotelis Tsirigos, Julio A Aguirre-Ghiso, Emily C Dykhuizen, Dan Hasson, Emily Bernstein.

  ARID2 is the most recurrently mutated SWI/SNF complex member in melanoma; however, its tumor-suppressive mechanisms in the context of the chromatin landscape remain to be elucidated. Here, we model ARID2 deficiency in melanoma cells, which results in defective PBAF complex assembly with a concomitant genomic redistribution of the BAF complex. Upon ARID2 depletion, a subset of PBAF and shared BAF-PBAF-occupied regions displays diminished chromatin accessibility and associated gene expression, while BAF-occupied enhancers gain chromatin accessibility and expression of genes linked to the process of invasion. As a function of altered accessibility, the genomic occupancy of melanoma-relevant transcription factors is affected and significantly correlates with the observed transcriptional changes. We further demonstrate that ARID2-deficient cells acquire the ability to colonize distal organs in multiple animal models. Taken together, our results reveal a role for ARID2 in mediating BAF and PBAF subcomplex chromatin dynamics with consequences for melanoma metastasis.

Keywords:  ARID2; BAF; CP: Cancer; PBAF; SWI/SNF; chromatin; invasion; melanoma; transcription factors

DOI:  https://doi.org/10.1016/j.celrep.2022.110637
Stem Cell Res. 2022 Mar 29. pii: S1873-5061(22)00119-2. [Epub ahead of print]61 102770

Idax and Rinf facilitate expression of Tet enzymes to promote neural and suppress trophectodermal programs during differentiation of embryonic stem cells.

Antoine Abou-Jaoude, Cheng-Yen Huang, Julio C Flores, Mirunalini Ravichandran, Run Lei, Stephanie Chrysanthou, Meelad M Dawlaty.

  The Inhibitor of disheveled and axin (Idax) and its ortholog the Retinoid inducible nuclear factor (Rinf) are DNA binding proteins with nuclear and cytoplasmic functions. Rinf is expressed in embryonic stem cells (ESCs) where it regulates transcription of the Ten-eleven translocation (Tet) enzymes, promoting neural and suppressing mesendoderm/trophectoderm differentiation. Here, we find that Idax, which is not expressed in ESCs, is induced upon differentiation. Like Rinf, Idax facilitates neural and silences trophectodermal programs. Individual or combined loss of Idax and Rinf led to downregulation of neural and upregulation of trophectoderm markers during differentiation of ESCs to embryoid bodies as well as during directed differentiation of ESCs to neural progenitor cells (NPCs) and trophoblast-like cells. These defects resemble those of Tet-deficient ESCs. Consistently, Tet genes are direct targets of Idax and Rinf, and loss of Idax and Rinf led to downregulation of Tet enzymes during ESC differentiation to NPCs and trophoblast-like cells. While Idax and Rinf single and double knockout (DKO) mice were viable and overtly normal, DKO embryos had reduced expression of several NPC markers in embryonic forebrains and deregulated expression of selected trophoblast markers in placentas. NPCs derived from DKO forebrains had reduced self-renewal while DKO placentas had increased junctional zone and reduced labyrinth layers. Together, our findings establish Idax and Rinf as regulators of Tet enzymes for proper differentiation of ESCs.

Keywords:  Differentiation; ESC; Idax; NPC; Rinf; Tet enzymes; Trophoblast

DOI:  https://doi.org/10.1016/j.scr.2022.102770
Cell Rep. 2022 Apr 05. pii: S2211-1247(22)00382-5. [Epub ahead of print]39(1): 110630

Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide.

Benjamin L Allen, Kim Quach, Taylor Jones, Cecilia B Levandowski, Christopher C Ebmeier, Jonathan D Rubin, Timothy Read, Robin D Dowell, Alanna Schepartz, Dylan J Taatjes.

  DNA-binding transcription factors (TFs) remain challenging to target with molecular probes. Many TFs function in part through interaction with Mediator, a 26-subunit complex that controls RNA polymerase II activity genome-wide. We sought to block p53 function by disrupting the p53-Mediator interaction. Through rational design and activity-based screening, we characterize a stapled peptide, with functional mimics of both p53 activation domains, that blocks p53-Mediator binding and selectively inhibits p53-dependent transcription in human cells; importantly, this "bivalent" peptide has negligible impact, genome-wide, on non-p53 target genes. Our proof-of-concept strategy circumvents the TF entirely and targets the TF-Mediator interface instead, with desired functional outcomes (i.e., selective inhibition of p53 activation). Furthermore, these results demonstrate that TF activation domains represent viable starting points for Mediator-targeting molecular probes, as an alternative to large compound libraries. Different TFs bind Mediator through different subunits, suggesting this strategy could be broadly applied to selectively alter gene expression programs.

Keywords:  AP-MS; CP: Molecular biology; ChIP-seq; Mediator complex; Nutlin-3a; RNA-seq; chemical biology; in vitro transcription; molecular probes; p53; proteomics; stapled peptide; transcription

DOI:  https://doi.org/10.1016/j.celrep.2022.110630
BMC Genomics. 2022 Apr 07. 23(Suppl 1): 272

FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.

Guan-Dong Shang, Zhou-Geng Xu, Mu-Chun Wan, Fu-Xiang Wang, Jia-Wei Wang.

   BACKGROUND: Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing and analyzing framework for inferring influential TFs based on ChIP-seq/ATAC-seq datasets.
RESULTS: Here, we introduce FindIT2 (Find Influential TFs and Targets), an R/Bioconductor package for annotating and processing high-throughput multi-omics data. FindIT2 supports a complete framework for annotating ChIP-seq/ATAC-seq peaks, identifying TF targets by the combination of ChIP-seq and RNA-seq datasets, and inferring influential TFs based on different types of data input. Moreover, benefited from the annotation framework based on Bioconductor, FindIT2 can be applied to any species with genomic annotations, which is particularly useful for the non-model species that are less well-studied.
CONCLUSION: FindIT2 provides a user-friendly and flexible framework to generate results at different levels according to the richness of the annotation information of user's species. FindIT2 is compatible with all the operating systems and is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor ( https://bioconductor.org/packages/devel/bioc/html/FindIT2.html ).

Keywords:  ATAC-seq; ChIP-seq; Chromatin accessibility; Gene regulation; R package; Transcription factor

DOI:  https://doi.org/10.1186/s12864-022-08506-8
Biochemistry. 2022 Apr 04.

H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes.

Nathaniel L Burge, Jenna L Thuma, Ziyong Z Hong, Kevin B Jamison, Jennifer J Ottesen, Michael G Poirier.

The linker histone H1 is a highly prevalent protein that compacts chromatin and regulates DNA accessibility and transcription. However, the mechanisms behind H1 regulation of transcription factor (TF) binding within nucleosomes are not well understood. Using in vitro fluorescence assays, we positioned fluorophores throughout human H1 and the nucleosome, then monitored the distance changes between H1 and the histone octamer, H1 and nucleosomal DNA, or nucleosomal DNA and the histone octamer to monitor the H1 movement during TF binding. We found that H1 remains bound to the nucleosome dyad, while the C terminal domain (CTD) releases the linker DNA during nucleosome partial unwrapping and TF binding. In addition, mutational studies revealed that a small 16 amino acid region at the beginning of the H1 CTD is largely responsible for altering nucleosome wrapping and regulating TF binding within nucleosomes. We then investigated physiologically relevant post-translational modifications (PTMs) in human H1 by preparing fully synthetic H1 using convergent hybrid phase native chemical ligation. Both individual PTMs and combinations of phosphorylation and citrullination of H1 had no detectable influence on nucleosome binding and nucleosome wrapping, and had only a minor impact on H1 regulation of TF occupancy within nucleosomes. This suggests that these H1 PTMs function by other mechanisms. Our results highlight the importance of the H1 CTD, in particular, the first 16 amino acids, in regulating nucleosome linker DNA dynamics and TF binding within the nucleosome.

DOI: https://doi.org/10.1021/acs.biochem.2c00001
Genome Res. 2022 Apr 08. pii: gr.275870.121. [Epub ahead of print]

Chromatin interaction aware gene regulatory modeling with graph attention networks.

Alireza Karbalayghareh, Merve Sahin, Christina S Leslie.

Linking distal enhancers to genes and modeling their impact on target gene expression are longstanding unresolved problems in regulatory genomics and critical for interpreting noncoding genetic variation. Here we present a new deep learning approach called GraphReg that exploits 3D interactions from chromosome conformation capture assays in order to predict gene expression from 1D epigenomic data or genomic DNA sequence. By using graph attention networks to exploit the connectivity of distal elements up to 2Mb away in the genome, GraphReg more faithfully models gene regulation and more accurately predicts gene expression levels than state-of-the-art deep learning methods for this task. Feature attribution used with GraphReg accurately identifies functional enhancers of genes, as validated by CRISPRi-FlowFISH and TAP-seq assays, outperforming both CNNs and the recently proposed Activity-by-Contact model. Sequence-based GraphReg also accurately predicts direct transcription factor (TF) targets as validated by CRISPRi TF knockout experiments via in silico ablation of TF binding motifs. GraphReg therefore represents an important advance in modeling the regulatory impact of epigenomic and sequence elements.

DOI: https://doi.org/10.1101/gr.275870.121
BMC Genomics. 2022 Apr 03. 23(1): 255

Elevated ASCL1 activity creates de novo regulatory elements associated with neuronal differentiation.

Laura M Woods, Fahad R Ali, Roshna Gomez, Igor Chernukhin, Daniel Marcos, Lydia M Parkinson, Ahmad N Abou Tayoun, Jason S Carroll, Anna Philpott.

   BACKGROUND: The pro-neural transcription factor ASCL1 is a master regulator of neurogenesis and a key factor necessary for the reprogramming of permissive cell types to neurons. Endogenously, ASCL1 expression is often associated with neuroblast stem-ness. Moreover, ASCL1-mediated reprogramming of fibroblasts to differentiated neurons is commonly achieved using artificially high levels of ASCL1 protein, where ASCL1 acts as an "on-target" pioneer factor. However, the genome-wide effects of enhancing ASCL1 activity in a permissive neurogenic environment has not been thoroughly investigated. Here, we overexpressed ASCL1 in the neuronally-permissive context of neuroblastoma (NB) cells where modest endogenous ASCL1 supports the neuroblast programme.
RESULTS: Increasing ASCL1 in neuroblastoma cells both enhances binding at existing ASCL1 sites and also leads to creation of numerous additional, lower affinity binding sites. These extensive genome-wide changes in ASCL1 binding result in significant reprogramming of the NB transcriptome, redirecting it from a proliferative neuroblastic state towards one favouring neuronal differentiation. Mechanistically, ASCL1-mediated cell cycle exit and differentiation can be increased further by preventing its multi-site phosphorylation, which is associated with additional changes in genome-wide binding and gene activation profiles.
CONCLUSIONS: Our findings show that enhancing ASCL1 activity in a neurogenic environment both increases binding at endogenous ASCL1 sites and also results in additional binding to new low affinity sites that favours neuronal differentiation over the proliferating neuroblast programme supported by the endogenous protein. These findings have important implications for controlling processes of neurogenesis in cancer and cellular reprogramming.

Keywords:  ASCL1; Differentiation; Induced neurons; Neuroblastoma; Reprogramming

DOI:  https://doi.org/10.1186/s12864-022-08495-8
Mol Cell. 2022 Mar 23. pii: S1097-2765(22)00218-0. [Epub ahead of print]

Single-cell profiling of transcriptome and histone modifications with EpiDamID.

Franka J Rang, Kim L de Luca, Sandra S de Vries, Christian Valdes-Quezada, Ellen Boele, Phong D Nguyen, Isabel Guerreiro, Yuko Sato, Hiroshi Kimura, Jeroen Bakkers, Jop Kind.

  Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins. Using these, we render the DamID technology compatible with the genome-wide identification of histone post-translational modifications. Importantly, this includes the possibility to jointly measure chromatin marks and transcription at the single-cell level. We use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. In addition, we map H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specific to notochord. Overall, EpiDamID is a new addition to a vast toolbox to study chromatin states during dynamic cellular processes.

Keywords:  DamID; chromatin; embryo development; epigenetics; gene regulation; histone post-translational modifications; multi-modal omics; single-cell genomics

DOI:  https://doi.org/10.1016/j.molcel.2022.03.009
Nucleic Acids Res. 2022 Apr 07. pii: gkac198. [Epub ahead of print]

Multivalent DNA and nucleosome acidic patch interactions specify VRK1 mitotic localization and activity.

Gabrielle R Budziszewski, Yani Zhao, Cathy J Spangler, Katarzyna M Kedziora, Michael R Williams, Dalal N Azzam, Aleksandra Skrajna, Yuka Koyama, Andrew P Cesmat, Holly C Simmons, Eyla C Arteaga, Joshua D Strauss, Dmitri Kireev, Robert K McGinty.

A key role of chromatin kinases is to phosphorylate histone tails during mitosis to spatiotemporally regulate cell division. Vaccinia-related kinase 1 (VRK1) is a serine-threonine kinase that phosphorylates histone H3 threonine 3 (H3T3) along with other chromatin-based targets. While structural studies have defined how several classes of histone-modifying enzymes bind to and function on nucleosomes, the mechanism of chromatin engagement by kinases is largely unclear. Here, we paired cryo-electron microscopy with biochemical and cellular assays to demonstrate that VRK1 interacts with both linker DNA and the nucleosome acidic patch to phosphorylate H3T3. Acidic patch binding by VRK1 is mediated by an arginine-rich flexible C-terminal tail. Homozygous missense and nonsense mutations of this acidic patch recognition motif in VRK1 are causative in rare adult-onset distal spinal muscular atrophy. We show that these VRK1 mutations interfere with nucleosome acidic patch binding, leading to mislocalization of VRK1 during mitosis, thus providing a potential new molecular mechanism for pathogenesis.

DOI: https://doi.org/10.1093/nar/gkac198
Nat Commun. 2022 Apr 06. 13(1): 1871

CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus.

Patricia A Clow, Menghan Du, Nathaniel Jillette, Aziz Taghbalout, Jacqueline J Zhu, Albert W Cheng.

Three-dimensional (3D) structures of the genome are dynamic, heterogeneous and functionally important. Live cell imaging has become the leading method for chromatin dynamics tracking. However, existing CRISPR- and TALE-based genomic labeling techniques have been hampered by laborious protocols and are ineffective in labeling non-repetitive sequences. Here, we report a versatile CRISPR/Casilio-based imaging method that allows for a nonrepetitive genomic locus to be labeled using one guide RNA. We construct Casilio dual-color probes to visualize the dynamic interactions of DNA elements in single live cells in the presence or absence of the cohesin subunit RAD21. Using a three-color palette, we track the dynamic 3D locations of multiple reference points along a chromatin loop. Casilio imaging reveals intercellular heterogeneity and interallelic asynchrony in chromatin interaction dynamics, underscoring the importance of studying genome structures in 4D.

DOI: https://doi.org/10.1038/s41467-022-29343-z
Nucleic Acids Res. 2022 Apr 05. pii: gkac226. [Epub ahead of print]

Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion.

Núria Serna-Pujol, Mónica Salinas-Pena, Francesca Mugianesi, François Le Dily, Marc A Marti-Renom, Albert Jordan.

Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.

DOI: https://doi.org/10.1093/nar/gkac226
Nat Commun. 2022 Apr 04. 13(1): 1807

SWI/SNF chromatin remodeler complex within the reward pathway is required for behavioral adaptations to stress.

Abdallah Zayed, Camille Baranowski, Anne-Claire Compagnion, Cécile Vernochet, Samah Karaki, Romain Durand-de Cuttoli, Estefani Saint-Jour, Soumee Bhattacharya, Fabio Marti, Peter Vanhoutte, Moshe Yaniv, Philippe Faure, Jacques Barik, Laurence Amar, François Tronche, Sébastien Parnaudeau.

Enduring behavioral changes upon stress exposure involve changes in gene expression sustained by epigenetic modifications in brain circuits, including the mesocorticolimbic pathway. Brahma (BRM) and Brahma Related Gene 1 (BRG1) are ATPase subunits of the SWI/SNF complexes involved in chromatin remodeling, a process essential to enduring plastic changes in gene expression. Here, we show that in mice, social defeat induces changes in BRG1 nuclear distribution. The inactivation of the Brg1/Smarca4 gene within dopamine-innervated regions or the constitutive inactivation of the Brm/Smarca2 gene leads to resilience to repeated social defeat and decreases the behavioral responses to cocaine without impacting midbrain dopamine neurons activity. Within striatal medium spiny neurons, Brg1 gene inactivation reduces the expression of stress- and cocaine-induced immediate early genes, increases levels of heterochromatin and at a global scale decreases chromatin accessibility. Altogether these data demonstrate the pivotal function of SWI/SNF complexes in behavioral and transcriptional adaptations to salient environmental challenges.

DOI: https://doi.org/10.1038/s41467-022-29380-8
Nucleic Acids Res. 2022 Apr 07. pii: gkac197. [Epub ahead of print]

Regulatory elements can be essential for maintaining broad chromatin organization and cell viability.

Ying Liu, Bo Ding, Lina Zheng, Ping Xu, Zhiheng Liu, Zhao Chen, Peiyao Wu, Ying Zhao, Qian Pan, Yu Guo, Wei Wang, Wensheng Wei.

Increasing evidence shows that promoters and enhancers could be related to 3D chromatin structure, thus affecting cellular functions. Except for their roles in forming canonical chromatin loops, promoters and enhancers have not been well studied regarding the maintenance of broad chromatin organization. Here, we focused on the active promoters/enhancers predicted to form many 3D contacts with other active promoters/enhancers (referred to as hotspots) and identified dozens of loci essential for cell growth and survival through CRISPR screening. We found that the deletion of an essential hotspot could lead to changes in broad chromatin organization and the expression of distal genes. We showed that the essentiality of hotspots does not result from their association with individual genes that are essential for cell viability but rather from their association with multiple dysregulated non-essential genes to synergistically impact cell fitness.

DOI: https://doi.org/10.1093/nar/gkac197
Nat Commun. 2022 Apr 06. 13(1): 1855

Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery.

Tian Zhou, Xinyi Zhu, Zhizhong Ye, Yong-Fei Wang, Chao Yao, Ning Xu, Mi Zhou, Jianyang Ma, Yuting Qin, Yiwei Shen, Yuanjia Tang, Zhihua Yin, Hong Xu, Yutong Zhang, Xiaoli Zang, Huihua Ding, Wanling Yang, Ya Guo, John B Harley, Bahram Namjou, Kenneth M Kaufman, Leah C Kottyan, Matthew T Weirauch, Guojun Hou, Nan Shen.

Despite strong evidence that human genetic variants affect the expression of many key transcription factors involved in autoimmune diseases, establishing biological links between non-coding risk variants and the gene targets they regulate remains a considerable challenge. Here, we combine genetic, epigenomic, and CRISPR activation approaches to screen for functional variants that regulate IRF8 expression. We demonstrate that the locus containing rs2280381 is a cell-type-specific enhancer for IRF8 that spatially interacts with the IRF8 promoter. Further, rs2280381 mediates IRF8 expression through enhancer RNA AC092723.1, which recruits TET1 to the IRF8 promoter regulating IRF8 expression by affecting methylation levels. The alleles of rs2280381 modulate PU.1 binding and chromatin state to regulate AC092723.1 and IRF8 expression differentially. Our work illustrates an integrative strategy to define functional genetic variants that regulate the expression of critical genes in autoimmune diseases and decipher the mechanisms underlying the dysregulation of IRF8 expression mediated by lupus risk variants.

DOI: https://doi.org/10.1038/s41467-022-29514-y
Elife. 2022 Apr 07. pii: e75244. [Epub ahead of print]11

Genetic loci and metabolic states associated with murine epigenetic aging.

Khyobeni Mozhui, Ake T Lu, Caesar Z Li, Amin Haghani, Jose Vladimir Sandoval-Sierra, Yibo Wu, Robert W Williams, Steve Horvath.

  Changes in DNA methylation (DNAm) are linked to aging. Here, we profile highly conserved CpGs in 339 predominantly female mice belonging to the BXD family for which we have deep longevity and genomic data. We use a 'pan-mammalian' microarray that provides a common platform for assaying the methylome across mammalian clades. We computed epigenetic clocks and tested associations with DNAm entropy, diet, weight, metabolic traits, and genetic variation. We describe the multifactorial variance of methylation at these CpGs, and show that high fat diet augments the age-associated changes. Entropy increases with age. The progression to disorder, particularly at CpGs that gain methylation over time, was predictive of genotype-dependent life expectancy. The longer-lived BXD strains had comparatively lower entropy at a given age. We identified two genetic loci that modulate rates of epigenetic age acceleration (EAA): one on chromosome (Chr) 11 that encompasses the Erbb2/Her2 oncogenic region, and a second on Chr19 that contains a cytochrome P450 cluster. Both loci harbor genes associated with EAA in humans including STXBP4, NKX2-3, and CUTC. Transcriptome and proteome analyses revealed associations with oxidation-reduction, metabolic, and immune response pathways. Our results highlight concordant loci for EAA in humans and mice, and demonstrate a tight coupling between the metabolic state and epigenetic aging.

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

DOI:  https://doi.org/10.7554/eLife.75244
Sci Signal. 2022 Apr 05. 15(728): eabm2496

The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17.

Daniele Chaves-Moreira, Marilyn A Mitchell, Cristina Arruza, Priyanka Rawat, Simone Sidoli, Robbin Nameki, Jessica Reddy, Rosario I Corona, Lena K Afeyan, Isaac A Klein, Sisi Ma, Boris Winterhoff, Gottfried E Konecny, Benjamin A Garcia, Donita C Brady, Kate Lawrenson, Patrice J Morin, Ronny Drapkin.

PAX8 is a master transcription factor that is essential during embryogenesis and promotes neoplastic growth. It is expressed by the secretory cells lining the female reproductive tract, and its deletion during development results in atresia of reproductive tract organs. Nearly all ovarian carcinomas express PAX8, and its knockdown results in apoptosis of ovarian cancer cells. To explore the role of PAX8 in these tissues, we purified the PAX8 protein complex from nonmalignant fallopian tube cells and high-grade serous ovarian carcinoma cell lines. We found that PAX8 was a member of a large chromatin remodeling complex and preferentially interacted with SOX17, another developmental transcription factor. Depleting either PAX8 or SOX17 from cancer cells altered the expression of factors involved in angiogenesis and functionally disrupted tubule and capillary formation in cell culture and mouse models. PAX8 and SOX17 in ovarian cancer cells promoted the secretion of angiogenic factors by suppressing the expression of SERPINE1, which encodes a proteinase inhibitor with antiangiogenic effects. The findings reveal a non-cell-autonomous function of these transcription factors in regulating angiogenesis in ovarian cancer.

DOI: https://doi.org/10.1126/scisignal.abm2496
Mol Cell. 2022 Mar 29. pii: S1097-2765(22)00256-8. [Epub ahead of print]

Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma.

Evgeny Deforzh, Erik J Uhlmann, Eashita Das, Aleksandra Galitsyna, Ramil Arora, Harini Saravanan, Rosalia Rabinovsky, Aditya D Wirawan, Nadiya M Teplyuk, Rachid El Fatimy, Sucika Perumalla, Anirudh Jairam, Zhiyun Wei, Leonid Mirny, Anna M Krichevsky.

  miR-10b is silenced in normal neuroglial cells of the brain but commonly activated in glioma, where it assumes an essential tumor-promoting role. We demonstrate that the entire miR-10b-hosting HOXD locus is activated in glioma via the cis-acting mechanism involving 3D chromatin reorganization and CTCF-cohesin-mediated looping. This mechanism requires two interacting lncRNAs, HOXD-AS2 and LINC01116, one associated with HOXD3/HOXD4/miR-10b promoter and another with the remote enhancer. Knockdown of either lncRNA in glioma cells alters CTCF and cohesin binding, abolishes chromatin looping, inhibits the expression of all genes within HOXD locus, and leads to glioma cell death. Conversely, in cortical astrocytes, enhancer activation is sufficient for HOXD/miR-10b locus reorganization, gene derepression, and neoplastic cell transformation. LINC01116 RNA is essential for this process. Our results demonstrate the interplay of two lncRNAs in the chromatin folding and concordant regulation of miR-10b and multiple HOXD genes normally silenced in astrocytes and triggering the neoplastic glial transformation.

Keywords:  CTCF; HOXD locus; chromatin loops; enhancer-promoter communication; glioblastoma; lncRNAs; low-grade glioma; miR-10b

DOI:  https://doi.org/10.1016/j.molcel.2022.03.018
EMBO Rep. 2022 Apr 04. e54721

Determinants of epigenetic resistance to HDAC inhibitors in dystrophic fibro-adipogenic progenitors.

Silvia Consalvi, Luca Tucciarone, Elisa Macrì, Marco De Bardi, Mario Picozza, Illari Salvatori, Alessandra Renzini, Sergio Valente, Antonello Mai, Viviana Moresi, Pier Lorenzo Puri.

  Pharmacological treatment of Duchenne muscular dystrophy (DMD) with histone deacetylase inhibitors (HDACi) is currently being tested in clinical trials; however, pre-clinical studies indicated that the beneficial effects of HDACi are restricted to early stages of disease. We show that FAPs from late-stage mdx mice exhibit aberrant HDAC activity and genome-wide alterations of histone acetylation that are not fully reversed by HDACi. In particular, combinatorial H3K27 and/or H3K9/14 hypo-acetylation at promoters of genes required for cell cycle activation and progression, as well as glycolysis, are associated with their downregulation in late-stage mdx FAPs. These alterations could not be reversed by HDACi, due to a general resistance to HDACi-induced H3K9/14 hyperacetylation. Conversely, H3K9/14 hyper-acetylation at promoters of Senescence Associated Secretory Phenotype (SASP) genes is associated with their upregulation in late-stage mdx FAPs; however, HDACi could reduce promoter acetylation and blunt SASP gene activation. These data reveal that during DMD progression FAPs develop disease-associated features reminiscent of cellular senescence, through epigenetically distinct and pharmacologically dissociable events. They also indicate that HDACi might retain anti-fibrotic effects at late stages of DMD.

Keywords:  FAPs; HDAC; duchenne muscular dystrophy; fibrosis; regeneration

DOI:  https://doi.org/10.15252/embr.202254721
Elife. 2022 Apr 08. pii: e71624. [Epub ahead of print]11

Multi-omic rejuvenation of human cells by maturation phase transient reprogramming.

Diljeet Gill, Aled Parry, Fátima Santos, Hanneke Okkenhaug, Christopher D Todd, Irene Hernando-Herraez, Thomas M Stubbs, Inês Milagre, Wolf Reik.

  Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming, somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first 'maturation phase transient reprogramming' (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells temporarily lose and then reacquire their fibroblast identity during MPTR, possibly as a result of epigenetic memory at enhancers and/or persistent expression of some fibroblast genes. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. The magnitude of rejuvenation instigated by MTPR appears substantially greater than that achieved in previous transient reprogramming protocols. In addition, MPTR fibroblasts produced youthful levels of collagen proteins, and showed partial functional rejuvenation of their migration speed. Finally, our work suggests that more extensive reprogramming does not necessarily result in greater rejuvenation but instead that optimal time windows exist for rejuvenating the transcriptome and the epigenome. Overall, we demonstrate that it is possible to separate rejuvenation from complete pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.

Keywords:  genetics; genomics; human; regenerative medicine; stem cells

DOI:  https://doi.org/10.7554/eLife.71624