bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2024‒03‒24
twenty-six papers selected by
Connor Rogerson, University of Cambridge
  1. H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation.
  2. The winged helix domain of MORF binds CpG islands and the TAZ2 domain of p300.
  3. Increased enhancer-promoter interactions during developmental enhancer activation in mammals.
  4. Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration.
  5. Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion.
  6. GAS41 modulates ferroptosis by anchoring NRF2 on chromatin.
  7. Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
  8. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis.
  9. SUMO-dependent transcriptional repression by Sox2 inhibits the proliferation of neural stem cells.
  10. Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes.
  11. Multicenter integrated analysis of noncoding CRISPRi screens.
  12. Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers.
  13. Exhaustive identification of genome-wide binding events of transcriptional regulators.
  14. The homeobox transcription factor DUXBL controls exit from totipotency.
  15. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding.
  16. Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation.
  17. FUS reads histone H3K36me3 to regulate alternative polyadenylation.
  18. STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma.
  19. Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma.
  20. Robust chromatin state annotation.
  21. A single-nuclei paired multiomic analysis of the human midbrain reveals age- and Parkinson's disease-associated glial changes.
  22. Childhood cancer mutagenesis caused by transposase-derived PGBD5.
  23. Two redundant transcription factor binding sites in a single enhancer are essential for mammalian sex determination.
  24. SIRT4 loss reprograms intestinal nucleotide metabolism to support proliferation following perturbation of homeostasis.
  25. The impact of DNA methylation on CTCF-mediated 3D genome organization.
  26. FOXL2 interaction with different binding partners regulates the dynamics of ovarian development.
  1. Mol Cell. 2024 Mar 15. pii: S1097-2765(24)00171-0. [Epub ahead of print]
    H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation.
    Naoki Kubo, Poshen B Chen, Rong Hu, Zhen Ye, Hiroyuki Sasaki, Bing Ren.
      Histone H3 lysine 4 mono-methylation (H3K4me1) marks poised or active enhancers. KMT2C (MLL3) and KMT2D (MLL4) catalyze H3K4me1, but their histone methyltransferase activities are largely dispensable for transcription during early embryogenesis in mammals. To better understand the role of H3K4me1 in enhancer function, we analyze dynamic enhancer-promoter (E-P) interactions and gene expression during neural differentiation of the mouse embryonic stem cells. We found that KMT2C/D catalytic activities were only required for H3K4me1 and E-P contacts at a subset of candidate enhancers, induced upon neural differentiation. By contrast, a majority of enhancers retained H3K4me1 in KMT2C/D catalytic mutant cells. Surprisingly, H3K4me1 signals at these KMT2C/D-independent sites were reduced after acute depletion of KMT2B, resulting in aggravated transcriptional defects. Our observations therefore implicate KMT2B in the catalysis of H3K4me1 at enhancers and provide additional support for an active role of H3K4me1 in enhancer-promoter interactions and transcription in mammalian cells.
    Keywords:  H3K4me1; KMT2B; KMT2C/D; MLL2; MLL3/4; chromatin contacts; differentiation; enhancer; gene regulation; histone methyltransferases
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.030
  2. iScience. 2024 Apr 19. 27(4): 109367
    The winged helix domain of MORF binds CpG islands and the TAZ2 domain of p300.
    Dustin C Becht, Akinori Kanai, Soumi Biswas, Mohamed Halawa, Lei Zeng, Khan L Cox, Michael G Poirier, Ming-Ming Zhou, Xiaobing Shi, Akihiko Yokoyama, Tatiana G Kutateladze.
      Acetylation of histones by lysine acetyltransferases (KATs) provides a fundamental mechanism by which chromatin structure and transcriptional programs are regulated. Here, we describe a dual binding activity of the first winged helix domain of human MORF KAT (MORFWH1) that recognizes the TAZ2 domain of p300 KAT (p300TAZ2) and CpG rich DNA sequences. Structural and biochemical studies identified distinct DNA and p300TAZ2 binding sites, allowing MORFWH1 to independently engage either ligand. Genomic data show that MORF/MOZWH1 colocalizes with H3K18ac, a product of enzymatic activity of p300, on CpG rich promoters of target genes. Our findings suggest a functional cooperation of MORF and p300 KATs in transcriptional regulation.
    Keywords:  Biochemistry; Structural biology
    DOI:  https://doi.org/10.1016/j.isci.2024.109367
  3. Nat Genet. 2024 Mar 20.
    Increased enhancer-promoter interactions during developmental enhancer activation in mammals.
    Zhuoxin Chen, Valentina Snetkova, Grace Bower, Sandra Jacinto, Benjamin Clock, Atrin Dizehchi, Iros Barozzi, Brandon J Mannion, Ana Alcaina-Caro, Javier Lopez-Rios, Diane E Dickel, Axel Visel, Len A Pennacchio, Evgeny Z Kvon.
      Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.
    DOI:  https://doi.org/10.1038/s41588-024-01681-2
  4. Cell Rep. 2024 Mar 21. pii: S2211-1247(24)00311-5. [Epub ahead of print]43(4): 113983
    Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration.
    Kenneth Wu, Namrita Dhillon, Antone Bajor, Sara Abrahamsson, Rohinton T Kamakaka.
      Transcriptional silencing in Saccharomyces cerevisiae involves the generation of a chromatin state that stably represses transcription. Using multiple reporter assays, a diverse set of upstream activating sequence enhancers and core promoters were investigated for their susceptibility to silencing. We show that heterochromatin stably silences only weak and stress-induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements, and the partial repression of these elements did not result in bistable expression states. Permutation analysis of enhancers and promoters indicates that both elements are targets of repression. Chromatin remodelers help specific regulatory elements to resist repression, most probably by altering nucleosome mobility and changing transcription burst duration. The strong enhancers/promoters can be repressed if silencer-bound Sir1 is increased. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating-type gene regulatory elements but not strong housekeeping gene regulatory sequences.
    Keywords:  CP: Molecular biology; Sir1; UAS enhancer; chromatin; core promoter; heterochromatin; nucleosomes; silencing; transcription; transcription burst
    DOI:  https://doi.org/10.1016/j.celrep.2024.113983
  5. Elife. 2024 Mar 19. pii: RP88564. [Epub ahead of print]12
    Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion.
    Davin Jeong, Guang Shi, Xin Li, D Thirumalai.
      Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss. Imaging experiments show that, at the single-cell level, TAD-like structures are present even without cohesin. To provide a structural basis for these findings, we first used polymer simulations to show that certain TADs with epigenetic switches across their boundaries survive after depletion of loops. More importantly, the three-dimensional structures show that many of the P-TADs have sharp physical boundaries. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and human colorectal carcinoma cell lines, which affirmed that epigenetic switches and physical boundaries (calculated using the predicted 3D structures using the data-driven HIPPS method that uses Hi-C as the input) explain the origin of the P-TADs. Single-cell structures display TAD-like features in the absence of cohesin that are remarkably similar to the findings in imaging experiments. Some P-TADs, with physical boundaries, are relevant to the retention of enhancer-promoter/promoter-promoter interactions. Overall, our study shows that preservation of a subset of TADs upon removing cohesin is a robust phenomenon that is valid across multiple cell lines.
    Keywords:  TAD features without cohesin; enhancer–promoter interactions; none; physics of living systems; preserved TADs; single-cell Hi-C
    DOI:  https://doi.org/10.7554/eLife.88564
  6. Nat Commun. 2024 Mar 21. 15(1): 2531
    GAS41 modulates ferroptosis by anchoring NRF2 on chromatin.
    Zhe Wang, Xin Yang, Delin Chen, Yanqing Liu, Zhiming Li, Shoufu Duan, Zhiguo Zhang, Xuejun Jiang, Brent R Stockwell, Wei Gu.
      YEATS domain-containing protein GAS41 is a histone reader and oncogene. Here, through genome-wide CRISPR-Cas9 screenings, we identify GAS41 as a repressor of ferroptosis. GAS41 interacts with NRF2 and is critical for NRF2 to activate its targets such as SLC7A11 for modulating ferroptosis. By recognizing the H3K27-acetylation (H3K27-ac) marker, GAS41 is recruited to the SLC7A11 promoter, independent of NRF2 binding. By bridging the interaction between NRF2 and the H3K27-ac marker, GAS41 acts as an anchor for NRF2 on chromatin in a promoter-specific manner for transcriptional activation. Moreover, the GAS41-mediated effect on ferroptosis contributes to its oncogenic role in vivo. These data demonstrate that GAS41 is a target for modulating tumor growth through ferroptosis. Our study reveals a mechanism for GAS41-mediated regulation in transcription by anchoring NRF2 on chromatin, and provides a model in which the DNA binding activity on chromatin by transcriptional factors (NRF2) can be directly regulated by histone markers (H3K27-ac).
    DOI:  https://doi.org/10.1038/s41467-024-46857-w
  7. Nature. 2024 Mar 20.
    Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
    Takuro Shioi, Suguru Hatazawa, Eriko Oya, Noriko Hosoya, Wataru Kobayashi, Mitsuo Ogasawara, Takehiko Kobayashi, Yoshimasa Takizawa, Hitoshi Kurumizaka.
      RAD51 is the central eukaryotic recombinase required for meiotic recombination and mitotic repair of double-strand DNA breaks (DSBs)1,2. However, the mechanism by which RAD51 functions at DSB sites in chromatin has remained elusive. Here we report the cryo-electron microscopy structures of human RAD51-nucleosome complexes, in which RAD51 forms ring and filament conformations. In the ring forms, the N-terminal lobe domains (NLDs) of RAD51 protomers are aligned on the outside of the RAD51 ring, and directly bind to the nucleosomal DNA. The nucleosomal linker DNA that contains the DSB site is recognized by the L1 and L2 loops-active centres that face the central hole of the RAD51 ring. In the filament form, the nucleosomal DNA is peeled by the RAD51 filament extension, and the NLDs of RAD51 protomers proximal to the nucleosome bind to the remaining nucleosomal DNA and histones. Mutations that affect nucleosome-binding residues of the RAD51 NLD decrease nucleosome binding, but barely affect DNA binding in vitro. Consistently, yeast Rad51 mutants with the corresponding mutations are substantially defective in DNA repair in vivo. These results reveal an unexpected function of the RAD51 NLD, and explain the mechanism by which RAD51 associates with nucleosomes, recognizes DSBs and forms the active filament in chromatin.
    DOI:  https://doi.org/10.1038/s41586-024-07196-4
  8. Nat Genet. 2024 Mar 21.
    Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis.
    Sneha Mitra, Rohan Malik, Wilfred Wong, Afsana Rahman, Alexander J Hartemink, Yuri Pritykin, Kushal K Dey, Christina S Leslie.
      We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC-seq co-assay) sequencing data. The approach uses regularized Poisson regression on tile-level accessibility data to jointly model all regulatory effects at a gene locus, avoiding the limitations of pairwise gene-peak correlations and dependence on peak calling. SCARlink outperformed existing gene scoring methods for imputing gene expression from chromatin accessibility across high-coverage multi-ome datasets while giving comparable to improved performance on low-coverage datasets. Shapley value analysis on trained models identified cell-type-specific gene enhancers that are validated by promoter capture Hi-C and are 11× to 15× and 5× to 12× enriched in fine-mapped eQTLs and fine-mapped genome-wide association study (GWAS) variants, respectively. We further show that SCARlink-predicted and observed gene expression vectors provide a robust way to compute a chromatin potential vector field to enable developmental trajectory analysis.
    DOI:  https://doi.org/10.1038/s41588-024-01689-8
  9. PLoS One. 2024 ;19(3): e0298818
    SUMO-dependent transcriptional repression by Sox2 inhibits the proliferation of neural stem cells.
    Elisa Marelli, Jaime Hughes, Paul J Scotting.
      Sox2 is known for its roles in maintaining the stem cell state of embryonic stem cells and neural stem cells. In particular, it has been shown to slow the proliferation of these cell types. It is also known for its effects as an activating transcription factor. Despite this, analysis of published studies shows that it represses as many genes as it activates. Here, we identify a new set of target genes that Sox2 represses in neural stem cells. These genes are associated with centrosomes, centromeres and other aspects of cell cycle control. In addition, we show that SUMOylation of Sox2 is necessary for the repression of these genes and for its repressive effects on cell proliferation. Together, these data suggest that SUMO-dependent repression of this group of target genes is responsible for the role of Sox2 in regulating the proliferation of neural stem cells.
    DOI:  https://doi.org/10.1371/journal.pone.0298818
  10. Cell Rep. 2024 Mar 21. pii: S2211-1247(24)00300-0. [Epub ahead of print]43(4): 113972
    Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes.
    Yajing Lyu, Yongkang Yang, Varen Talwar, Haiquan Lu, Chelsey Chen, Shaima Salman, Elizabeth E Wicks, Tina Yi-Ting Huang, Daiana Drehmer, Yufeng Wang, Qiaozhu Zuo, Emmanuel Datan, Walter Jackson, Dominic Dordai, Ru Wang, Gregg L Semenza.
      Hypoxia-inducible factor 1 (HIF-1) is a transcriptional activator that mediates cellular adaptation to decreased oxygen availability. HIF-1 recruits chromatin-modifying enzymes leading to changes in histone acetylation, citrullination, and methylation at target genes. Here, we demonstrate that hypoxia-inducible gene expression in estrogen receptor (ER)-positive MCF7 and ER-negative SUM159 human breast cancer cells requires the histone H2A/H2B chaperone facilitates chromatin transcription (FACT) and the H2B ubiquitin ligase RING finger protein 20/40 (RNF20/40). Knockdown of FACT or RNF20/40 expression leads to decreased transcription initiation and elongation at HIF-1 target genes. Mechanistically, FACT and RNF20/40 are recruited to hypoxia response elements (HREs) by HIF-1 and stabilize binding of HIF-1 (and each other) at HREs. Hypoxia induces the monoubiquitination of histone H2B at lysine 120 at HIF-1 target genes in an HIF-1-dependent manner. Together, these findings delineate a cooperative molecular mechanism by which FACT and RNF20/40 stabilize multiprotein complex formation at HREs and mediate histone ubiquitination to facilitate HIF-1 transcriptional activity.
    Keywords:  CP: Cancer; CP: Molecular biology; H2B monoubiquitination; H2B-K120ub1; SPT16; SSRP1; histone chaperone; histone modifying enzymes; nucleosomes; transcription elongation; transcription initiation; ubiquitin ligase
    DOI:  https://doi.org/10.1016/j.celrep.2024.113972
  11. Nat Methods. 2024 Mar 19.
    Multicenter integrated analysis of noncoding CRISPRi screens.
    David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay-Smith, Benjamin R Doughty, Idan Gabdank, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly.
      The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
    DOI:  https://doi.org/10.1038/s41592-024-02216-7
  12. Elife. 2024 Mar 18. pii: RP91433. [Epub ahead of print]12
    Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers.
    Jee Min Kim, Claudia C Carcamo, Sina Jazani, Zepei Xie, Xinyu A Feng, Maryam Yamadi, Matthew Poyton, Katie L Holland, Jonathan B Grimm, Luke D Lavis, Taekjip Ha, Carl Wu.
      Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
    Keywords:  ISW2; RSC; chromatin remodelers; chromosomes; gene expression; molecular biophysics; none; optical tweezers; single molecule; structural biology; target search
    DOI:  https://doi.org/10.7554/eLife.91433
  13. Nucleic Acids Res. 2024 Mar 18. pii: gkae180. [Epub ahead of print]
    Exhaustive identification of genome-wide binding events of transcriptional regulators.
    Anna Nordin, Pierfrancesco Pagella, Gianluca Zambanini, Claudio Cantù.
      Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
    DOI:  https://doi.org/10.1093/nar/gkae180
  14. Nat Genet. 2024 Mar 20.
    The homeobox transcription factor DUXBL controls exit from totipotency.
    Maria Vega-Sendino, Felipe F Lüttmann, Teresa Olbrich, Yanpu Chen, Carsten Kuenne, Paula Stein, Desiree Tillo, Grace I Carey, Jiasheng Zhong, Virginia Savy, Lenka Radonova, Tianlin Lu, Bechara Saykali, Kee-Pyo Kim, Catherine N Domingo, Leah Schüler, Stefan Günther, Mette Bentsen, Darko Bosnakovski, Hans Schöler, Michael Kyba, Tapan K Maity, Lisa M Jenkins, Mario Looso, Carmen J Williams, Johnny Kim, Sergio Ruiz.
      In mice, exit from the totipotent two-cell (2C) stage embryo requires silencing of the 2C-associated transcriptional program. However, the molecular mechanisms involved in this process remain poorly understood. Here we demonstrate that the 2C-specific transcription factor double homeobox protein (DUX) mediates an essential negative feedback loop by inducing the expression of DUXBL to promote this silencing. We show that DUXBL gains accessibility to DUX-bound regions specifically upon DUX expression. Furthermore, we determine that DUXBL interacts with TRIM24 and TRIM33, members of the TRIM superfamily involved in gene silencing, and colocalizes with them in nuclear foci upon DUX expression. Importantly, DUXBL overexpression impairs 2C-associated transcription, whereas Duxbl inactivation in mouse embryonic stem cells increases DUX-dependent induction of the 2C-transcriptional program. Consequently, DUXBL deficiency in embryos results in sustained expression of 2C-associated transcripts leading to early developmental arrest. Our study identifies DUXBL as an essential regulator of totipotency exit enabling the first divergence of cell fates.
    DOI:  https://doi.org/10.1038/s41588-024-01692-z
  15. Brief Bioinform. 2024 Jan 22. pii: bbae096. [Epub ahead of print]25(2):
    scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding.
    Ziheng Duan, Siwei Xu, Shushrruth Sai Srinivasan, Ahyeon Hwang, Che Yu Lee, Feng Yue, Mark Gerstein, Yu Luan, Matthew Girgenti, Jing Zhang.
      Dynamic compartmentalization of eukaryotic DNA into active and repressed states enables diverse transcriptional programs to arise from a single genetic blueprint, whereas its dysregulation can be strongly linked to a broad spectrum of diseases. While single-cell Hi-C experiments allow for chromosome conformation profiling across many cells, they are still expensive and not widely available for most labs. Here, we propose an alternate approach, scENCORE, to computationally reconstruct chromatin compartments from the more affordable and widely accessible single-cell epigenetic data. First, scENCORE constructs a long-range epigenetic correlation graph to mimic chromatin interaction frequencies, where nodes and edges represent genome bins and their correlations. Then, it learns the node embeddings to cluster genome regions into A/B compartments and aligns different graphs to quantify chromatin conformation changes across conditions. Benchmarking using cell-type-matched Hi-C experiments demonstrates that scENCORE can robustly reconstruct A/B compartments in a cell-type-specific manner. Furthermore, our chromatin confirmation switching studies highlight substantial compartment-switching events that may introduce substantial regulatory and transcriptional changes in psychiatric disease. In summary, scENCORE allows accurate and cost-effective A/B compartment reconstruction to delineate higher-order chromatin structure heterogeneity in complex tissues.
    Keywords:  chromatin compartments; graph embedding; single-cell epigenetics
    DOI:  https://doi.org/10.1093/bib/bbae096
  16. Commun Biol. 2024 Mar 21. 7(1): 351
    Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation.
    Ilaria Aurigemma, Olga Lanzetta, Andrea Cirino, Sara Allegretti, Gabriella Lania, Rosa Ferrentino, Varsha Poondi Krishnan, Claudia Angelini, Elizabeth Illingworth, Antonio Baldini.
      Endothelial cells (EC) differentiate from multiple sources, including the cardiopharyngeal mesoderm, which gives rise also to cardiac and branchiomeric muscles. The enhancers activated during endothelial differentiation within the cardiopharyngeal mesoderm are not completely known. Here, we use a cardiogenic mesoderm differentiation model that activates an endothelial transcription program to identify endothelial regulatory elements activated in early cardiogenic mesoderm. Integrating chromatin remodeling and gene expression data with available single-cell RNA-seq data from mouse embryos, we identify 101 putative regulatory elements of EC genes. We then apply a machine-learning strategy, trained on validated enhancers, to predict enhancers. Using this computational assay, we determine that 50% of these sequences are likely enhancers, some of which are already reported. We also identify a smaller set of regulatory elements of well-known EC genes and validate them using genetic and epigenetic perturbation. Finally, we integrate multiple data sources and computational tools to search for transcriptional factor binding motifs. In conclusion, we show EC regulatory sequences with a high likelihood to be enhancers, and we validate a subset of them using computational and cell culture models. Motif analyses show that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC regulation in cardiopharyngeal mesoderm.
    DOI:  https://doi.org/10.1038/s42003-024-06017-8
  17. Nucleic Acids Res. 2024 Mar 18. pii: gkae184. [Epub ahead of print]
    FUS reads histone H3K36me3 to regulate alternative polyadenylation.
    Junqi Jia, Haonan Fan, Xinyi Wan, Yuan Fang, Zhuoning Li, Yin Tang, Yanjun Zhang, Jun Huang, Dong Fang.
      Complex organisms generate differential gene expression through the same set of DNA sequences in distinct cells. The communication between chromatin and RNA regulates cellular behavior in tissues. However, little is known about how chromatin, especially histone modifications, regulates RNA polyadenylation. In this study, we found that FUS was recruited to chromatin by H3K36me3 at gene bodies. The H3K36me3 recognition of FUS was mediated by the proline residues in the ZNF domain. After these proline residues were mutated or H3K36me3 was abolished, FUS dissociated from chromatin and bound more to RNA, resulting in an increase in polyadenylation sites far from stop codons genome-wide. A proline mutation corresponding to a mutation in amyotrophic lateral sclerosis contributed to the hyperactivation of mitochondria and hyperdifferentiation in mouse embryonic stem cells. These findings reveal that FUS is an H3K36me3 reader protein that links chromatin-mediated alternative polyadenylation to human disease.
    DOI:  https://doi.org/10.1093/nar/gkae184
  18. Cell Rep Med. 2024 Mar 19. pii: S2666-3791(24)00118-6. [Epub ahead of print]5(3): 101472
    STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma.
    Nicole Prutsch, Shuning He, Alla Berezovskaya, Adam D Durbin, Neekesh V Dharia, Kelsey A Maher, Jamie D Matthews, Lucy Hare, Suzanne D Turner, Kimberly Stegmaier, Lukas Kenner, Olaf Merkel, A Thomas Look, Brian J Abraham, Mark W Zimmerman.
      Anaplastic large cell lymphoma (ALCL) is an aggressive, CD30+ T cell lymphoma of children and adults. ALK fusion transcripts or mutations in the JAK-STAT pathway are observed in most ALCL tumors, but the mechanisms underlying tumorigenesis are not fully understood. Here, we show that dysregulated STAT3 in ALCL cooccupies enhancers with master transcription factors BATF3, IRF4, and IKZF1 to form a core regulatory circuit that establishes and maintains the malignant cell state in ALCL. Critical downstream targets of this network in ALCL cells include the protooncogene MYC, which requires active STAT3 to facilitate high levels of MYC transcription. The core autoregulatory transcriptional circuitry activity is reinforced by MYC binding to the enhancer regions associated with STAT3 and each of the core regulatory transcription factors. Thus, activation of STAT3 provides the crucial link between aberrant tyrosine kinase signaling and the core transcriptional machinery that drives tumorigenesis and creates therapeutic vulnerabilities in ALCL.
    DOI:  https://doi.org/10.1016/j.xcrm.2024.101472
  19. Nat Commun. 2024 Mar 21. 15(1): 2513
    Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma.
    Daniel A Ang, Jean-Michel Carter, Kamalakshi Deka, Joel H L Tan, Jianbiao Zhou, Qingfeng Chen, Wee Joo Chng, Nathan Harmston, Yinghui Li.
      In multiple myeloma, abnormal plasma cells establish oncogenic niches within the bone marrow by engaging the NF-κB pathway to nurture their survival while they accumulate pro-proliferative mutations. Under these conditions, many cases eventually develop genetic abnormalities endowing them with constitutive NF-κB activation. Here, we find that sustained NF-κB/p52 levels resulting from such mutations favours the recruitment of enhancers beyond the normal B-cell repertoire. Furthermore, through targeted disruption of p52, we characterise how such enhancers are complicit in the formation of super-enhancers and the establishment of cis-regulatory interactions with myeloma dependencies during constitutive activation of p52. Finally, we functionally validate the pathological impact of these cis-regulatory modules on cell and tumour phenotypes using in vitro and in vivo models, confirming RGS1 as a p52-dependent myeloma driver. We conclude that the divergent epigenomic reprogramming enforced by aberrant non-canonical NF-κB signalling potentiates transcriptional programs beneficial for multiple myeloma progression.
    DOI:  https://doi.org/10.1038/s41467-024-46728-4
  20. Genome Res. 2024 Mar 21. pii: gr.278343.123. [Epub ahead of print]
    Robust chromatin state annotation.
    Mehdi Foroozandeh Shahraki, Marjan Farahbod, Maxwell W Libbrecht.
      With the goal of mapping genomic activity, international projects have recently measured epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations produced by segmentation and genome annotation (SAGA) methods have emerged as the predominant way to summarize these epigenomic data sets in order to annotate the genome. These chromatin state annotations are essential for many genomic tasks, including identifying active regulatory elements and interpreting disease-associated genetic variation. However, despite the widespread applications of SAGA methods, no principled approach exists to evaluate the statistical significance of chromatin state assignments. Here, we propose the first method for assigning calibrated confidence scores to chromatin state annotations. Toward this goal, we performed a comprehensive evaluation of the reproducibility of the two most widely used existing SAGA methods, ChromHMM and Segway. We found that their predictions are frequently irreproducible. For example, when applying the same SAGA method on two sets of experimental replicates, 27-69% of predicted enhancers fail to replicate. This suggests that a substantial fraction of predicted elements in existing chromatin state annotations cannot be relied upon. To remedy this problem, we introduce SAGAconf, a method for assigning a measure of confidence (r-value) to chromatin state annotations. SAGAconf works with any SAGA method and assigns an r-value to each genomic bin of a chromatin state annotation that represents the probability that the label of this bin will be reproduced in a replicated experiment. Thus, SAGAconf allows a researcher to select only the reliable predictions from a chromatin annotation for use in downstream analyses.
    DOI:  https://doi.org/10.1101/gr.278343.123
  21. Nat Aging. 2024 Mar;4(3): 364-378
    A single-nuclei paired multiomic analysis of the human midbrain reveals age- and Parkinson's disease-associated glial changes.
    Levi Adams, Min Kyung Song, Samantha Yuen, Yoshiaki Tanaka, Yoon-Seong Kim.
      Age is the primary risk factor for Parkinson's disease (PD), but how aging changes the expression and regulatory landscape of the brain remains unclear. Here we present a single-nuclei multiomic study profiling shared gene expression and chromatin accessibility of young, aged and PD postmortem midbrain samples. Combined multiomic analysis along a pseudopathogenesis trajectory reveals that all glial cell types are affected by age, but microglia and oligodendrocytes are further altered in PD. We present evidence for a disease-associated oligodendrocyte subtype and identify genes lost over the aging and disease process, including CARNS1, that may predispose healthy cells to develop a disease-associated phenotype. Surprisingly, we found that chromatin accessibility changed little over aging or PD within the same cell types. Peak-gene association patterns, however, are substantially altered during aging and PD, identifying cell-type-specific chromosomal loci that contain PD-associated single-nucleotide polymorphisms. Our study suggests a previously undescribed role for oligodendrocytes in aging and PD.
    DOI:  https://doi.org/10.1038/s43587-024-00583-6
  22. Sci Adv. 2024 Mar 22. 10(12): eadn4649
    Childhood cancer mutagenesis caused by transposase-derived PGBD5.
    Makiko Yamada, Ross R Keller, Rodrigo Lopez Gutierrez, Daniel Cameron, Hiromichi Suzuki, Reeti Sanghrajka, Jake Vaynshteyn, Jeffrey Gerwin, Francesco Maura, William Hooper, Minita Shah, Nicolas Robine, Phillip Demarest, N Sumru Bayin, Luz Jubierre Zapater, Casie Reed, Steven Hébert, Ignas Masilionis, Ronan Chaligne, Nicholas D Socci, Michael D Taylor, Claudia L Kleinman, Alexandra L Joyner, G Praveen Raju, Alex Kentsis.
      Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling is sufficient to enforce cerebellar granule cell progenitor-like cell states, which exhibit Pgbd5-dependent expression of distinct DNA repair and neurodevelopmental factors. Mouse medulloblastomas expressing Pgbd5 have increased numbers of somatic structural DNA rearrangements, some of which carry PGBD5-specific sequences at their breakpoints. Similar sequence breakpoints recurrently affect somatic DNA rearrangements of known tumor suppressors and oncogenes in medulloblastomas in 329 children. This identifies PGBD5 as a medulloblastoma mutator and provides a genetic mechanism for the generation of oncogenic DNA rearrangements in childhood cancer.
    DOI:  https://doi.org/10.1126/sciadv.adn4649
  23. Nucleic Acids Res. 2024 Mar 18. pii: gkae178. [Epub ahead of print]
    Two redundant transcription factor binding sites in a single enhancer are essential for mammalian sex determination.
    Meshi Ridnik, Elisheva Abberbock, Veronica Alipov, Shelly Ziv Lhermann, Shoham Kaufman, Maor Lubman, Francis Poulat, Nitzan Gonen.
      Male development in mammals depends on the activity of the two SOX gene: Sry and Sox9, in the embryonic testis. As deletion of Enhancer 13 (Enh13) of the Sox9 gene results in XY male-to-female sex reversal, we explored the critical elements necessary for its function and hence, for testis and male development. Here, we demonstrate that while microdeletions of individual transcription factor binding sites (TFBS) in Enh13 lead to normal testicular development, combined microdeletions of just two SRY/SOX binding motifs can alone fully abolish Enh13 activity leading to XY male-to-female sex reversal. This suggests that for proper male development to occur, these few nucleotides of non-coding DNA must be intact. Interestingly, we show that depending on the nature of these TFBS mutations, dramatically different phenotypic outcomes can occur, providing a molecular explanation for the distinct clinical outcomes observed in patients harboring different variants in the same enhancer.
    DOI:  https://doi.org/10.1093/nar/gkae178
  24. Cell Rep. 2024 Mar 19. pii: S2211-1247(24)00303-6. [Epub ahead of print]43(4): 113975
    SIRT4 loss reprograms intestinal nucleotide metabolism to support proliferation following perturbation of homeostasis.
    Sarah A Tucker, Song-Hua Hu, Sejal Vyas, Albert Park, Shakchhi Joshi, Aslihan Inal, Tiffany Lam, Emily Tan, Kevin M Haigis, Marcia C Haigis.
      The intestine is a highly metabolic tissue, but the metabolic programs that influence intestinal crypt proliferation, differentiation, and regeneration are still emerging. Here, we investigate how mitochondrial sirtuin 4 (SIRT4) affects intestinal homeostasis. Intestinal SIRT4 loss promotes cell proliferation in the intestine following ionizing radiation (IR). SIRT4 functions as a tumor suppressor in a mouse model of intestinal cancer, and SIRT4 loss drives dysregulated glutamine and nucleotide metabolism in intestinal adenomas. Intestinal organoids lacking SIRT4 display increased proliferation after IR stress, along with increased glutamine uptake and a shift toward de novo nucleotide biosynthesis over salvage pathways. Inhibition of de novo nucleotide biosynthesis diminishes the growth advantage of SIRT4-deficient organoids after IR stress. This work establishes SIRT4 as a modulator of intestinal metabolism and homeostasis in the setting of DNA-damaging stress.
    Keywords:  CP: Cancer; SIRT4; glutamine; intestinal organoids; irradiation; nucleotide biosynthesis; nucleotide metabolism; sirtuin
    DOI:  https://doi.org/10.1016/j.celrep.2024.113975
  25. Nat Struct Mol Biol. 2024 Mar;31(3): 404-412
    The impact of DNA methylation on CTCF-mediated 3D genome organization.
    Ana Monteagudo-Sánchez, Daan Noordermeer, Maxim V C Greenberg.
      Cytosine DNA methylation is a highly conserved epigenetic mark in eukaryotes. Although the role of DNA methylation at gene promoters and repetitive elements has been extensively studied, the function of DNA methylation in other genomic contexts remains less clear. In the nucleus of mammalian cells, the genome is spatially organized at different levels, and strongly influences myriad genomic processes. There are a number of factors that regulate the three-dimensional (3D) organization of the genome, with the CTCF insulator protein being among the most well-characterized. Pertinently, CTCF binding has been reported as being DNA methylation-sensitive in certain contexts, perhaps most notably in the process of genomic imprinting. Therefore, it stands to reason that DNA methylation may play a broader role in the regulation of chromatin architecture. Here we summarize the current understanding that is relevant to both the mammalian DNA methylation and chromatin architecture fields and attempt to assess the extent to which DNA methylation impacts the folding of the genome. The focus is in early embryonic development and cellular transitions when the epigenome is in flux, but we also describe insights from pathological contexts, such as cancer, in which the epigenome and 3D genome organization are misregulated.
    DOI:  https://doi.org/10.1038/s41594-024-01241-6
  26. Sci Adv. 2024 Mar 22. 10(12): eadl0788
    FOXL2 interaction with different binding partners regulates the dynamics of ovarian development.
    Roberta Migale, Michelle Neumann, Richard Mitter, Mahmoud-Reza Rafiee, Sophie Wood, Jessica Olsen, Robin Lovell-Badge.
      The transcription factor FOXL2 is required in ovarian somatic cells for female fertility. Differential timing of Foxl2 deletion, in embryonic versus adult mouse ovary, leads to distinctive outcomes, suggesting different roles across development. Here, we comprehensively investigated FOXL2's role through a multi-omics approach to characterize gene expression dynamics and chromatin accessibility changes, coupled with genome-wide identification of FOXL2 targets and on-chromatin interacting partners in somatic cells across ovarian development. We found that FOXL2 regulates more targets postnatally, through interaction with factors regulating primordial follicle formation and steroidogenesis. Deletion of one interactor, ubiquitin-specific protease 7 (Usp7), results in impairment of somatic cell differentiation, germ cell nest breakdown, and ovarian development, leading to sterility. Our datasets constitute a comprehensive resource for exploration of the molecular mechanisms of ovarian development and causes of female infertility.
    DOI:  https://doi.org/10.1126/sciadv.adl0788
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