bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2024–07–21
eightteen papers selected by
Connor Rogerson, University of Cambridge
  1. Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape.
  2. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory.
  3. ARID1A safeguards the canalization of the cell fate decision during osteoclastogenesis.
  4. Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force.
  5. Position-dependent function of human sequence-specific transcription factors.
  6. Symbolic recording of signalling and cis-regulatory element activity to DNA.
  7. Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer.
  8. Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.
  9. R-loop resolution by ARIP4 helicase promotes androgen-mediated transcription induction.
  10. MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer data.
  11. Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach.
  12. Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome.
  13. Identification of plant transcriptional activation domains.
  14. MLL-AF9 regulates transcriptional initiation in mixed lineage leukemic cells.
  15. BACH2 regulates diversification of regulatory and proinflammatory chromatin states in TH17 cells.
  16. Competition between two HUSH complexes orchestrates the immune response to retroelement invasion.
  17. Single-cell total-RNA profiling unveils regulatory hubs of transcription factors.
  18. Non-coding variants impact cis-regulatory coordination in a cell type-specific manner.
  1. Nat Commun. 2024 Jul 15. 15(1): 5937
    Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape.
    Lele Song, Qinglan Li, Lingbo Xia, Arushi Eesha Sahay, Qi Qiu, Yuanyuan Li, Haitao Li, Kotaro Sasaki, Katalin Susztak, Hao Wu, Liling Wan.
      How disruptions to normal cell differentiation link to tumorigenesis remains incompletely understood. Wilms tumor, an embryonal tumor associated with disrupted organogenesis, often harbors mutations in epigenetic regulators, but their role in kidney development remains unexplored. Here, we show at single-cell resolution that a Wilms tumor-associated mutation in the histone acetylation reader ENL disrupts kidney differentiation in mice by rewiring the gene regulatory landscape. Mutant ENL promotes nephron progenitor commitment while restricting their differentiation by dysregulating transcription factors such as Hox clusters. It also induces abnormal progenitors that lose kidney-associated chromatin identity. Furthermore, mutant ENL alters the transcriptome and chromatin accessibility of stromal progenitors, resulting in hyperactivation of Wnt signaling. The impacts of mutant ENL on both nephron and stroma lineages lead to profound kidney developmental defects and postnatal mortality in mice. Notably, a small molecule inhibiting mutant ENL's histone acetylation binding activity largely reverses these defects. This study provides insights into how mutations in epigenetic regulators disrupt kidney development and suggests a potential therapeutic approach.
    DOI:  https://doi.org/10.1038/s41467-024-50171-w
  2. Mol Cell. 2024 Jul 10. pii: S1097-2765(24)00532-X. [Epub ahead of print]
    Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory.
    Emily R Feierman, Sean Louzon, Nicholas A Prescott, Tracy Biaco, Qingzeng Gao, Qi Qiu, Kyuhyun Choi, Katherine C Palozola, Anna J Voss, Shreya D Mehta, Camille N Quaye, Katherine T Lynch, Marc V Fuccillo, Hao Wu, Yael David, Erica Korb.
      Histone proteins affect gene expression through multiple mechanisms, including through exchange with histone variants. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. Most notably, widely expressed variants of H2B remain elusive. We applied recently developed antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters, and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Further, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a mechanism linking histone variants to chromatin accessibility, transcriptional regulation, neuronal function, and memory. This work further identifies a widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
    Keywords:  H2B; H2BE; chromatin; chromatin accessibility; epigenetics; histone; histone variant; memory; neuron; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2024.06.025
  3. Nat Commun. 2024 Jul 17. 15(1): 5994
    ARID1A safeguards the canalization of the cell fate decision during osteoclastogenesis.
    Jiahui Du, Yili Liu, Jinrui Sun, Enhui Yao, Jingyi Xu, Xiaolin Wu, Ling Xu, Mingliang Zhou, Guangzheng Yang, Xinquan Jiang.
      Chromatin remodeler ARID1A regulates gene transcription by modulating nucleosome positioning and chromatin accessibility. While ARID1A-mediated stage and lineage-restricted gene regulation during cell fate canalization remains unresolved. Using osteoclastogenesis as a model, we show that ARID1A transcriptionally safeguards the osteoclast (OC) fate canalization during proliferation-differentiation switching at single-cell resolution. Notably, ARID1A is indispensable for the transcriptional apparatus condensates formation with coactivator BRD4/lineage-specifying transcription factor (TF) PU.1 at Nfatc1 super-enhancer during safeguarding the OC fate canalization. Besides, the antagonist function between ARID1A-cBAF and BRD9-ncBAF complex during osteoclastogenesis has been validated with in vitro assay and compound mutant mouse model. Furthermore, the antagonistic function of ARID1A-"accelerator" and BRD9-"brake" both depend on coactivator BRD4-"clutch" during osteoclastogenesis. Overall, these results uncover sophisticated cooperation between chromatin remodeler ARID1A, coactivator, and lineage-specifying TF at super-enhancer of lineage master TF in a condensate manner, and antagonist between distinct BAF complexes in the proper and balanced cell fate canalization.
    DOI:  https://doi.org/10.1038/s41467-024-50225-z
  4. Cell Rep. 2024 Jul 10. pii: S2211-1247(24)00791-5. [Epub ahead of print] 114462
    Mechanomemory of nucleoplasm and RNA polymerase II after chromatin stretching by a microinjected magnetic nanoparticle force.
    Fazlur Rashid, Sadia Amin Kabbo, Ning Wang.
      Increasing evidence suggests that the mechanics of chromatin and nucleoplasm regulate gene transcription and nuclear function. However, how the chromatin and nucleoplasm sense and respond to forces remains elusive. Here, we employed a strategy of applying forces directly to the chromatin of a cell via a microinjected 200-nm anti-H2B-antibody-coated ferromagnetic nanoparticle (FMNP) and an anti-immunoglobulin G (IgG)-antibody-coated or an uncoated FMNP. The chromatin behaved as a viscoelastic gel-like structure and the nucleoplasm was a softer viscoelastic structure at loading frequencies of 0.1-5 Hz. Protein diffusivity of the chromatin, nucleoplasm, and RNA polymerase II (RNA Pol II) and RNA Pol II activity were upregulated in a chromatin-stretching-dependent manner and stayed upregulated for tens of minutes after force cessation. Chromatin stiffness increased, but the mechanomemory duration of chromatin diffusivity decreased, with substrate stiffness. These findings may provide a mechanomemory mechanism of transcription upregulation and have implications on cell and nuclear functions.
    Keywords:  CP: Cell biology; CP: Molecular biology; RNA polymerase II activity; cell memory; chromatin memory; chromatin stretching; ferromagnetic nanoparticle; force cessation; mechanomemory; mechanotransduction; nuclear functions; nuclear memory
    DOI:  https://doi.org/10.1016/j.celrep.2024.114462
  5. Nature. 2024 Jul 17.
    Position-dependent function of human sequence-specific transcription factors.
    Sascha H Duttke, Carlos Guzman, Max Chang, Nathaniel P Delos Santos, Bayley R McDonald, Jialei Xie, Aaron F Carlin, Sven Heinz, Christopher Benner.
      Patterns of transcriptional activity are encoded in our genome through regulatory elements such as promoters or enhancers that, paradoxically, contain similar assortments of sequence-specific transcription factor (TF) binding sites1-3. Knowledge of how these sequence motifs encode multiple, often overlapping, gene expression programs is central to understanding gene regulation and how mutations in non-coding DNA manifest in disease4,5. Here, by studying gene regulation from the perspective of individual transcription start sites (TSSs), using natural genetic variation, perturbation of endogenous TF protein levels and massively parallel analysis of natural and synthetic regulatory elements, we show that the effect of TF binding on transcription initiation is position dependent. Analysing TF-binding-site occurrences relative to the TSS, we identified several motifs with highly preferential positioning. We show that these patterns are a combination of a TF's distinct functional profiles-many TFs, including canonical activators such as NRF1, NFY and Sp1, activate or repress transcription initiation depending on their precise position relative to the TSS. As such, TFs and their spacing collectively guide the site and frequency of transcription initiation. More broadly, these findings reveal how similar assortments of TF binding sites can generate distinct gene regulatory outcomes depending on their spatial configuration and how DNA sequence polymorphisms may contribute to transcription variation and disease and underscore a critical role for TSS data in decoding the regulatory information of our genome.
    DOI:  https://doi.org/10.1038/s41586-024-07662-z
  6. Nature. 2024 Jul 17.
    Symbolic recording of signalling and cis-regulatory element activity to DNA.
    Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F Nathans, Beth Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure.
      Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes (symbols) into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging signal transduction pathway-responsive cis-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities. By coupling ENGRAM to sequential genome editing via DNA Typewriter1, we stably record information about the temporal dynamics of two orthogonal signalling pathways to genomic DNA. Finally we apply ENGRAM to integratively record the transient activity of nearly 100 transcription factor consensus motifs across daily windows spanning the differentiation of mouse embryonic stem cells into gastruloids, an in vitro model of early mammalian development. Although these are proof-of-concept experiments and much work remains to fully realize the possibilities, the symbolic recording of biological signals or states within cells, to the genome and over time, has broad potential to complement contemporary paradigms for how we make measurements in biological systems.
    DOI:  https://doi.org/10.1038/s41586-024-07706-4
  7. Cancer Cell. 2024 Jul 17. pii: S1535-6108(24)00237-X. [Epub ahead of print]
    Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer.
    Leslie Duplaquet, Kevin So, Alexander W Ying, Shreoshi Pal Choudhuri, Xinyue Li, Grace D Xu, Yixiang Li, Xintao Qiu, Rong Li, Shilpa Singh, Xiaoli S Wu, Seth Hamilton, Victor D Chien, Qi Liu, Jun Qi, Tim D D Somerville, Hillary M Heiling, Emanuele Mazzola, Yenarae Lee, Thomas Zoller, Christopher R Vakoc, John G Doench, William C Forrester, Tinya Abrams, Henry W Long, Matthew J Niederst, Benjamin J Drapkin, Cigall Kadoch, Matthew G Oser.
      Small cell lung cancers (SCLCs) are composed of heterogeneous subtypes marked by lineage-specific transcription factors, including ASCL1, NEUROD1, and POU2F3. POU2F3-positive SCLCs, ∼12% of all cases, are uniquely dependent on POU2F3 itself; as such, approaches to attenuate POU2F3 expression may represent new therapeutic opportunities. Here using genome-scale screens for regulators of POU2F3 expression and SCLC proliferation, we define mSWI/SNF complexes as top dependencies specific to POU2F3-positive SCLC. Notably, chemical disruption of mSWI/SNF ATPase activity attenuates proliferation of all POU2F3-positive SCLCs, while disruption of non-canonical BAF (ncBAF) via BRD9 degradation is effective in pure non-neuroendocrine POU2F3-SCLCs. mSWI/SNF targets to and maintains accessibility over gene loci central to POU2F3-mediated gene regulatory networks. Finally, clinical-grade pharmacologic disruption of SMARCA4/2 ATPases and BRD9 decreases POU2F3-SCLC tumor growth and increases survival in vivo. These results demonstrate mSWI/SNF-mediated governance of the POU2F3 oncogenic program and suggest mSWI/SNF inhibition as a therapeutic strategy for POU2F3-positive SCLCs.
    Keywords:  BRD9; FHD-286; FHD-60; OCA-T1; OCA-T2; POU2F3; SMARCD1; mSWI/SNF; neuroendocrine; small cell lung cancer
    DOI:  https://doi.org/10.1016/j.ccell.2024.06.012
  8. Mol Cell. 2024 Jul 09. pii: S1097-2765(24)00529-X. [Epub ahead of print]
    Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.
    Cheng Xu, Holly Kleinschmidt, Jianyu Yang, Erik M Leith, Jenna Johnson, Song Tan, Shaun Mahony, Lu Bai.
      Despite the unique ability of pioneer factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called chromatin immunoprecipitation with integrated synthetic oligonucleotides (ChIP-ISO) to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1, in human A549 cells. Combining ChIP-ISO with in vitro and neural network analyses, we find that (1) FOXA1 binding is strongly affected by co-binding transcription factors (TFs) AP-1 and CEBPB; (2) FOXA1 and AP-1 show binding cooperativity in vitro; (3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin; and (4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.
    Keywords:  ChIP-ISO; binding cooperativity; binding specificity; chromatin; pioneer factor; synthetic DNA library; transcription factor
    DOI:  https://doi.org/10.1016/j.molcel.2024.06.022
  9. Sci Adv. 2024 Jul 19. 10(29): eadm9577
    R-loop resolution by ARIP4 helicase promotes androgen-mediated transcription induction.
    Raissa Regina Ng, Zhongyang Lin, Yanmin Zhang, Shih Chieh Ti, Asif Javed, Jason Wing Hon Wong, Qingming Fang, Justin Wai Chung Leung, Alex Hin Ning Tang, Michael Shing Yan Huen.
      Pausing of RNA polymerase II (Pol II) at transcription start sites (TSSs) primes target genes for productive elongation. Coincidentally, DNA double-strand breaks (DSBs) enrich at highly transcribed and Pol II-paused genes, although their interplay remains undefined. Using androgen receptor (AR) signaling as a model, we have uncovered AR-interacting protein 4 (ARIP4) helicase as a driver of androgen-dependent transcription induction. Chromatin immunoprecipitation sequencing analysis revealed that ARIP4 preferentially co-occupies TSSs with paused Pol II. Moreover, we found that ARIP4 complexes with topoisomerase II beta and mediates transient DSB formation upon hormone stimulation. Accordingly, ARIP4 deficiency compromised release of paused Pol II and resulted in R-loop accumulation at a panel of highly transcribed AR target genes. Last, we showed that ARIP4 binds and unwinds R-loops in vitro and that its expression positively correlates with prostate cancer progression. We propose that androgen stimulation triggers ARIP4-mediated unwinding of R-loops at TSSs, enforcing Pol II pause release to effectively drive an androgen-dependent expression program.
    DOI:  https://doi.org/10.1126/sciadv.adm9577
  10. Nat Commun. 2024 Jul 17. 15(1): 6027
    MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer data.
    Theodore Sakellaropoulos, Catherine Do, Guimei Jiang, Giulia Cova, Peter Meyn, Dacia Dimartino, Sitharam Ramaswami, Adriana Heguy, Aristotelis Tsirigos, Jane A Skok.
      Aberrations in the capacity of DNA/chromatin modifiers and transcription factors to bind non-coding regions can lead to changes in gene regulation and impact disease phenotypes. However, identifying distal regulatory elements and connecting them with their target genes remains challenging. Here, we present MethNet, a pipeline that integrates large-scale DNA methylation and gene expression data across multiple cancers, to uncover cis regulatory elements (CREs) in a 1 Mb region around every promoter in the genome. MethNet identifies clusters of highly ranked CREs, referred to as 'hubs', which contribute to the regulation of multiple genes and significantly affect patient survival. Promoter-capture Hi-C confirmed that highly ranked associations involve physical interactions between CREs and their gene targets, and CRISPR interference based single-cell RNA Perturb-seq validated the functional impact of CREs. Thus, MethNet-identified CREs represent a valuable resource for unraveling complex mechanisms underlying gene expression, and for prioritizing the verification of predicted non-coding disease hotspots.
    DOI:  https://doi.org/10.1038/s41467-024-50380-3
  11. Mol Cell. 2024 Jul 09. pii: S1097-2765(24)00528-8. [Epub ahead of print]
    Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach.
    Liang Lu, Xiaoting Zhang, Yuenan Zhou, Zuokun Shi, Xiwen Xie, Xinyue Zhang, Liaoliao Gao, Anbo Fu, Cong Liu, Bo He, Xushen Xiong, Yafei Yin, Qingqing Wang, Chengqi Yi, Xiaoyu Li.
      5-methylcytosine (m5C) is a prevalent RNA modification crucial for gene expression regulation. However, accurate and sensitive m5C sites identification remains challenging due to severe RNA degradation and reduced sequence complexity during bisulfite sequencing (BS-seq). Here, we report m5C-TAC-seq, a bisulfite-free approach combining TET-assisted m5C-to-f5C oxidation with selective chemical labeling, therefore enabling direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites. With m5C-TAC-seq, we comprehensively profiled the m5C methylomes in human and mouse cells, identifying a substantially larger number of confident m5C sites. Through perturbing potential m5C methyltransferases, we deciphered the responsible enzymes for most m5C sites, including the characterization of NSUN5's involvement in mRNA m5C deposition. Additionally, we characterized m5C dynamics during mESC differentiation. Notably, the mild reaction conditions and preservation of nucleotide composition in m5C-TAC-seq allow m5C detection in chromatin-associated RNAs. The accurate and robust m5C-TAC-seq will advance research into m5C methylation functional investigation.
    Keywords:  5-methylcytosine; RNA modification; base resolution; bisulfite-free; chromatin-associated RNA; enzyme-assisted chemical labeling; epitranscriptomics; m(5)C methyltransferase
    DOI:  https://doi.org/10.1016/j.molcel.2024.06.021
  12. Nat Methods. 2024 Jul 18.
    Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome.
    Chao Dong, Xiaoxuan Meng, Tong Zhang, Zhifang Guo, Yaxi Liu, Peihuang Wu, Shiwei Chen, Fanqi Zhou, Yanni Ma, Haiqing Xiong, Shaokun Shu, Aibin He.
      Studies of molecular and cellular functions of small-molecule inhibitors in cancer treatment, eliciting effects by targeting genome and epigenome associated proteins, requires measurement of drug-target engagement in single-cell resolution. Here we present EpiChem for in situ single-cell joint mapping of small molecules and multimodal epigenomic landscape. We demonstrate single-cell co-assays of three small molecules together with histone modifications, chromatin accessibility or target proteins in human colorectal cancer (CRC) organoids. Integrated multimodal analysis reveals diverse drug interactions in the context of chromatin states within heterogeneous CRC organoids. We further reveal drug genomic binding dynamics and adaptive epigenome across cell types after small-molecule drug treatment in CRC organoids. This method provides a unique tool to exploit the mechanisms of cell type-specific drug actions.
    DOI:  https://doi.org/10.1038/s41592-024-02360-0
  13. Nature. 2024 Jul 17.
    Identification of plant transcriptional activation domains.
    Nicholas Morffy, Lisa Van den Broeck, Caelan Miller, Ryan J Emenecker, John A Bryant, Tyler M Lee, Katelyn Sageman-Furnas, Edward G Wilkinson, Sunita Pathak, Sanjana R Kotha, Angelica Lam, Saloni Mahatma, Vikram Pande, Aman Waoo, R Clay Wright, Alex S Holehouse, Max V Staller, Rosangela Sozzani, Lucia C Strader.
      Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.
    DOI:  https://doi.org/10.1038/s41586-024-07707-3
  14. J Biol Chem. 2024 Jul 11. pii: S0021-9258(24)02067-2. [Epub ahead of print] 107566
    MLL-AF9 regulates transcriptional initiation in mixed lineage leukemic cells.
    Zimei Yang, Ge Zhang, Ruoyu Zhao, Tian Tian, Junhong Zhi, Gang Wei, Robert G Roeder, Lili Jing, Ming Yu.
      MLL-fusion proteins (MLL-FPs) are believed to maintain gene activation and induce mixed lineage leukemia (MLL) through aberrantly stimulating transcriptional elongation, but the underlying mechanisms are incompletely understood. Here we show that both MLL1 and AF9, one of the major fusion partners of MLL1, mainly occupy promoters and distal intergenic regions, exhibiting chromatin occupancy patterns resembling that of RNA polymerase II (Pol II) in HEL, a human cell line without MLL1 arrangement (MLLr). MLL1 and AF9 only co-regulate over a dozen genes despite of their co-occupancy on thousands of genes. They do not interact with each other, and their chromatin occupancy is also independent of each other. Moreover, AF9 deficiency in HEL cells decreases global TBP occupancy while decreases CDK9 occupancy on a small number of genes, suggesting an accessory role of AF9 in CDK9 recruitment and a possible major role in transcriptional initiation via initiation factor recruitment. Importantly, MLL1 and MLL-AF9 occupy promoters and distal intergenic regions, exhibiting identical chromatin occupancy patterns in MLL cells, and MLL-AF9 deficiency decreased occupancy of TBP and TFIIE on major target genes of MLL-AF9 in iMA9, a murine acute myeloid leukemia (AML) cell line inducibly expressing MLL-AF9, suggesting that it can also regulate initiation. These results suggest that there is no difference between MLL1 and MLL-AF9 with respect to location and size of occupancy sites, contrary to what people have believed, and that MLL-AF9 may also regulate transcriptional initiation in addition to widely-believed elongation.
    Keywords:  AF9; MLL-AF9; MLL1; initiation; mixed lineage leukemia; super elongation complex
    DOI:  https://doi.org/10.1016/j.jbc.2024.107566
  15. Nat Immunol. 2024 Jul 15.
    BACH2 regulates diversification of regulatory and proinflammatory chromatin states in TH17 cells.
    Pratiksha I Thakore, Alexandra Schnell, Linglin Huang, Maryann Zhao, Yu Hou, Elena Christian, Sarah Zaghouani, Chao Wang, Vasundhara Singh, Anvita Singaraju, Rajesh Kumar Krishnan, Deneen Kozoriz, Sai Ma, Venkat Sankar, Samuele Notarbartolo, Jason D Buenrostro, Federica Sallusto, Nikolaos A Patsopoulos, Orit Rozenblatt-Rosen, Vijay K Kuchroo, Aviv Regev.
      Interleukin-17 (IL-17)-producing helper T (TH17) cells are heterogenous and consist of nonpathogenic TH17 (npTH17) cells that contribute to tissue homeostasis and pathogenic TH17 (pTH17) cells that mediate tissue inflammation. Here, we characterize regulatory pathways underlying TH17 heterogeneity and discover substantial differences in the chromatin landscape of npTH17 and pTH17 cells both in vitro and in vivo. Compared to other CD4+ T cell subsets, npTH17 cells share accessible chromatin configurations with regulatory T cells, whereas pTH17 cells exhibit features of both npTH17 cells and type 1 helper T (TH1) cells. Integrating single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq), we infer self-reinforcing and mutually exclusive regulatory networks controlling different cell states and predicted transcription factors regulating TH17 cell pathogenicity. We validate that BACH2 promotes immunomodulatory npTH17 programs and restrains proinflammatory TH1-like programs in TH17 cells in vitro and in vivo. Furthermore, human genetics implicate BACH2 in multiple sclerosis. Overall, our work identifies regulators of TH17 heterogeneity as potential targets to mitigate autoimmunity.
    DOI:  https://doi.org/10.1038/s41590-024-01901-1
  16. Mol Cell. 2024 Jul 06. pii: S1097-2765(24)00527-6. [Epub ahead of print]
    Competition between two HUSH complexes orchestrates the immune response to retroelement invasion.
    Joshua Miguel C Danac, Rachael E Matthews, Akhila Gungi, Chuyan Qin, Harriet Parsons, Robin Antrobus, Richard T Timms, Iva A Tchasovnikarova.
      The human silencing hub (HUSH) preserves genome integrity through the epigenetic repression of invasive genetic elements. However, despite our understanding of HUSH as an obligate complex of three subunits, only loss of MPP8 or Periphilin, but not TASOR, triggers interferon signaling following derepression of endogenous retroelements. Here, we resolve this paradox by characterizing a second HUSH complex that shares MPP8 and Periphilin but assembles around TASOR2, an uncharacterized paralog of TASOR. Whereas HUSH represses LINE-1 retroelements marked by the repressive histone modification H3K9me3, HUSH2 is recruited by the transcription factor IRF2 to repress interferon-stimulated genes. Mechanistically, HUSH-mediated retroelement silencing sequesters the limited pool of the shared subunits MPP8 and Periphilin, preventing TASOR2 from forming HUSH2 complexes and hence relieving the HUSH2-mediated repression of interferon-stimulated genes. Thus, competition between two HUSH complexes intertwines retroelement silencing with the induction of an immune response, coupling epigenetic and immune aspects of genome defense.
    Keywords:  HUSH; HUSH2; IRF2; LINE-1; chromatin; epigenetics; immune response; interferon; retroelement; transposable elements
    DOI:  https://doi.org/10.1016/j.molcel.2024.06.020
  17. Nat Commun. 2024 Jul 15. 15(1): 5941
    Single-cell total-RNA profiling unveils regulatory hubs of transcription factors.
    Yichi Niu, Jiayi Luo, Chenghang Zong.
      Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from unspliced RNA to spliced RNA (i.e., mature RNA) to degradation. To feed this kinetic analysis, simultaneous measurement of unspliced RNA and spliced RNA in single cells is greatly desired. However, the majority of single-cell RNA-seq chemistry primarily captures mature RNA species to measure gene expressions. Here, we develop a one-step total-RNA chemistry-based single-cell RNA-seq method: snapTotal-seq. We benchmark this method with multiple single-cell RNA-seq assays in their performance in kinetic analysis of cell cycle by RNA velocity. Next, with LASSO regression between transcription factors, we identify the critical regulatory hubs mediating the cell cycle dynamics. We also apply snapTotal-seq to profile the oncogene-induced senescence and identify the key regulatory hubs governing the entry of senescence. Furthermore, from the comparative analysis of unspliced RNA and spliced RNA, we identify a significant portion of genes whose expression changes occur in spliced RNA but not to the same degree in unspliced RNA, indicating these gene expression changes are mainly controlled by post-transcriptional regulation. Overall, we demonstrate that snapTotal-seq can provide enriched information about gene regulation, especially during the transition between cell states.
    DOI:  https://doi.org/10.1038/s41467-024-50291-3
  18. Genome Biol. 2024 Jul 18. 25(1): 190
    Non-coding variants impact cis-regulatory coordination in a cell type-specific manner.
    Olga Pushkarev, Guido van Mierlo, Judith Franziska Kribelbauer, Wouter Saelens, Vincent Gardeux, Bart Deplancke.
       BACKGROUND: Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual epigenomic variation to identify groups of covariable regulatory elements, referred to as chromatin modules (CMs). While CM mapping allows to investigate the relationship between chromatin modularity and gene expression, the computational principles used for CM identification vary in their application and outcomes.
    RESULTS: We comprehensively evaluate and streamline existing CM mapping tools and present guidelines for optimal utilization of epigenome data from a diverse population of individuals to assess regulatory coordination across the human genome. We showcase the effectiveness of our recommended practices by analyzing distinct cell types and demonstrate cell type specificity of CRE interactions in CMs and their relevance for gene expression. Integration of genotype information revealed that many non-coding disease-associated variants affect the activity of CMs in a cell type-specific manner by affecting the binding of cell type-specific transcription factors. We provide example cases that illustrate in detail how CMs can be used to deconstruct GWAS loci, assess variable expression of cell surface receptors in immune cells, and reveal how genetic variation can impact the expression of prognostic markers in chronic lymphocytic leukemia.
    CONCLUSIONS: Our study presents an optimal strategy for CM mapping and reveals how CMs capture the coordination of CREs and its impact on gene expression. Non-coding genetic variants can disrupt this coordination, and we highlight how this may lead to disease predisposition in a cell type-specific manner.
    Keywords:   Cis-regulatory interactions; Epigenomics; Gene regulation; Genome-wide association studies; Quantitative trait loci
    DOI:  https://doi.org/10.1186/s13059-024-03333-4
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