bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2024–10–13
25 papers selected by
Connor Rogerson, University of Cambridge
  1. SRF promotes long-range chromatin loop formation and stem cell pluripotency.
  2. Transcriptional coactivator MED15 is required for beta cell maturation.
  3. A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.
  4. Temporally distinct 3D multi-omic dynamics in the developing human brain.
  5. HNF1β bookmarking involves Topoisomerase 1 activation and DNA topology relaxation in mitotic chromatin.
  6. scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells.
  7. The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation.
  8. Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation.
  9. Structural mechanism of HP1⍺-dependent transcriptional repression and chromatin compaction.
  10. HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding.
  11. Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters.
  12. Mycobacterial HelD connects RNA polymerase recycling with transcription initiation.
  13. Genome-wide mapping of native co-localized G4s and R-loops in living cells.
  14. Enhancer reprogramming underlies therapeutic utility of a SMARCA2 degrader in SMARCA4 mutant cancer.
  15. Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice.
  16. SATB1 prevents immune cell infiltration by regulating chromatin organization and gene expression of a chemokine gene cluster in T cells.
  17. Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy.
  18. Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate.
  19. The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1.
  20. Optimization of the Irf8 +32-kb enhancer disrupts dendritic cell lineage segregation.
  21. Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
  22. HES1 potentiates high salt stress response as an enhancer of NFAT5-DNA binding.
  23. Practical approaches for visualization of endogenous enhancer-promoter interactions in a single nucleus through chromatin labeling.
  24. scATAcat: cell-type annotation for scATAC-seq data.
  25. Base-excision repair pathway regulates transcription-replication conflicts in pancreatic ductal adenocarcinoma.
  1. Cell Rep. 2024 Oct 10. pii: S2211-1247(24)01197-5. [Epub ahead of print]43(10): 114846
    SRF promotes long-range chromatin loop formation and stem cell pluripotency.
    Pavel Tsaytler, Gaby Blaess, Manuela Scholze-Wittler, David Meierhofer, Lars Wittler, Frederic Koch, Bernhard G Herrmann.
      Serum response factor (SRF) is a transcription factor essential for cell proliferation, differentiation, and migration and is required for primitive streak and mesoderm formation in the embryo. The canonical roles of SRF are mediated by a diverse set of context-dependent cofactors. Here, we show that SRF physically interacts with CTCF and cohesin subunits at topologically associating domain (TAD) boundaries and loop anchors. SRF promotes long-range chromatin loop formation and contributes to TAD insulation. In embryonic stem cells (ESCs), SRF associates with SOX2 and NANOG and contributes to the formation of three-dimensional (3D) pluripotency hubs. Our findings reveal additional roles of SRF in higher-order chromatin organization.
    Keywords:  CP: Molecular biology; CP: Stem cell research; CTCF; NANOG; OSN enhancers; SOX2; SRF; TAD insulation; chromatin loops; chromatin organization; long-range contact regulation; pluripotency
    DOI:  https://doi.org/10.1016/j.celrep.2024.114846
  2. Nat Commun. 2024 Oct 08. 15(1): 8711
    Transcriptional coactivator MED15 is required for beta cell maturation.
    Alex Z Kadhim, Ben Vanderkruk, Samantha Mar, Meixia Dan, Katarina Zosel, Eric E Xu, Rachel J Spencer, Shugo Sasaki, Xuanjin Cheng, Shannon L J Sproul, Thilo Speckmann, Cuilan Nian, Robyn Cullen, Rocky Shi, Dan S Luciani, Bradford G Hoffman, Stefan Taubert, Francis C Lynn.
      Mediator, a co-regulator complex required for RNA Polymerase II activity, interacts with tissue-specific transcription factors to regulate development and maintain homeostasis. We observe reduced Mediator subunit MED15 expression in endocrine hormone-producing pancreatic islets isolated from people living with type 2 diabetes and sought to understand how MED15 and Mediator control gene expression programs important for the function of insulin-producing β-cells. Here we show that Med15 is expressed during mouse β-cell development and maturation. Knockout of Med15 in mouse β-cells causes defects in β-cell maturation without affecting β-cell mass or insulin expression. ChIP-seq and co-immunoprecipitation analyses found that Med15 binds β-cell transcription factors Nkx6-1 and NeuroD1 to regulate key β-cell maturation genes. In support of a conserved role during human development, human embryonic stem cell-derived β-like cells, genetically engineered to express high levels of MED15, express increased levels of maturation markers. We provide evidence of a conserved role for Mediator in β-cell maturation and demonstrate an additional layer of control that tunes β-cell transcription factor function.
    DOI:  https://doi.org/10.1038/s41467-024-52801-9
  3. Nat Commun. 2024 Oct 10. 15(1): 8793
    A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.
    Samuel Abassah-Oppong, Matteo Zoia, Brandon J Mannion, Raquel Rouco, Virginie Tissières, Cailyn H Spurrell, Virginia Roland, Fabrice Darbellay, Anja Itum, Julie Gamart, Tabitha A Festa-Daroux, Carly S Sullivan, Michael Kosicki, Eddie Rodríguez-Carballo, Yoko Fukuda-Yuzawa, Riana D Hunter, Catherine S Novak, Ingrid Plajzer-Frick, Stella Tran, Jennifer A Akiyama, Diane E Dickel, Javier Lopez-Rios, Iros Barozzi, Guillaume Andrey, Axel Visel, Len A Pennacchio, John Cobb, Marco Osterwalder.
      Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development. We identify the gene desert as a regulatory hub containing more than 15 distinct enhancers recapitulating anatomical subdomains of Shox2 expression. Ablation of the gene desert leads to embryonic lethality due to Shox2 depletion in the cardiac sinus venosus, caused in part by the loss of a specific distal enhancer. The gene desert is also required for stylopod morphogenesis, mediated via distributed proximal limb enhancers. In summary, our study establishes a multi-layered role of the Shox2 gene desert in orchestrating pleiotropic developmental expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.
    DOI:  https://doi.org/10.1038/s41467-024-53009-7
  4. Nature. 2024 Oct 09.
    Temporally distinct 3D multi-omic dynamics in the developing human brain.
    Matthew G Heffel, Jingtian Zhou, Yi Zhang, Dong-Sung Lee, Kangcheng Hou, Oier Pastor-Alonso, Kevin D Abuhanna, Joseph Galasso, Colin Kern, Chu-Yi Tai, Carlos Garcia-Padilla, Mahsa Nafisi, Yi Zhou, Anthony D Schmitt, Terence Li, Maximilian Haeussler, Brittney Wick, Martin Jinye Zhang, Fangming Xie, Ryan S Ziffra, Eran A Mukamel, Eleazar Eskin, Tomasz J Nowakowski, Jesse R Dixon, Bogdan Pasaniuc, Joseph R Ecker, Quan Zhu, Bogdan Bintu, Mercedes F Paredes, Chongyuan Luo.
      The human hippocampus and prefrontal cortex play critical roles in learning and cognition1,2, yet the dynamic molecular characteristics of their development remain enigmatic. Here we investigated the epigenomic and three-dimensional chromatin conformational reorganization during the development of the hippocampus and prefrontal cortex, using more than 53,000 joint single-nucleus profiles of chromatin conformation and DNA methylation generated by single-nucleus methyl-3C sequencing (snm3C-seq3)3. The remodelling of DNA methylation is temporally separated from chromatin conformation dynamics. Using single-cell profiling and multimodal single-molecule imaging approaches, we have found that short-range chromatin interactions are enriched in neurons, whereas long-range interactions are enriched in glial cells and non-brain tissues. We reconstructed the regulatory programs of cell-type development and differentiation, finding putatively causal common variants for schizophrenia strongly overlapping with chromatin loop-connected, cell-type-specific regulatory regions. Our data provide multimodal resources for studying gene regulatory dynamics in brain development and demonstrate that single-cell three-dimensional multi-omics is a powerful approach for dissecting neuropsychiatric risk loci.
    DOI:  https://doi.org/10.1038/s41586-024-08030-7
  5. Cell Rep. 2024 Oct 08. pii: S2211-1247(24)01156-2. [Epub ahead of print]43(10): 114805
    HNF1β bookmarking involves Topoisomerase 1 activation and DNA topology relaxation in mitotic chromatin.
    Alessia Bagattin, Salvina Laura Tammaccaro, Magali Chiral, Munevver Parla Makinistoglu, Nicolas Zimmermann, Jonathan Lerner, Serge Garbay, Nicolas Kuperwasser, Marco Pontoglio.
      HNF1β (HNF1B) is a transcription factor frequently mutated in patients with developmental renal disease. It binds to mitotic chromatin and reactivates gene expression after mitosis, a phenomenon referred to as bookmarking. Using a crosslinking method that circumvents the artifacts of formaldehyde, we demonstrate that HNF1β remains associated with chromatin in a sequence-specific way in both interphase and mitosis. We identify an HNF1β-interacting protein, BTBD2, that enables the interaction and activation of Topoisomerase 1 (TOP1) exclusively during mitosis. Our study identifies a shared microhomology domain between HNF1β and TOP1, where a mutation, found in "maturity onset diabetes of the young" patients, disrupts their interaction. Importantly, HNF1β recruits TOP1 and induces DNA relaxation around HNF1β mitotic chromatin sites, elucidating its crucial role in chromatin remodeling and gene reactivation after mitotic exit. These findings shed light on how HNF1β reactivates target gene expression after mitosis, providing insights into its crucial role in maintenance of cellular identity.
    Keywords:  BTBD2; CP: Genomics; CP: Molecular biology; ChIP-seq; DNA topology; HNF1B; TOP1; epigenetics; mitotic bookmarking; renal disease; transcription
    DOI:  https://doi.org/10.1016/j.celrep.2024.114805
  6. Nat Methods. 2024 Oct 07.
    scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells.
    Qingqing Li, Yuqing Guo, Zixin Wu, Xueqiang Xu, Zhenhuan Jiang, Shuyue Qi, Zhenyu Liu, Lu Wen, Fuchou Tang.
      Chromatin modifications are fundamental epigenetic marks that determine genome functions, but it remains challenging to profile those of repetitive elements and complex genomic regions. Here, we develop scNanoSeq-CUT&Tag, a streamlined method, by adapting modified cleavage under targets and tagmentation (CUT&Tag) to the nanopore sequencing platform for genome-wide chromatin modification profiling within individual cells. We show that scNanoSeq-CUT&Tag can accurately profile histone marks and transcription factor occupancy patterns at single-cell resolution as well as distinguish different cell types. scNanoSeq-CUT&Tag efficiently maps the allele-specific chromatin modifications and allows analysis of their neighboring region co-occupancy patterns within individual cells. Moreover, scNanoSeq-CUT&Tag can accurately detect chromatin modifications for individual copies of repetitive elements in both human and mouse genomes. Overall, we prove that scNanoSeq-CUT&Tag is a valuable single-cell tool for efficiently profiling histone marks and transcription factor occupancies, especially for previously poorly studied complex genomic regions and blacklist genomic regions.
    DOI:  https://doi.org/10.1038/s41592-024-02453-w
  7. Mol Cell. 2024 Oct 01. pii: S1097-2765(24)00772-X. [Epub ahead of print]
    The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation.
    Joydeb Sinha, Jan F Nickels, Abby R Thurm, Connor H Ludwig, Bella N Archibald, Michaela M Hinks, Jun Wan, Dong Fang, Lacramioara Bintu.
      Histone H3.3 is frequently mutated in tumors, with the lysine 36 to methionine mutation (K36M) being a hallmark of chondroblastomas. While it is known that H3.3K36M changes the epigenetic landscape, its effects on gene expression dynamics remain unclear. Here, we use a synthetic reporter to measure the effects of H3.3K36M on silencing and epigenetic memory after recruitment of the ZNF10 Krüppel-associated box (KRAB) domain, part of the largest class of human repressors and associated with H3K9me3 deposition. We find that H3.3K36M, which decreases H3K36 methylation and increases histone acetylation, leads to a decrease in epigenetic memory and promoter methylation weeks after KRAB release. We propose a model for establishment and maintenance of epigenetic memory, where the H3K36 methylation pathway is necessary to maintain histone deacetylation and convert H3K9me3 domains into DNA methylation for stable epigenetic memory. Our quantitative model can inform oncogenic mechanisms and guide development of epigenetic editing tools.
    Keywords:  DNA methylation; H3.3K36M; H3K36me2; H3K36me3; KRAB; NSD1; SETD2; epigenetic memory; heterochromatin; oncohistone
    DOI:  https://doi.org/10.1016/j.molcel.2024.09.015
  8. Genome Biol. 2024 Oct 10. 25(1): 263
    Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation.
    Gerry A Shipman, Reinnier Padilla, Cynthia Horth, Bo Hu, Eric Bareke, Francisca N Vitorino, Joanna M Gongora, Benjamin A Garcia, Chao Lu, Jacek Majewski.
       BACKGROUND: Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecular agents collectively shape the H3K36me landscape is unclear.
    RESULTS: We use mouse mesenchymal stem cells to perturb the H3K36me methyltransferases (K36MTs) and infer the activities of the five most prominent enzymes: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it may also deposit H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other (K36MTs) prime gene bodies with lower methylation states ahead of transcription. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor.
    CONCLUSIONS: Within genes, SETD2 primarily deposits H3K36me3, while the other K36MTs deposit H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1 > NSD2 > NSD3 > ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.
    Keywords:  ASH1L; Epigenetics; H3K36 methylation; NSD1; NSD2; NSD3; SETD2; Transcription
    DOI:  https://doi.org/10.1186/s13059-024-03415-3
  9. Structure. 2024 Oct 03. pii: S0969-2126(24)00382-4. [Epub ahead of print]
    Structural mechanism of HP1⍺-dependent transcriptional repression and chromatin compaction.
    Vladyslava Sokolova, Jacob Miratsky, Vladimir Svetlov, Michael Brenowitz, John Vant, Tyler S Lewis, Kelly Dryden, Gahyun Lee, Shayan Sarkar, Evgeny Nudler, Abhishek Singharoy, Dongyan Tan.
      Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. Here, we present the cryoelectron microscopy (cryo-EM) structure of an HP1α dimer bound to an H2A.Z-nucleosome, revealing two distinct HP1α-nucleosome interfaces. The primary HP1α binding site is located at the N terminus of histone H3, specifically at the trimethylated lysine 9 (K9me3) region, while a secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. Our study offers a model for HP1α-mediated heterochromatin maintenance and gene silencing. It also sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
    Keywords:  HP; MDFF; cryo-EM; heterochromatin; histone methylation; histone variant; nucleosome
    DOI:  https://doi.org/10.1016/j.str.2024.09.013
  10. Mol Cell. 2024 Oct 03. pii: S1097-2765(24)00775-5. [Epub ahead of print]
    HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding.
    Evgeny Deforzh, Prakash Kharel, Yanhong Zhang, Anton Karelin, Abdellatif El Khayari, Pavel Ivanov, Anna M Krichevsky.
      The role of long non-coding RNAs (lncRNAs) in malignant cell transformation remains elusive. We previously identified an enhancer-associated lncRNA, LINC01116 (named HOXDeRNA), as a transformative factor converting human astrocytes into glioma-like cells. Employing a combination of CRISPR editing, chromatin isolation by RNA purification coupled with sequencing (ChIRP-seq), in situ mapping RNA-genome interactions (iMARGI), chromatin immunoprecipitation sequencing (ChIP-seq), HiC, and RNA/DNA FISH, we found that HOXDeRNA directly binds to CpG islands within the promoters of 35 glioma-specific transcription factors (TFs) distributed throughout the genome, including key stem cell TFs SOX2, OLIG2, POU3F2, and ASCL1, liberating them from PRC2 repression. This process requires a distinct RNA quadruplex structure and other segments of HOXDeRNA, interacting with EZH2 and CpGs, respectively. Subsequent transformation activates multiple oncogenes (e.g., EGFR, miR-21, and WEE1), driven by the SOX2- and OLIG2-dependent glioma-specific super enhancers. These results help reconstruct the sequence of events underlying the process of astrocyte transformation, highlighting HOXDeRNA's central genome-wide activity and suggesting a shared RNA-dependent mechanism in otherwise heterogeneous and multifactorial gliomagenesis.
    Keywords:  CpG; PRC2; astrocytes; enhancer RNA; glioma; long non-coding RNA; rG4; stem cells; super enhancers; transcription factors
    DOI:  https://doi.org/10.1016/j.molcel.2024.09.018
  11. Mol Cell. 2024 Oct 05. pii: S1097-2765(24)00771-8. [Epub ahead of print]
    Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters.
    Rajendra K C, Ruiying Cheng, Sihang Zhou, Simon Lizarazo, Duncan J Smith, Kevin Van Bortle.
      The transcriptional interplay of human RNA polymerase I (RNA Pol I), RNA Pol II, and RNA Pol III remains largely uncharacterized due to limited integrative genomic analyses for all three enzymes. To address this gap, we applied a uniform framework to quantify global RNA Pol I, RNA Pol II, and RNA Pol III occupancies and identify both canonical and noncanonical patterns of gene localization. Most notably, our survey captures unexpected RNA Pol III recruitment at promoters of specific protein-coding genes. We show that such RNA Pol III-occupied promoters are enriched for small nascent RNAs terminating in a run of 4 Ts-a hallmark of RNA Pol III termination indicative of constrained RNA Pol III transcription. Taken further, RNA Pol III disruption generally reduces the expression of RNA Pol III-occupied protein-coding genes, suggesting RNA Pol III recruitment and transcription enhance RNA Pol II activity. These findings resemble analogous patterns of RNA Pol II activity at RNA Pol III-transcribed genes, altogether uncovering a reciprocal form of crosstalk between RNA Pol II and RNA Pol III.
    Keywords:  La chaperone; RNA Pol II; RNA Pol III; RPPH1; gene regulation; nc111; nc143; nc96; tRNA; transcriptome
    DOI:  https://doi.org/10.1016/j.molcel.2024.09.019
  12. Nat Commun. 2024 Oct 09. 15(1): 8740
    Mycobacterial HelD connects RNA polymerase recycling with transcription initiation.
    Tomáš Kovaľ, Nabajyoti Borah, Petra Sudzinová, Barbora Brezovská, Hana Šanderová, Viola Vaňková Hausnerová, Alena Křenková, Martin Hubálek, Mária Trundová, Kristýna Adámková, Jarmila Dušková, Marek Schwarz, Jana Wiedermannová, Jan Dohnálek, Libor Krásný, Tomáš Kouba.
      Mycobacterial HelD is a transcription factor that recycles stalled RNAP by dissociating it from nucleic acids and, if present, from the antibiotic rifampicin. The rescued RNAP, however, must disengage from HelD to participate in subsequent rounds of transcription. The mechanism of release is unknown. We show that HelD from Mycobacterium smegmatis forms a complex with RNAP associated with the primary sigma factor σA and transcription factor RbpA but not CarD. We solve several structures of RNAP-σA-RbpA-HelD without and with promoter DNA. These snapshots capture HelD during transcription initiation, describing mechanistic aspects of HelD release from RNAP and its protective effect against rifampicin. Biochemical evidence supports these findings, defines the role of ATP binding and hydrolysis by HelD in the process, and confirms the rifampicin-protective effect of HelD. Collectively, these results show that when HelD is present during transcription initiation, the process is protected from rifampicin until the last possible moment.
    DOI:  https://doi.org/10.1038/s41467-024-52891-5
  13. Elife. 2024 Oct 11. pii: RP99026. [Epub ahead of print]13
    Genome-wide mapping of native co-localized G4s and R-loops in living cells.
    Ting Liu, Xing Shen, Yijia Ren, Hongyu Lu, Yu Liu, Chong Chen, Lin Yu, Zhihong Xue.
      The interplay between G4s and R-loops are emerging in regulating DNA repair, replication, and transcription. A comprehensive picture of native co-localized G4s and R-loops in living cells is currently lacking. Here, we describe the development of HepG4-seq and an optimized HBD-seq methods, which robustly capture native G4s and R-loops, respectively, in living cells. We successfully employed these methods to establish comprehensive maps of native co-localized G4s and R-loops in human HEK293 cells and mouse embryonic stem cells (mESCs). We discovered that co-localized G4s and R-loops are dynamically altered in a cell type-dependent manner and are largely localized at active promoters and enhancers of transcriptional active genes. We further demonstrated the helicase Dhx9 as a direct and major regulator that modulates the formation and resolution of co-localized G4s and R-loops. Depletion of Dhx9 impaired the self-renewal and differentiation capacities of mESCs by altering the transcription of co-localized G4s and R-loops -associated genes. Taken together, our work established that the endogenous co-localized G4s and R-loops are prevalently persisted in the regulatory regions of active genes and are involved in the transcriptional regulation of their linked genes, opening the door for exploring broader roles of co-localized G4s and R-loops in development and disease.
    Keywords:  Dhx9; HBD-seq; HepG4-seq; R-loops; biochemistry; chemical biology; co-localized G4s; genetics; genomics; human; mouse; native G-quadruplex; native R-loop
    DOI:  https://doi.org/10.7554/eLife.99026
  14. Cell Chem Biol. 2024 Oct 01. pii: S2451-9456(24)00396-9. [Epub ahead of print]
    Enhancer reprogramming underlies therapeutic utility of a SMARCA2 degrader in SMARCA4 mutant cancer.
    Sasikumar Kotagiri, Nicholas Blazanin, Yuanxin Xi, Yanyan Han, Md Qudratullah, Xiaobing Liang, Yawen Wang, Poonam Pandey, Hira Mazhar, Truong Nguyen Lam, Anand Kamal Singh, Jing Wang, Yonathan Lissanu.
      Genomic studies have identified frequent mutations in subunits of the SWI/SNF (switch/sucrose non-fermenting) chromatin remodeling complex including SMARCA4 and ARID1A in non-small cell lung cancer (NSCLC). Genetic evidence indicates that the paralog SMARCA2 is synthetic lethal to SMARCA4 suggesting SMARCA2 is a valuable therapeutic target. However, the discovery of selective inhibitors of SMARCA2 has been challenging. Here, we utilized structure-activity relationship (SAR) studies to develop YD23, a potent and selective proteolysis targeting chimera (PROTAC) targeting SMARCA2. Mechanistically, we show that SMARCA2 degradation induces reprogramming of the enhancer landscape in SMARCA4-mutant cells with loss of chromatin accessibility at enhancers of genes involved in cell proliferation. Furthermore, we identified YAP/TEADas key partners to SMARCA2 in driving growth of SMARCA4-mutant cells. Finally, we show that YD23 has potent tumor growth inhibitory activity in SMARCA4-mutant xenografts. These findings provide the mechanistic basis for development of SMARCA2 degraders as synthetic lethal therapeutics against SMARCA4-mutant lung cancers.
    Keywords:  PROTAC; SMARCA2; SMARCA4; SWI/SNF; YAP/TEAD; cell cycle; enhancer accessibility; gene regulation; lung cancer; synthetic lethality
    DOI:  https://doi.org/10.1016/j.chembiol.2024.09.004
  15. Genome Biol. 2024 Oct 10. 25(1): 262
    Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice.
    Yu Chang, Jiahan Liu, Minrong Guo, Weizhi Ouyang, Jiapei Yan, Lizhong Xiong, Xingwang Li.
       BACKGROUND: In response to drought stress (DS), plants undergo complex processes that entail significant transcriptome reprogramming. However, the intricate relationship between the dynamic alterations in the three-dimensional (3D) genome and the modulation of gene co-expression in drought responses remains a relatively unexplored area.
    RESULTS: In this study, we reconstruct high-resolution 3D genome maps based on genomic regions marked by H3K9ac, an active histone modification that dynamically responds to soil water variations in rice. We discover a genome-wide disconnection of 3D genome contact upon DS with over 10,000 chromatin loops lost, which are partially recovered in the subsequent re-watering. Loops integrating promoter-promoter interactions (PPI) contribute to gene expression in addition to basal H3K9ac modifications. Moreover, H3K9ac-marked promoter regions with high affinities in mediating PPIs, termed as super-promoter regions (SPRs), integrate spatially clustered PPIs in a super-enhancer-like manner. Interestingly, the knockout mutation of OsbZIP23, a well-defined DS-responsive transcription factor, leads to the disassociation of over 80% DS-specific PPIs and decreased expression of the corresponding genes under DS. As a case study, we show how OsbZIP23 integrates the PPI cluster formation and the co-expression of four dehydrin genes, RAB16A-D, through targeting the RAB16C SPR in a stress signaling-dependent manner.
    CONCLUSIONS: Our high-resolution 3D genome maps unveil the principles and details of dynamic genome folding in response to water supply variations and illustrate OsbZIP23 as an indispensable integrator of the yet unique 3D genome organization that is essential for gene co-expression under DS in rice.
    Keywords:  Chromatin interaction; Drought stress; H3K9ac; Rice; Super-promoter region
    DOI:  https://doi.org/10.1186/s13059-024-03408-2
  16. Commun Biol. 2024 Oct 11. 7(1): 1304
    SATB1 prevents immune cell infiltration by regulating chromatin organization and gene expression of a chemokine gene cluster in T cells.
    Bao Wang, Qian Bian.
      SATB1, a key regulator of T cell development, governs lineage-specific transcriptional programs upon T cell activation. The absence of SATB1 has been linked to the initiation and progression of autoimmunity. However, its precise roles in this process remain incompletely understood. Here we show that conditional knockout of Satb1 in CD4+ T cells in mice led to T cell hyperactivation and inflammatory cell infiltration across multiple organs. Transcriptional profiling on activated T cells revealed that the loss of SATB1 led to aberrant upregulation of CC chemokines. Treating Satb1 conditional knockout mice with CC chemokine receptor inhibitor alleviated inflammatory cell infiltration. Intriguingly, SATB1's transcriptional regulation of chemokine genes could not be attributed to its direct binding to chemokine promoters. Instead, SATB1 exerted its regulatory effects by controlling higher-order chromatin organization at a CC chemokine locus. The loss of SATB1 led to the emergence of a new chromatin domain encompassing the Ccl3, Ccl4, Ccl5, Ccl6, and Ccl9 genes and a distal enhancer, resulting in increased contacts between the enhancer and all five chemokine genes, thus inducing their upregulation. Collectively, these results demonstrate that SATB1 protects organs from immune cell infiltration by regulating chemokine expression, providing valuable insights into the development of autoimmunity-related phenotypes.
    DOI:  https://doi.org/10.1038/s42003-024-07021-8
  17. Sci Adv. 2024 Oct 11. 10(41): eadq0479
    Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy.
    Yongchun Zhang, Dimitris Karagiannis, Helu Liu, Mi Lin, Yinshan Fang, Ming Jiang, Xiao Chen, Supriya Suresh, Haidi Huang, Junjun She, Feiyu Shi, Jiangying Liu, Dan Luo, J Carlos Angel, Guangtan Lin, Patrick Yang, Wael El-Rifai, Alexander Zaika, Anthony E Oro, Kuancan Liu, Anil K Rustgi, Timothy C Wang, Chao Lu, Jianwen Que.
      While cell fate determination and maintenance are important in establishing and preserving tissue identity and function during development, aberrant cell fate transition leads to cancer cell heterogeneity and resistance to treatment. Here, we report an unexpected role for the transcription factor p63 (Trp63/TP63) in the fate choice of the squamous versus neuroendocrine lineage in esophageal development and malignancy. Deletion of p63 results in extensive neuroendocrine differentiation in the developing mouse esophagus and esophageal progenitors derived from human embryonic stem cells. In human esophageal neuroendocrine carcinoma (eNEC) cells, p63 is transcriptionally silenced by EZH2-mediated H3K27 trimethylation (H3K27me3). Up-regulation of the major p63 isoform ΔNp63α, through either ectopic expression or EZH2 inhibition, promotes squamous transdifferentiation of eNEC cells. Together, these findings uncover p63 as a rheostat in coordinating the transition between squamous and neuroendocrine cell fates during esophageal development and tumor progression.
    DOI:  https://doi.org/10.1126/sciadv.adq0479
  18. Cell Rep. 2024 Oct 03. pii: S2211-1247(24)01158-6. [Epub ahead of print]43(10): 114807
    Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate.
    Thorsten Schaefer, Nitish Mittal, Hui Wang, Meric Ataman, Silvia Candido, Jonas Lötscher, Sergiy Velychko, Lionel Tintignac, Thomas Bock, Anastasiya Börsch, Jochen Baßler, Tata Nageswara Rao, Jakub Zmajkovic, Sarah Roffeis, Jordan Löliger, Francis Jacob, Alain Dumlin, Christoph Schürch, Alexander Schmidt, Radek C Skoda, Matthias P Wymann, Christoph Hess, Hans R Schöler, Holm Zaehres, Ed Hurt, Mihaela Zavolan, Claudia Lengerke.
      Stemness and pluripotency are mediated by transcriptional master regulators that promote self-renewal and repress cell differentiation, among which is the high-mobility group (HMG) box transcription factor SOX2. Dysregulated SOX2 expression, by contrast, leads to transcriptional aberrations relevant to oncogenic transformation, cancer progression, metastasis, therapy resistance, and relapse. Here, we report a post-transcriptional mechanism by which the cytosolic pool of SOX2 contributes to these events in an unsuspected manner. Specifically, a low-complexity region within SOX2's C-terminal segment connects to the ribosome to modulate the expression of cognate downstream factors. Independent of nuclear structures or DNA, this C-terminal functionality alone changes metabolic properties and induces non-adhesive growth when expressed in the cytosol of SOX2 knockout cells. We thus propose a revised model of SOX2 action where nuclear and cytosolic fractions cooperate to impose cell fate decisions via both transcriptional and translational mechanisms.
    Keywords:  CP: Developmental biology; CP: Molecular biology; SOX2; cancer; differentiation; ribosome; stem cell; translation
    DOI:  https://doi.org/10.1016/j.celrep.2024.114807
  19. Nat Cancer. 2024 Oct 11.
    The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1.
    Rodrigo Romero, Tinyi Chu, Tania J González Robles, Perianne Smith, Yubin Xie, Harmanpreet Kaur, Sara Yoder, Huiyong Zhao, Chenyi Mao, Wenfei Kang, Maria V Pulina, Kayla E Lawrence, Anuradha Gopalan, Samir Zaidi, Kwangmin Yoo, Jungmin Choi, Ning Fan, Olivia Gerstner, Wouter R Karthaus, Elisa DeStanchina, Kelly V Ruggles, Peter M K Westcott, Ronan Chaligné, Dana Pe'er, Charles L Sawyers.
      Lineage plasticity is a hallmark of cancer progression that impacts therapy outcomes, yet the mechanisms mediating this process remain unclear. Here, we introduce a versatile in vivo platform to interrogate neuroendocrine lineage transformation throughout prostate cancer progression. Transplanted mouse prostate organoids with human-relevant driver mutations (Rb1-/-; Trp53-/-; cMyc+ or Pten-/-; Trp53-/-; cMyc+) develop adenocarcinomas, but only those with Rb1 deletion advance to aggressive, ASCL1+ neuroendocrine prostate cancer (NEPC) resistant to androgen receptor signaling inhibitors. Notably, this transition requires an in vivo microenvironment not replicated by conventional organoid culture. Using multiplexed immunofluorescence and spatial transcriptomics, we reveal that ASCL1+ cells arise from KRT8+ luminal cells, progressing into transcriptionally heterogeneous ASCL1+;KRT8- NEPC. Ascl1 loss in established NEPC causes transient regression followed by recurrence, but its deletion before transplantation abrogates lineage plasticity, resulting in castration-sensitive adenocarcinomas. This dynamic model highlights the importance of therapy timing and offers a platform to identify additional lineage plasticity drivers.
    DOI:  https://doi.org/10.1038/s43018-024-00838-6
  20. Nat Immunol. 2024 Oct 07.
    Optimization of the Irf8 +32-kb enhancer disrupts dendritic cell lineage segregation.
    Feiya Ou, Tian-Tian Liu, Pritesh Desai, Stephen T Ferris, Sunkyung Kim, Haolin Shen, Ray A Ohara, Suin Jo, Jing Chen, J Luke Postoak, Siling Du, Michael S Diamond, Theresa L Murphy, Kenneth M Murphy.
      Autoactivation of lineage-determining transcription factors mediates bistable expression, generating distinct cell phenotypes essential for complex body plans. Classical type 1 dendritic cell (cDC1) and type 2 dendritic cell (cDC2) subsets provide nonredundant functions for defense against distinct immune challenges. Interferon regulatory factor 8 (IRF8), the cDC1 lineage-determining transcription factor, undergoes autoactivation in cDC1 progenitors to establish cDC1 identity, yet its expression is downregulated during cDC2 differentiation by an unknown mechanism. This study reveals that the Irf8 +32-kb enhancer, responsible for IRF8 autoactivation, is naturally suboptimized with low-affinity IRF8 binding sites. Introducing multiple high-affinity IRF8 sites into the Irf8 +32-kb enhancer causes a gain-of-function effect, leading to erroneous IRF8 autoactivation in specified cDC2 progenitors, redirecting them toward cDC1 and a novel hybrid DC subset with mixed-lineage phenotypes. Further, this also causes a loss-of-function effect, reducing Irf8 expression in cDC1s. These developmental alterations critically impair both cDC1-dependent and cDC2-dependent arms of immunity. Collectively, our findings underscore the significance of enhancer suboptimization in the developmental segregation of cDCs required for normal immune function.
    DOI:  https://doi.org/10.1038/s41590-024-01976-w
  21. Elife. 2024 Oct 09. pii: RP94833. [Epub ahead of print]13
    Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
    Aurélie Anne-Gaëlle Gabriel, Julien Racle, Maryline Falquet, Camilla Jandus, David Gfeller.
      Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement represents a mixed signal from multiple cell types. In this work, we derive reliable chromatin accessibility marker peaks and reference profiles for most non-malignant cell types frequently observed in the microenvironment of human tumors. We then integrate these data into the EPIC deconvolution framework (Racle et al., 2017) to quantify cell-type heterogeneity in bulk ATAC-Seq data. Our EPIC-ATAC tool accurately predicts non-malignant and malignant cell fractions in tumor samples. When applied to a human breast cancer cohort, EPIC-ATAC accurately infers the immune contexture of the main breast cancer subtypes.
    Keywords:  ATAC-Seq; bulk deconvolution; cancer biology; chromatin accessibility; computational biology; human; systems biology; tumor microenvironment
    DOI:  https://doi.org/10.7554/eLife.94833
  22. Commun Biol. 2024 Oct 09. 7(1): 1290
    HES1 potentiates high salt stress response as an enhancer of NFAT5-DNA binding.
    Hiroki Ryuno, Yusuke Hanafusa, Takao Fujisawa, Motoyuki Ogawa, Hiroki Adachi, Isao Naguro, Hidenori Ichijo.
      High salt conditions and subsequent hyperosmolarity are injurious cellular stresses that can activate immune signaling. Nuclear factor of activated T-cells 5 (NFAT5) is an essential transcription factor that induces osmoprotective genes such as aldose reductase (AR) and betaine-GABA transporter 1 (BGT1). High salt stress-mediated NFAT5 activation is also reported to accelerate the inflammatory response and autoimmune diseases. However, the systemic regulation of NFAT5 remains unclear. Here, we performed a genome-wide siRNA screen to comprehensively identify the regulators of NFAT5. We monitored NFAT5 nuclear translocation and identified one of the Notch signaling effectors, Hairy and enhancer of split-1 (HES1), as a positive regulator of NFAT5. HES1 was induced by high salinity via ERK signaling and facilitated NFAT5 recruitment to its target promoter region, resulting in the proper induction of osmoprotective genes and cytoprotection under high salt stress. These findings suggest that, though HES1 is well known as a transcriptional repressor, it positively regulates NFAT5-dependent transcription in the context of a high salinity/hyperosmotic response.
    DOI:  https://doi.org/10.1038/s42003-024-06997-7
  23. Mol Cells. 2024 Oct 07. pii: S1016-8478(24)00146-8. [Epub ahead of print] 100121
    Practical approaches for visualization of endogenous enhancer-promoter interactions in a single nucleus through chromatin labeling.
    Gunhee Park, Won-Ki Cho.
      Recent studies highlight the critical role of nuclear genome organization in regulating gene expression. Dynamic changes in the hierarchical structure of chromatin modulate transcription by influencing the recruitment of transcription factors and altering the epigenetic landscape. Among these regulatory mechanisms, enhancer-promoter (E-P) interactions are of particular importance. Enhancers physically interact with the promoters of target genes, a process mediated by various co-activators, which facilitates the transfer of enhancer-bound transcription factors and ultimately leads to transcriptional bursting. While next-generation sequencing techniques have provided significant insights into the features of E-P interactions, the effects of cell-to-cell heterogeneity and the physical dynamics of these interactions remain poorly understood due to the lack of spatiotemporal information. In this article, we introduce a platform that enables imaging-based approaches to visualize E-P interactions at the single-cell level.
    Keywords:  CRISPR; Chromatin labeling; E-P interaction; MS2 tagging; TetO-TetR
    DOI:  https://doi.org/10.1016/j.mocell.2024.100121
  24. NAR Genom Bioinform. 2024 Sep;6(4): lqae135
    scATAcat: cell-type annotation for scATAC-seq data.
    Aybuge Altay, Martin Vingron.
      Cells whose accessibility landscape has been profiled with scATAC-seq cannot readily be annotated to a particular cell type. In fact, annotating cell-types in scATAC-seq data is a challenging task since, unlike in scRNA-seq data, we lack knowledge of 'marker regions' which could be used for cell-type annotation. Current annotation methods typically translate accessibility to expression space and rely on gene expression patterns. We propose a novel approach, scATAcat, that leverages characterized bulk ATAC-seq data as prototypes to annotate scATAC-seq data. To mitigate the inherent sparsity of single-cell data, we aggregate cells that belong to the same cluster and create pseudobulk. To demonstrate the feasibility of our approach we collected a number of datasets with respective annotations to quantify the results and evaluate performance for scATAcat. scATAcat is available as a python package at https://github.com/aybugealtay/scATAcat.
    DOI:  https://doi.org/10.1093/nargab/lqae135
  25. Cell Rep. 2024 Oct 04. pii: S2211-1247(24)01171-9. [Epub ahead of print]43(10): 114820
    Base-excision repair pathway regulates transcription-replication conflicts in pancreatic ductal adenocarcinoma.
    Fan Meng, Tiane Li, Anup K Singh, Yingying Wang, Marc Attiyeh, Fatemeh Kohram, Qianhua Feng, Yun R Li, Binghui Shen, Terence Williams, Yilun Liu, Mustafa Raoof.
      Oncogenic mutations (such as in KRAS) can dysregulate transcription and replication, leading to transcription-replication conflicts (TRCs). Here, we demonstrate that TRCs are enriched in human pancreatic ductal adenocarcinoma (PDAC) compared to other common solid tumors or normal cells. Several orthogonal approaches demonstrated that TRCs are oncogene dependent. A small interfering RNA (siRNA) screen identified several factors in the base-excision repair (BER) pathway as main regulators of TRCs in PDAC cells. Inhibitors of BER pathway (methoxyamine and CRT) enhanced TRCs. Mechanistically, BER pathway inhibition severely altered RNA polymerase II (RNAPII) and R-loop dynamics at nascent DNA, causing RNAPII trapping and contributing to enhanced TRCs. The ensuing DNA damage activated the ATR-Chk1 pathway. Co-treatment with ATR inhibitor (VX970) and BER inhibitor (methoxyamine) at clinically relevant doses synergistically enhanced DNA damage and reduced cell proliferation in PDAC cells. The study provides mechanistic insights into the regulation of TRCs in PDAC by the BER pathway, which has biologic and therapeutic implications.
    Keywords:  ATR pathway; CP: Cancer; CP: Molecular biology; DNA repair; R-loops; base excision repair; oncogene-induced replication stress; pancreatic cancer; replication stress; transcription replication conflict
    DOI:  https://doi.org/10.1016/j.celrep.2024.114820
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