bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2023–08–20
nineteen papers selected by
Connor Rogerson, University of Cambridge
  1. High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription.
  2. Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression.
  3. Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC.
  4. SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data.
  5. Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms.
  6. Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency.
  7. Predicting the impact of sequence motifs on gene regulation using single-cell data.
  8. FOXA1 O-GlcNAcylation-mediated transcriptional switch governs metastasis capacity in breast cancer.
  9. GATA2 mitotic bookmarking is required for definitive haematopoiesis.
  10. Cell-specific and shared regulatory elements control a multigene locus active in mammary and salivary glands.
  11. Archival single-cell genomics reveals persistent subclones during DCIS progression.
  12. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.
  13. Inhibition of Ezh2 redistributes bivalent domains within transcriptional regulators associated with WNT and Hedgehog pathways in osteoblasts.
  14. In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis.
  15. RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation.
  16. Simultaneous profiling of chromatin architecture and transcription in single cells.
  17. KDM6A epigenetically regulates subtype plasticity in small cell lung cancer.
  18. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin.
  19. Transient naive reprogramming corrects hiPS cells functionally and epigenetically.
  1. Nat Commun. 2023 Aug 17. 14(1): 4971
    High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription.
    Annkatrin Bressin, Olga Jasnovidova, Mirjam Arnold, Elisabeth Altendorfer, Filip Trajkovski, Thomas A Kratz, Joanna E Handzlik, Denes Hnisz, Andreas Mayer.
      Gene transcription by RNA polymerase II (Pol II) is under control of promoters and distal regulatory elements known as enhancers. Enhancers are themselves transcribed by Pol II correlating with their activity. How enhancer transcription is regulated and coordinated with transcription at target genes has remained unclear. Here, we developed a high-sensitive native elongating transcript sequencing approach, called HiS-NET-seq, to provide an extended high-resolution view on transcription, especially at lowly transcribed regions such as enhancers. HiS-NET-seq uncovers new transcribed enhancers in human cells. A multi-omics analysis shows that genome-wide enhancer transcription depends on the BET family protein BRD4. Specifically, BRD4 co-localizes to enhancer and promoter-proximal gene regions, and is required for elongation activation at enhancers and their genes. BRD4 keeps a set of enhancers and genes in proximity through long-range contacts. From these studies BRD4 emerges as a general regulator of enhancer transcription that may link transcription at enhancers and genes.
    DOI:  https://doi.org/10.1038/s41467-023-40633-y
  2. Cell Rep. 2023 Aug 11. pii: S2211-1247(23)00990-7. [Epub ahead of print]42(8): 112979
    Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression.
    Xinhong Liu, Xiangzheng Liu, Yingxue Du, Di Zou, Chen Tian, Yong Li, Xun Lan, Charles J David, Qianwen Sun, Mo Chen.
      KRAS is the most commonly mutated oncogene in human cancer, and mutant KRAS is responsible for over 90% of pancreatic ductal adenocarcinoma (PDAC), the most lethal cancer. Here, we show that RNA polymerase II-associated factor 1 complex (PAF1C) is specifically required for survival of PDAC but not normal adult pancreatic cells. We show that PAF1C maintains cancer cell genomic stability by restraining overaccumulation of enhancer RNAs (eRNAs) and promoter upstream transcripts (PROMPTs) driven by mutant Kras. Loss of PAF1C leads to cancer-specific lengthening and accumulation of pervasive transcripts on chromatin and concomitant aberrant R-loop formation and DNA damage, which, in turn, trigger cell death. We go on to demonstrate that the global transcriptional hyperactivation driven by Kras signaling during tumorigenesis underlies the specific demand for PAF1C by cancer cells. Our work provides insights into how enhancer transcription hyperactivation causes general transcription factor addiction during tumorigenesis.
    Keywords:  CP: Cancer; CP: Molecular biology; DNA damage; PAF1 complex; R-loop; enhancer RNA; pancreatic ductal adenocarcinoma; transcription addiction
    DOI:  https://doi.org/10.1016/j.celrep.2023.112979
  3. Blood. 2023 Aug 18. pii: blood.2023021120. [Epub ahead of print]
    Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC.
    Shruthi Subramanian, Julie A I Thoms, Yizhou Huang, Carina Paola Cornejo Paramo, Forrest Charles Koch, Sebastien Jacquelin, Sylvie Shen, Emma Song, Swapna Joshi, Christopher Peter Brownlee, Petter S Woll, Diego Chacon-Fajardo, Dominik Beck, David J Curtis, Kenneth Yehson, Vicki Antonenas, Tracey O'Brien, Annette Trickett, Jason A Powell, Ian D Lewis, Stuart M Pitson, Maher K Gandhi, Steven W Lane, Fatemeh Vafaee, Emily Wong, Berthold Gottgens, Hamid Rokny, Jason Wing Hon Wong, John E Pimanda.
      Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - bind regulatory elements in bulk CD34+ HSPCs. However, whether specific heptad-TF combinations have distinct roles in regulating hematopoietic differentiation remained unknown. We mapped genome-wide chromatin contacts (HiC, H3K27ac HiChIP), chromatin modifications (H3K4me3, H3K27ac, H3K27me3) and 10 TF binding profiles (the Heptad, PU.1, CTCF, and STAG2) in HSPC subsets (HSC-MPP, CMP, GMP, MEP) and found that TF occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type-specific gene expression. Distinct regulatory elements were enriched with specific heptad-TF combinations, including stem-cell-specific elements with ERG, and myeloid- and erythroid-specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. Furthermore, heptad-occupied regions in HSPCs were subsequently bound by lineage-defining TFs such as PU.1 and GATA1, suggesting that heptad factors may prime regulatory elements for use in mature cell types. We also found that enhancers with cell-type-specific heptad occupancy shared a common grammar with respect to TF binding motifs, suggesting that combinatorial binding of specific TF complexes was at least partially regulated by features encoded in specific DNA sequence motifs. Taken together, this study provides a comprehensive characterisation of the gene regulatory landscape in rare subpopulations of human HSPCs. The accompanying datasets should serve as a valuable resource for understanding adult hematopoiesis and a framework for analysing aberrant regulatory networks in leukemic cells.
    DOI:  https://doi.org/10.1182/blood.2023021120
  4. Nat Commun. 2023 Aug 12. 14(1): 4873
    SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data.
    Lindsay Lee, Hongyu Yu, Bojing Blair Jia, Adam Jussila, Chenxu Zhu, Jiawen Chen, Liangqi Xie, Antonina Hafner, Shreya Mishra, Duan Dennis Wang, Caterina Strambio-De-Castillia, Alistair Boettiger, Bing Ren, Yun Li, Ming Hu.
      Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtains comparable results of chromatin loops across datasets generated from diverse imaging technologies. SnapFISH is freely available at https://github.com/HuMingLab/SnapFISH .
    DOI:  https://doi.org/10.1038/s41467-023-40658-3
  5. Mol Cell. 2023 Aug 08. pii: S1097-2765(23)00567-1. [Epub ahead of print]
    Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms.
    Kota Nagasaka, Iain F Davidson, Roman R Stocsits, Wen Tang, Gordana Wutz, Paul Batty, Melanie Panarotto, Gabriele Litos, Alexander Schleiffer, Daniel W Gerlich, Jan-Michael Peters.
      Cohesin connects CTCF-binding sites and other genomic loci in cis to form chromatin loops and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here, we describe a cohesin hinge mutant that can extrude DNA into loops but is unable to mediate cohesion in human cells. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin's cohesion and loop extrusion activities can be partially separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wild-type cohesin. This suggests that cohesion establishment and cohesin's interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.
    Keywords:  CTCF; DNA loop extrusion; TADs; chromatin architectures; cohesin; cohesion
    DOI:  https://doi.org/10.1016/j.molcel.2023.07.024
  6. Sci Adv. 2023 Aug 18. 9(33): eadg7997
    Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency.
    Fatemeh Mirzadeh Azad, Eduard A Struys, Victoria Wingert, Luciana Hannibal, Ken Mills, Joop H Jansen, Daniel B Longley, Hendrik G Stunnenberg, Yaser Atlasi.
      Understanding mechanisms of epigenetic regulation in embryonic stem cells (ESCs) is of fundamental importance for stem cell and developmental biology. Here, we identify Spic, a member of the ETS family of transcription factors (TFs), as a marker of ground state pluripotency. We show that Spic is rapidly induced in ground state ESCs and in response to extracellular signal-regulated kinase (ERK) inhibition. We find that SPIC binds to enhancer elements and stabilizes NANOG binding to chromatin, particularly at genes involved in choline/one-carbon (1C) metabolism such as Bhmt, Bhmt2, and Dmgdh. Gain-of-function and loss-of-function experiments revealed that Spic controls 1C metabolism and the flux of S-adenosyl methionine to S-adenosyl-L-homocysteine (SAM-to-SAH), thereby, modulating the levels of H3R17me2 and H3K4me3 histone marks in ESCs. Our findings highlight betaine-dependent 1C metabolism as a hallmark of ground state pluripotency primarily activated by SPIC. These findings underscore the role of uncharacterized auxiliary TFs in linking cellular metabolism to epigenetic regulation in ESCs.
    DOI:  https://doi.org/10.1126/sciadv.adg7997
  7. Genome Biol. 2023 08 15. 24(1): 189
    Predicting the impact of sequence motifs on gene regulation using single-cell data.
    Jacob Hepkema, Nicholas Keone Lee, Benjamin J Stewart, Siwat Ruangroengkulrith, Varodom Charoensawan, Menna R Clatworthy, Martin Hemberg.
      The binding of transcription factors at proximal promoters and distal enhancers is central to gene regulation. Identifying regulatory motifs and quantifying their impact on expression remains challenging. Using a convolutional neural network trained on single-cell data, we infer putative regulatory motifs and cell type-specific importance. Our model, scover, explains 29% of the variance in gene expression in multiple mouse tissues. Applying scover to distal enhancers identified using scATAC-seq from the developing human brain, we identify cell type-specific motif activities in distal enhancers. Scover can identify regulatory motifs and their importance from single-cell data where all parameters and outputs are easily interpretable.
    DOI:  https://doi.org/10.1186/s13059-023-03021-9
  8. Sci Adv. 2023 Aug 18. 9(33): eadg7112
    FOXA1 O-GlcNAcylation-mediated transcriptional switch governs metastasis capacity in breast cancer.
    Yajie Liu, Kairan Yu, Xiaotian Kong, Keren Zhang, Lingyan Wang, Nana Zhang, Qiushi Chen, Mingshan Niu, Wenli Li, Xiaomin Zhong, Sijin Wu, Jianing Zhang, Yubo Liu.
      FOXA1, a transcription factor involved in epigenetic reprogramming, is crucial for breast cancer progression. However, the mechanisms by which FOXA1 achieves its oncogenic functions remain elusive. Here, we demonstrate that the O-linked β-N-acetylglucosamine modification (O-GlcNAcylation) of FOXA1 promotes breast cancer metastasis by orchestrating the transcription of numerous metastasis regulators. O-GlcNAcylation at Thr432, Ser441, and Ser443 regulates the stability of FOXA1 and promotes its assembly with chromatin. O-GlcNAcylation shapes the FOXA1 interactome, especially triggering the recruitment of the transcriptional repressor methyl-CpG binding protein 2 and consequently stimulating FOXA1 chromatin-binding sites to switch to chromatin loci of adhesion-related genes, including EPB41L3 and COL9A2. Site-specific depletion of O-GlcNAcylation on FOXA1 affects the expression of various downstream genes and thus inhibits breast cancer proliferation and metastasis both in vitro and in vivo. Our data establish the importance of aberrant FOXA1 O-GlcNAcylation in breast cancer progression and indicate that targeting O-GlcNAcylation is a therapeutic strategy for metastatic breast cancer.
    DOI:  https://doi.org/10.1126/sciadv.adg7112
  9. Nat Commun. 2023 Aug 14. 14(1): 4645
    GATA2 mitotic bookmarking is required for definitive haematopoiesis.
    Rita Silvério-Alves, Ilia Kurochkin, Anna Rydström, Camila Vazquez Echegaray, Jakob Haider, Matthew Nicholls, Christina Rode, Louise Thelaus, Aida Yifter Lindgren, Alexandra Gabriela Ferreira, Rafael Brandão, Jonas Larsson, Marella F T R de Bruijn, Javier Martin-Gonzalez, Carlos-Filipe Pereira.
      In mitosis, most transcription factors detach from chromatin, but some are retained and bookmark genomic sites. Mitotic bookmarking has been implicated in lineage inheritance, pluripotency and reprogramming. However, the biological significance of this mechanism in vivo remains unclear. Here, we address mitotic retention of the hemogenic factors GATA2, GFI1B and FOS during haematopoietic specification. We show that GATA2 remains bound to chromatin throughout mitosis, in contrast to GFI1B and FOS, via C-terminal zinc finger-mediated DNA binding. GATA2 bookmarks a subset of its interphase targets that are co-enriched for RUNX1 and other regulators of definitive haematopoiesis. Remarkably, homozygous mice harbouring the cyclin B1 mitosis degradation domain upstream Gata2 partially phenocopy knockout mice. Degradation of GATA2 at mitotic exit abolishes definitive haematopoiesis at aorta-gonad-mesonephros, placenta and foetal liver, but does not impair yolk sac haematopoiesis. Our findings implicate GATA2-mediated mitotic bookmarking as critical for definitive haematopoiesis and highlight a dependency on bookmarkers for lineage commitment.
    DOI:  https://doi.org/10.1038/s41467-023-40391-x
  10. Nat Commun. 2023 Aug 17. 14(1): 4992
    Cell-specific and shared regulatory elements control a multigene locus active in mammary and salivary glands.
    Hye Kyung Lee, Michaela Willi, Chengyu Liu, Lothar Hennighausen.
      Regulation of high-density loci harboring genes with different cell-specificities remains a puzzle. Here we investigate a locus that evolved through gene duplication and contains eight genes and 20 candidate regulatory elements, including one super-enhancer. Casein genes (Csn1s1, Csn2, Csn1s2a, Csn1s2b, Csn3) are expressed in mammary glands, induced 10,000-fold during pregnancy and account for 50% of mRNAs during lactation, Prr27 and Fdcsp are salivary-specific and Odam has dual specificity. We probed the function of 12 candidate regulatory elements, individually and in combination, in the mouse genome. The super-enhancer is essential for the expression of Csn3, Csn1s2b, Odam and Fdcsp but largely dispensable for Csn1s1, Csn2 and Csn1s2a. Csn3 activation also requires its own local enhancer. Synergism between local enhancers and cytokine-responsive promoter elements facilitates activation of Csn2 during pregnancy. Our work identifies the regulatory complexity of a multigene locus with an ancestral super-enhancer active in mammary and salivary tissue and local enhancers and promoter elements unique to mammary tissue.
    DOI:  https://doi.org/10.1038/s41467-023-40712-0
  11. Cell. 2023 Aug 10. pii: S0092-8674(23)00802-4. [Epub ahead of print]
    Archival single-cell genomics reveals persistent subclones during DCIS progression.
    Grand Challenge PRECISION Consortium
      Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.
    Keywords:  Arc-well; FFPE material; archival samples; breast cancer; ductal carcinoma in situ recurrence; premalignancies; single-cell DNA sequencing; tumor evolution
    DOI:  https://doi.org/10.1016/j.cell.2023.07.024
  12. Mol Cell. 2023 Aug 17. pii: S1097-2765(23)00564-6. [Epub ahead of print]83(16): 2872-2883.e7
    Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.
    Stephen Abini-Agbomson, Kristjan Gretarsson, Rochelle M Shih, Laura Hsieh, Tracy Lou, Pablo De Ioannes, Nikita Vasilyev, Rachel Lee, Miao Wang, Matthew D Simon, Jean-Paul Armache, Evgeny Nudler, Geeta Narlikar, Shixin Liu, Chao Lu, Karim-Jean Armache.
      SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/H4K20me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation. It is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes, suggesting that the enzyme likely has uncharacterized non-catalytic activities. Our cryoelectron microscopy (cryo-EM), biochemical, biophysical, and cellular analyses reveal how SUV420H1 recognizes its nucleosome substrates, and how histone variant H2A.Z stimulates its catalytic activity. SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from the histone octamer, which is a non-catalytic activity. We hypothesize that this regulates the accessibility of large macromolecular complexes to chromatin. We show that SUV420H1 can promote chromatin condensation, another non-catalytic activity that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.
    Keywords:  DNA repair; H4K20 methylation; SUV420H1; chromatin; chromatin condensation; chromatin epigenetics; heterochromatin; histone lysine methyltransferase; histone variant H2A.Z; nucleosomes
    DOI:  https://doi.org/10.1016/j.molcel.2023.07.020
  13. J Biol Chem. 2023 Aug 10. pii: S0021-9258(23)02183-X. [Epub ahead of print] 105155
    Inhibition of Ezh2 redistributes bivalent domains within transcriptional regulators associated with WNT and Hedgehog pathways in osteoblasts.
    Margarita E Carrasco, Roman Thaler, Gino Nardocci, Amel Dudakovic, Andre J van Wijnen.
      Bivalent epigenomic regulatory domains containing both activating histone 3 lysine 4 (H3K4me3) and repressive lysine 27 (H3K27me3) trimethylation are associated with key developmental genes. These bivalent domains repress transcription in the absence of differentiation signals but maintain regulatory genes in a poised state to allow for timely activation. Previous studies demonstrated that enhancer of zeste homolog 2 (Ezh2), a histone 3 lysine 27 (H3K27) methyltransferase, suppresses osteogenic differentiation and that inhibition of Ezh2 enhances commitment of osteoblast progenitors in vitro and bone formation in vivo. Here, we examined the mechanistic effects of Tazemetostat (EPZ6438), an FDA approved Ezh2 inhibitor for epithelioid sarcoma treatment, because this drug could potentially be repurposed to stimulate osteogenesis for clinical indications. We find that Tazemetostat reduces H3K27me3 marks in bivalent domains in enhancers required for bone formation and stimulates maturation of MC3T3 pre-osteoblasts. Furthermore, Tazemetostat activates bivalent genes associated with the Wingless/Integrated (WNT), Adenylyl cyclase (cAMP) and Hedgehog (Hh) signaling pathways based on transcriptomic (RNA-seq) and epigenomic (ChIP-seq) data. Functional analyses using selective pathway inhibitors and silencing RNAs demonstrate that the WNT and Hh pathways modulate osteogenic differentiation after Ezh2 inhibition. Strikingly, we show that loss of the Hh-responsive transcriptional regulator Gli1, but not Gli2, synergizes with Tazemetostat to accelerate osteoblast differentiation. These studies establish epigenetic cooperativity of Ezh2, Hh-Gli1 signaling, and bivalent regulatory genes in suppressing osteogenesis. Our findings may have important translational ramifications for anabolic applications requiring bone mass accrual and/or reverse bone loss.
    Keywords:  Bivalent domains; EPZ6438; Ezh2; enhancer of zeste homolog; epigenetics; histone methylation; osteoblast; osteogenesis
    DOI:  https://doi.org/10.1016/j.jbc.2023.105155
  14. Nat Genet. 2023 Aug 14.
    In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis.
    David Lara-Astiaso, Ainhoa Goñi-Salaverri, Julen Mendieta-Esteban, Nisha Narayan, Cynthia Del Valle, Torsten Gross, George Giotopoulos, Tumas Beinortas, Mar Navarro-Alonso, Laura Pilar Aguado-Alvaro, Jon Zazpe, Francesco Marchese, Natalia Torrea, Isabel A Calvo, Cecile K Lopez, Diego Alignani, Aitziber Lopez, Borja Saez, Jake P Taylor-King, Felipe Prosper, Nikolaus Fortelny, Brian J P Huntly.
      Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.
    DOI:  https://doi.org/10.1038/s41588-023-01471-2
  15. Dev Cell. 2023 Aug 08. pii: S1534-5807(23)00365-9. [Epub ahead of print]
    RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation.
    Danya J Martell, Hope E Merens, Alexis Caulier, Claudia Fiorini, Jacob C Ulirsch, Robert Ietswaart, Karine Choquet, Giovanna Graziadei, Valentina Brancaleoni, Maria Domenica Cappellini, Caroline Scott, Nigel Roberts, Melanie Proven, Noémi B A Roy, Christian Babbs, Douglas R Higgs, Vijay G Sankaran, L Stirling Churchman.
      Controlled release of promoter-proximal paused RNA polymerase II (RNA Pol II) is crucial for gene regulation. However, studying RNA Pol II pausing is challenging, as pause-release factors are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H, which encodes SPT5, in individuals with β-thalassemia. During erythropoiesis in healthy human cells, cell cycle genes were highly paused as cells transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, RNA Pol II pause release was globally disrupted, and as cells began transitioning from progenitors to precursors, differentiation was delayed, accompanied by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, identifying a role for RNA Pol II pausing in temporally coordinating the cell cycle and erythroid differentiation.
    Keywords:  RNA Pol II pausing; SPT5; SUPT5H; cell cycle; differentiation; erythropoiesis; hemoglobin; human genetic variation; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.devcel.2023.07.018
  16. Nat Struct Mol Biol. 2023 Aug 14.
    Simultaneous profiling of chromatin architecture and transcription in single cells.
    Jiale Qu, Jun Sun, Cai Zhao, Xinyi Liu, Xinyao Zhang, Shaoshuai Jiang, Chao Wei, Haopeng Yu, Xiaoxi Zeng, Lili Fan, Junjun Ding.
      The three-dimensional structure of chromatin plays a crucial role in development and disease, both of which are associated with transcriptional changes. However, given the heterogeneity in single-cell chromatin architecture and transcription, the regulatory relationship between the three-dimensional chromatin structure and gene expression is difficult to explain based on bulk cell populations. Here we develop a single-cell, multimodal, omics method allowing the simultaneous detection of chromatin architecture and messenger RNA expression by sequencing (single-cell transcriptome sequencing (scCARE-seq)). Applying scCARE-seq to examine chromatin architecture and transcription from 2i to serum single mouse embryonic stem cells, we observe improved separation of cell clusters compared with single-cell chromatin conformation capture. In addition, after defining the cell-cycle phase of each cell through chromatin architecture extracted by scCARE-seq, we find that periodic changes in chromatin architecture occur in parallel with transcription during the cell cycle. These findings highlight the potential of scCARE-seq to facilitate comprehensive analyses that may boost our understanding of chromatin architecture and transcription in the same single cell.
    DOI:  https://doi.org/10.1038/s41594-023-01066-9
  17. Nat Cell Biol. 2023 Aug 17.
    KDM6A epigenetically regulates subtype plasticity in small cell lung cancer.
    Leslie Duplaquet, Yixiang Li, Matthew A Booker, Yingtian Xie, Sarah Naomi Olsen, Radhika A Patel, Deli Hong, Charlie Hatton, Thomas Denize, Emily Walton, Yasmin N Laimon, Rong Li, Yijia Jiang, Roderick T Bronson, Jackson Southard, Shuqiang Li, Sabina Signoretti, Xintao Qiu, Paloma Cejas, Scott A Armstrong, Henry W Long, Michael Y Tolstorukov, Michael C Haffner, Matthew G Oser.
      Small cell lung cancer (SCLC) exists broadly in four molecular subtypes: ASCL1, NEUROD1, POU2F3 and Inflammatory. Initially, SCLC subtypes were thought to be mutually exclusive, but recent evidence shows intra-tumoural subtype heterogeneity and plasticity between subtypes. Here, using a CRISPR-based autochthonous SCLC genetically engineered mouse model to study the consequences of KDM6A/UTX inactivation, we show that KDM6A inactivation induced plasticity from ASCL1 to NEUROD1 resulting in SCLC tumours that express both ASCL1 and NEUROD1. Mechanistically, KDM6A normally maintains an active chromatin state that favours the ASCL1 subtype with its loss decreasing H3K4me1 and increasing H3K27me3 at enhancers of neuroendocrine genes leading to a cell state that is primed for ASCL1-to-NEUROD1 subtype switching. This work identifies KDM6A as an epigenetic regulator that controls ASCL1 to NEUROD1 subtype plasticity and provides an autochthonous SCLC genetically engineered mouse model to model ASCL1 and NEUROD1 subtype heterogeneity and plasticity, which is found in 35-40% of human SCLCs.
    DOI:  https://doi.org/10.1038/s41556-023-01210-z
  18. Cancer Cell. 2023 Aug 13. pii: S1535-6108(23)00253-2. [Epub ahead of print]
    Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin.
    Clinical Proteomic Tumor Analysis Consortium
      DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development and is closely intertwined with other genetic alterations. Here, we leveraged multi-omic profiling of 687 tumors and matched non-involved adjacent tissues from the kidney, brain, pancreas, lung, head and neck, and endometrium to identify aberrant methylation associated with RNA and protein abundance changes and build a Pan-Cancer catalog. We uncovered lineage-specific epigenetic drivers including hypomethylated FGFR2 in endometrial cancer. We showed that hypermethylated STAT5A is associated with pervasive regulon downregulation and immune cell depletion, suggesting that epigenetic regulation of STAT5A expression constitutes a molecular switch for immunosuppression in squamous tumors. We further demonstrated that methylation subtype-enrichment information can explain cell-of-origin, intra-tumor heterogeneity, and tumor phenotypes. Overall, we identified cis-acting DNA methylation events that drive transcriptional and translational changes, shedding light on the tumor's epigenetic landscape and the role of its cell-of-origin.
    DOI:  https://doi.org/10.1016/j.ccell.2023.07.013
  19. Nature. 2023 Aug 16.
    Transient naive reprogramming corrects hiPS cells functionally and epigenetically.
    Sam Buckberry, Xiaodong Liu, Daniel Poppe, Jia Ping Tan, Guizhi Sun, Joseph Chen, Trung Viet Nguyen, Alex de Mendoza, Jahnvi Pflueger, Thomas Frazer, Dulce B Vargas-Landín, Jacob M Paynter, Nathan Smits, Ning Liu, John F Ouyang, Fernando J Rossello, Hun S Chy, Owen J L Rackham, Andrew L Laslett, James Breen, Geoffrey J Faulkner, Christian M Nefzger, Jose M Polo, Ryan Lister.
      Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function1-8. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.
    DOI:  https://doi.org/10.1038/s41586-023-06424-7
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