bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2024–01–07
twenty-two papers selected by
Connor Rogerson, University of Cambridge
  1. Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.
  2. Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions.
  3. Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.
  4. Single-cell joint profiling of multiple epigenetic proteins and gene transcription.
  5. p300 is an obligate integrator of combinatorial transcription factor inputs.
  6. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation.
  7. DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation.
  8. Repression of latent NF-κB enhancers by PDX1 regulates β cell functional heterogeneity.
  9. Histone lactylation couples cellular metabolism with developmental gene regulatory networks.
  10. The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer.
  11. FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy.
  12. Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage.
  13. Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.
  14. Structure of the ISW1a complex bound to the dinucleosome.
  15. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex.
  16. Chromatin gene-gene loops support the cross-regulation of genes with related function.
  17. Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors.
  18. DNA looping mediates cooperative transcription activation.
  19. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology.
  20. Pioneer factor Pax7 initiates two-step cell-cycle-dependent chromatin opening.
  21. STAT3 and SOX-5 induce BRG1-mediated chromatin remodeling of RORCE2 in Th17 cells.
  22. Power-law behavior of transcriptional bursting regulated by enhancer-promoter communication.
  1. Genome Biol. 2024 Jan 02. 25(1): 2
    Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.
    George Hunt, Roshan Vaid, Sergei Pirogov, Alexander Pfab, Christoph Ziegenhain, Rickard Sandberg, Johan Reimegård, Mattias Mannervik.
       BACKGROUND: Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhancers and promoters in a chromatin context, but how the chromatin landscape influences transcription is not fully understood.
    RESULTS: Here we comprehensively resolve differential transcriptional and chromatin states during Drosophila DV patterning. We find that RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue-invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues.
    CONCLUSIONS: The data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. Our results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues.
    DOI:  https://doi.org/10.1186/s13059-023-03135-0
  2. Nat Commun. 2024 Jan 02. 15(1): 15
    Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions.
    Phoebe Lut Fei Tam, Ming Fung Cheung, Lu Yan Chan, Danny Leung.
      SETDB1 is an essential histone methyltransferase that deposits histone H3 lysine 9 trimethylation (H3K9me3) to transcriptionally repress genes and repetitive elements. The function of differential H3K9me3 enrichment between cell-types remains unclear. Here, we demonstrate mutual exclusivity of H3K9me3 and CTCF across mouse tissues from different developmental timepoints. We analyze SETDB1 depleted cells and discover that H3K9me3 prevents aberrant CTCF binding independently of DNA methylation and H3K9me2. Such sites are enriched with SINE B2 retrotransposons. Moreover, analysis of higher-order genome architecture reveals that large chromatin structures including topologically associated domains and subnuclear compartments, remain intact in SETDB1 depleted cells. However, chromatin loops and local 3D interactions are disrupted, leading to transcriptional changes by modifying pre-existing chromatin landscapes. Specific genes with altered expression show differential interactions with dysregulated cis-regulatory elements. Collectively, we find that cell-type specific targets of SETDB1 maintain cellular identities by modulating CTCF binding, which shape nuclear architecture and transcriptomic networks.
    DOI:  https://doi.org/10.1038/s41467-023-44578-0
  3. Nat Commun. 2024 Jan 02. 15(1): 35
    Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.
    Linhua Sun, Jingru Zhou, Xiao Xu, Yi Liu, Ni Ma, Yutong Liu, Wenchao Nie, Ling Zou, Xing Wang Deng, Hang He.
      Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.
    DOI:  https://doi.org/10.1038/s41467-023-44347-z
  4. Sci Adv. 2024 Jan 05. 10(1): eadi3664
    Single-cell joint profiling of multiple epigenetic proteins and gene transcription.
    Haiqing Xiong, Qianhao Wang, Chen C Li, Aibin He.
      Sculpting the epigenome with a combination of histone modifications and transcription factor occupancy determines gene transcription and cell fate specification. Here, we first develop uCoTarget, utilizing a split-pool barcoding strategy for realizing ultrahigh-throughput single-cell joint profiling of multiple epigenetic proteins. Through extensive optimization for sensitivity and multimodality resolution, we demonstrate that uCoTarget enables simultaneous detection of five histone modifications (H3K27ac, H3K4me3, H3K4me1, H3K36me3, and H3K27me3) in 19,860 single cells. We applied uCoTarget to the in vitro generation of hematopoietic stem/progenitor cells (HSPCs) from human embryonic stem cells, presenting multimodal epigenomic profiles in 26,418 single cells. uCoTarget reveals establishment of pairing of HSPC enhancers (H3K27ac) and promoters (H3K4me3) and RUNX1 engagement priming for H3K27ac activation along the HSPC path. We then develop uCoTargetX, an expansion of uCoTarget to simultaneously measure transcriptome and multiple epigenome targets. Together, our methods enable generalizable, versatile multimodal profiles for reconstructing comprehensive epigenome and transcriptome landscapes and analyzing the regulatory interplay at single-cell level.
    DOI:  https://doi.org/10.1126/sciadv.adi3664
  5. Mol Cell. 2023 Dec 19. pii: S1097-2765(23)01023-7. [Epub ahead of print]
    p300 is an obligate integrator of combinatorial transcription factor inputs.
    John J Ferrie, Jonathan P Karr, Thomas G W Graham, Gina M Dailey, Gloria Zhang, Robert Tjian, Xavier Darzacq.
      Transcription coactivators are proteins or protein complexes that mediate transcription factor (TF) function. However, they lack DNA-binding capacity, prompting the question of how they engage target loci. Three non-exclusive hypotheses have been posited: coactivators are recruited by complexing with TFs, by binding histones through epigenetic reader domains, or by partitioning into condensates through their extensive intrinsically disordered regions. Using p300 as a prototypical coactivator, we systematically mutated its annotated domains and show by single-molecule tracking in live U2OS cells that coactivator-chromatin binding depends entirely on combinatorial binding of multiple TF-interaction domains. Furthermore, we demonstrate that acetyltransferase activity opposes p300-chromatin association and that the N-terminal TF-interaction domains regulate that activity. Single TF-interaction domains are insufficient for chromatin binding and regulation of catalytic activity, implying a principle that we speculate could broadly apply to eukaryotic gene regulation: a TF must act in coordination with other TFs to recruit coactivator activity.
    Keywords:  coactivator; gene regulation; live-cell imaging; p300; single-molecule tracking; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2023.12.004
  6. Nat Cell Biol. 2024 Jan 05.
    Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation.
    Carmen Bravo González-Blas, Irina Matetovici, Hanne Hillen, Ibrahim Ihsan Taskiran, Roel Vandepoel, Valerie Christiaens, Leticia Sansores-García, Elisabeth Verboven, Gert Hulselmans, Suresh Poovathingal, Jonas Demeulemeester, Nikoleta Psatha, David Mauduit, Georg Halder, Stein Aerts.
      In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulatory code. Here, using a combination of single-cell multiomics, spatial omics, massively parallel reporter assays and deep learning, we mapped enhancer-gene regulatory networks across mouse liver cell types. We found that zonation affects gene expression and chromatin accessibility in hepatocytes, among other cell types. These states are driven by the repressors TCF7L1 and TBX3, alongside other core hepatocyte transcription factors, such as HNF4A, CEBPA, FOXA1 and ONECUT1. To examine the architecture of the enhancers driving these cell states, we trained a hierarchical deep learning model called DeepLiver. Our study provides a multimodal understanding of the regulatory code underlying hepatocyte identity and their zonation state that can be used to engineer enhancers with specific activity levels and zonation patterns.
    DOI:  https://doi.org/10.1038/s41556-023-01316-4
  7. Nat Struct Mol Biol. 2024 Jan 04.
    DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation.
    Mathieu Schulz, Aurélie Teissandier, Elena De La Mata Santaella, Mélanie Armand, Julian Iranzo, Fatima El Marjou, Pierre Gestraud, Marius Walter, Sarah Kinston, Berthold Göttgens, Maxim V C Greenberg, Deborah Bourc'his.
      As embryonic stem cells (ESCs) transition from naive to primed pluripotency during early mammalian development, they acquire high DNA methylation levels. During this transition, the germline is specified and undergoes genome-wide DNA demethylation, while emergence of the three somatic germ layers is preceded by acquisition of somatic DNA methylation levels in the primed epiblast. DNA methylation is essential for embryogenesis, but the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Here, using culture modeling of cellular transitions, we found that DNA methylation-free mouse ESCs with triple DNA methyltransferase knockout (TKO) progressed through the continuum of pluripotency states but demonstrated skewed differentiation abilities toward neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells, even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that neural and germline lineages are linked by a similar enhancer dynamic upon exit from the naive state, defined by common sets of transcription factors, including methyl-sensitive ones, that fail to be decommissioned in the absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of the preferred differentiation route during early development.
    DOI:  https://doi.org/10.1038/s41594-023-01162-w
  8. Cell Metab. 2024 Jan 02. pii: S1550-4131(23)00451-5. [Epub ahead of print]36(1): 90-102.e7
    Repression of latent NF-κB enhancers by PDX1 regulates β cell functional heterogeneity.
    Benjamin J Weidemann, Biliana Marcheva, Mikoto Kobayashi, Chiaki Omura, Marsha V Newman, Yumiko Kobayashi, Nathan J Waldeck, Mark Perelis, Louise Lantier, Owen P McGuinness, Kathryn Moynihan Ramsey, Roland W Stein, Joseph Bass.
      Interactions between lineage-determining and activity-dependent transcription factors determine single-cell identity and function within multicellular tissues through incompletely known mechanisms. By assembling a single-cell atlas of chromatin state within human islets, we identified β cell subtypes governed by either high or low activity of the lineage-determining factor pancreatic duodenal homeobox-1 (PDX1). β cells with reduced PDX1 activity displayed increased chromatin accessibility at latent nuclear factor κB (NF-κB) enhancers. Pdx1 hypomorphic mice exhibited de-repression of NF-κB and impaired glucose tolerance at night. Three-dimensional analyses in tandem with chromatin immunoprecipitation (ChIP) sequencing revealed that PDX1 silences NF-κB at circadian and inflammatory enhancers through long-range chromatin contacts involving SIN3A. Conversely, Bmal1 ablation in β cells disrupted genome-wide PDX1 and NF-κB DNA binding. Finally, antagonizing the interleukin (IL)-1β receptor, an NF-κB target, improved insulin secretion in Pdx1 hypomorphic islets. Our studies reveal functional subtypes of single β cells defined by a gradient in PDX1 activity and identify NF-κB as a target for insulinotropic therapy.
    Keywords:  IL-1β; NF-κB; PDX1; chromatin; circadian; diabetes; inflammation; insulin; p65; β cells
    DOI:  https://doi.org/10.1016/j.cmet.2023.11.018
  9. Nat Commun. 2024 Jan 02. 15(1): 90
    Histone lactylation couples cellular metabolism with developmental gene regulatory networks.
    Fjodor Merkuri, Megan Rothstein, Marcos Simoes-Costa.
      Embryonic cells exhibit diverse metabolic states. Recent studies have demonstrated that metabolic reprogramming drives changes in cell identity by affecting gene expression. However, the connection between cellular metabolism and gene expression remains poorly understood. Here we report that glycolysis-regulated histone lactylation couples the metabolic state of embryonic cells with chromatin organization and gene regulatory network (GRN) activation. We found that lactylation marks genomic regions of glycolytic embryonic tissues, like the neural crest (NC) and pre-somitic mesoderm. Histone lactylation occurs in the loci of NC genes as these cells upregulate glycolysis. This process promotes the accessibility of active enhancers and the deployment of the NC GRN. Reducing the deposition of the mark by targeting LDHA/B leads to the downregulation of NC genes and the impairment of cell migration. The deposition of lactyl-CoA on histones at NC enhancers is supported by a mechanism that involves transcription factors SOX9 and YAP/TEAD. These findings define an epigenetic mechanism that integrates cellular metabolism with the GRNs that orchestrate embryonic development.
    DOI:  https://doi.org/10.1038/s41467-023-44121-1
  10. Nat Struct Mol Biol. 2024 Jan 05.
    The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer.
    Joanna Achinger-Kawecka, Clare Stirzaker, Neil Portman, Elyssa Campbell, Kee-Ming Chia, Qian Du, Geraldine Laven-Law, Shalima S Nair, Aliza Yong, Ashleigh Wilkinson, Samuel Clifton, Heloisa H Milioli, Sarah Alexandrou, C Elizabeth Caldon, Jenny Song, Amanda Khoury, Braydon Meyer, Wenhan Chen, Ruth Pidsley, Wenjia Qu, Julia M W Gee, Anthony Schmitt, Emily S Wong, Theresa E Hickey, Elgene Lim, Susan J Clark.
      Three-dimensional (3D) epigenome remodeling is an important mechanism of gene deregulation in cancer. However, its potential as a target to counteract therapy resistance remains largely unaddressed. Here, we show that epigenetic therapy with decitabine (5-Aza-mC) suppresses tumor growth in xenograft models of pre-clinical metastatic estrogen receptor positive (ER+) breast tumor. Decitabine-induced genome-wide DNA hypomethylation results in large-scale 3D epigenome deregulation, including de-compaction of higher-order chromatin structure and loss of boundary insulation of topologically associated domains. Significant DNA hypomethylation associates with ectopic activation of ER-enhancers, gain in ER binding, creation of new 3D enhancer-promoter interactions and concordant up-regulation of ER-mediated transcription pathways. Importantly, long-term withdrawal of epigenetic therapy partially restores methylation at ER-enhancer elements, resulting in a loss of ectopic 3D enhancer-promoter interactions and associated gene repression. Our study illustrates the potential of epigenetic therapy to target ER+ endocrine-resistant breast cancer by DNA methylation-dependent rewiring of 3D chromatin interactions, which are associated with the suppression of tumor growth.
    DOI:  https://doi.org/10.1038/s41594-023-01181-7
  11. Nat Cell Biol. 2024 Jan 04.
    FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy.
    Vera A van der Weijden, Maximilian Stötzel, Dhanur P Iyer, Beatrix Fauler, Elzbieta Gralinska, Mohammed Shahraz, David Meierhofer, Martin Vingron, Steffen Rulands, Theodore Alexandrov, Thorsten Mielke, Aydan Bulut-Karslioglu.
      Mammalian developmental timing is adjustable in vivo by preserving pre-implantation embryos in a dormant state called diapause. Inhibition of the growth regulator mTOR (mTORi) pauses mouse development in vitro, yet how embryonic dormancy is maintained is not known. Here we show that mouse embryos in diapause are sustained by using lipids as primary energy source. In vitro, supplementation of embryos with the metabolite L-carnitine balances lipid consumption, puts the embryos in deeper dormancy and boosts embryo longevity. We identify FOXO1 as an essential regulator of the energy balance in dormant embryos and propose, through meta-analyses of dormant cell signatures, that it may be a common regulator of dormancy across adult tissues. Our results lift a constraint on in vitro embryo survival and suggest that lipid metabolism may be a critical metabolic transition relevant for longevity and stem cell function across tissues.
    DOI:  https://doi.org/10.1038/s41556-023-01325-3
  12. iScience. 2024 Jan 19. 27(1): 108624
    Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage.
    Alexandra Mancheno-Ferris, Clément Immarigeon, Alexia Rivero, David Depierre, Naomi Schickele, Olivier Fosseprez, Nicolas Chanard, Gabriel Aughey, Priscilla Lhoumaud, Julien Anglade, Tony Southall, Serge Plaza, François Payre, Olivier Cuvier, Cédric Polesello.
      The transcription factor Shavenbaby (Svb), the only member of the OvoL family in Drosophila, controls the fate of various epithelial embryonic cells and adult stem cells. Post-translational modification of Svb produces two protein isoforms, Svb-ACT and Svb-REP, which promote adult intestinal stem cell renewal or differentiation, respectively. To define Svb mode of action, we used engineered cell lines and develop an unbiased method to identify Svb target genes across different contexts. Within a given cell type, Svb-ACT and Svb-REP antagonistically regulate the expression of a set of target genes, binding specific enhancers whose accessibility is constrained by chromatin landscape. Reciprocally, Svb-REP can influence local chromatin marks of active enhancers to help repressing target genes. Along the intestinal lineage, the set of Svb target genes progressively changes, together with chromatin accessibility. We propose that Svb-ACT-to-REP transition promotes enterocyte differentiation of intestinal stem cells through direct gene regulation and chromatin remodeling.
    Keywords:  Cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2023.108624
  13. Nat Struct Mol Biol. 2024 Jan 04.
    Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.
    Yunye Zhu, Irina O Vvedenskaya, Sing-Hoi Sze, Bryce E Nickels, Craig D Kaplan.
      Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, nucleoside triphosphate substrate levels and RNA polymerase II (Pol II) activity to TSS selection by 'promoter scanning' in Saccharomyces cerevisiae (Pol II MAssively Systematic Transcript End Readout, 'Pol II MASTER'). Using Pol II MASTER, we measure the efficiency of Pol II initiation at 1,000,000 individual TSS sequences in a defined promoter context. Pol II MASTER confirms proposed critical qualities of S. cerevisiae TSS -8, -1 and +1 positions, quantitatively, in a controlled promoter context. Pol II MASTER extends quantitative analysis to surrounding sequences and determines that they tune initiation over a wide range of efficiencies. These results enabled the development of a predictive model for initiation efficiency based on sequence. We show that genetic perturbation of Pol II catalytic activity alters initiation efficiency mostly independently of TSS sequence, but selectively modulates preference for the initiating nucleotide. Intriguingly, we find that Pol II initiation efficiency is directly sensitive to guanosine-5'-triphosphate levels at the first five transcript positions and to cytosine-5'-triphosphate and uridine-5'-triphosphate levels at the second position genome wide. These results suggest individual nucleoside triphosphate levels can have transcript-specific effects on initiation, representing a cryptic layer of potential regulation at the level of Pol II biochemical properties. The results establish Pol II MASTER as a method for quantitative dissection of transcription initiation in eukaryotes.
    DOI:  https://doi.org/10.1038/s41594-023-01171-9
  14. Nat Struct Mol Biol. 2024 Jan 04.
    Structure of the ISW1a complex bound to the dinucleosome.
    Lifei Li, Kangjing Chen, Youyang Sia, Pengjing Hu, Youpi Ye, Zhucheng Chen.
      Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment.
    DOI:  https://doi.org/10.1038/s41594-023-01174-6
  15. Cell Rep. 2024 Jan 03. pii: S2211-1247(23)01650-9. [Epub ahead of print]43(1): 113639
    Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex.
    Etienne Dubiez, Erika Pellegrini, Maja Finderup Brask, William Garland, Anne-Emmanuelle Foucher, Karine Huard, Torben Heick Jensen, Stephen Cusack, Jan Kadlec.
      The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes with diverse "effectors" that promote either productive or destructive outcomes. Combining AlphaFold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18, and other effectors compete for binding to ARS2. In ternary CBC-ARS2 complexes with PHAX, NCBP3, or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.
    Keywords:  CP: Molecular biology; RNA biogenesis; RNA degradation; cryo-EM; protein complexes
    DOI:  https://doi.org/10.1016/j.celrep.2023.113639
  16. Mol Cell. 2023 Dec 21. pii: S1097-2765(23)01042-0. [Epub ahead of print]
    Chromatin gene-gene loops support the cross-regulation of genes with related function.
    Tim Pollex, Raquel Marco-Ferreres, Lucia Ciglar, Yad Ghavi-Helm, Adam Rabinowitz, Rebecca Rodriguez Viales, Christoph Schaub, Aleksander Jankowski, Charles Girardot, Eileen E M Furlong.
      Chromatin loops between gene pairs have been observed in diverse contexts in both flies and vertebrates. Combining high-resolution Capture-C, DNA fluorescence in situ hybridization, and genetic perturbations, we dissect the functional role of three loops between genes with related function during Drosophila embryogenesis. By mutating the loop anchor (but not the gene) or the gene (but not loop anchor), we disentangle loop formation and gene expression and show that the 3D proximity of paralogous gene loci supports their co-regulation. Breaking the loop leads to either an attenuation or enhancement of expression and perturbs their relative levels of expression and cross-regulation. Although many loops appear constitutive across embryogenesis, their function can change in different developmental contexts. Taken together, our results indicate that chromatin gene-gene loops act as architectural scaffolds that can be used in different ways in different contexts to fine-tune the coordinated expression of genes with related functions and sustain their cross-regulation.
    Keywords:  Hi-C; TADs; chromatin loops; chromatin organization; cross-regulation; embryogenesis; gene expression; genome topology; paralogs; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2023.12.023
  17. Cell Rep. 2023 Dec 30. pii: S2211-1247(23)01640-6. [Epub ahead of print]43(1): 113629
    Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors.
    Dimitris Karagiannis, Warren Wu, Albert Li, Makiko Hayashi, Xiao Chen, Michaela Yip, Vaibhav Mangipudy, Xinjing Xu, Francisco J Sánchez-Rivera, Yadira M Soto-Feliciano, Jiangbin Ye, Thales Papagiannakopoulos, Chao Lu.
      The interplay between metabolism and chromatin signaling is implicated in cancer progression. However, whether and how metabolic reprogramming in tumors generates chromatin vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor aberrant activation of the NRF2 antioxidant pathway, which drives aggressive and chemo-resistant disease. Using a chromatin-focused CRISPR screen, we report that NRF2 activation sensitizes LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDACs). This association is observed across cultured cells, mouse models, and patient-derived xenografts. Integrative epigenomic, transcriptomic, and metabolomic analysis demonstrates that HDAC inhibition causes widespread redistribution of H4ac and its reader protein, which transcriptionally downregulates metabolic enzymes. This results in reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest NRF2 activation as a potential biomarker for effective repurposing of HDAC inhibitors to treat solid tumors.
    Keywords:  CP: Cancer; HDAC inhibitors; NRF2 pathway; cancer epigenetics; cancer metabolism; cancer targeted therapy; epigenetic reprogramming; lung cancer
    DOI:  https://doi.org/10.1016/j.celrep.2023.113629
  18. Nat Struct Mol Biol. 2024 Jan 04.
    DNA looping mediates cooperative transcription activation.
    Shu-Jing Han, Yong-Liang Jiang, Lin-Lin You, Li-Qiang Shen, Xiaoxian Wu, Feng Yang, Ning Cui, Wen-Wen Kong, Hui Sun, Ke Zhou, Hui-Chao Meng, Zhi-Peng Chen, Yuxing Chen, Yu Zhang, Cong-Zhao Zhou.
      Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria.
    DOI:  https://doi.org/10.1038/s41594-023-01149-7
  19. Development. 2024 Jan 01. pii: dev202249. [Epub ahead of print]151(1):
    Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology.
    Jared A Tangeman, Sofia M Rebull, Erika Grajales-Esquivel, Jacob M Weaver, Stacy Bendezu-Sayas, Michael L Robinson, Salil A Lachke, Katia Del Rio-Tsonis.
      Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataracts. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq and CUT&RUN-seq to discover previously unreported mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Furthermore, we identify an epigenetic paradigm of cellular differentiation, defined by progressive loss of the H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
    Keywords:  FGF; Lens; MAF; Multiomics; PRC2; Single-cell
    DOI:  https://doi.org/10.1242/dev.202249
  20. Nat Struct Mol Biol. 2024 Jan 04.
    Pioneer factor Pax7 initiates two-step cell-cycle-dependent chromatin opening.
    Arthur Gouhier, Justine Dumoulin-Gagnon, Vincent Lapointe-Roberge, Juliette Harris, Aurelio Balsalobre, Jacques Drouin.
      Pioneer transcription factors direct cell differentiation by deploying new enhancer repertoires through their unique ability to target and initiate remodelling of closed chromatin. The initial steps of their action remain undefined, although pioneers have been shown to interact with nucleosomal target DNA and with some chromatin-remodeling complexes. We now define the sequence of events that enables the pioneer Pax7 with its unique abilities. Chromatin condensation exerted by linker histone H1 is the first constraint on Pax7 recruitment, and this establishes the initial speed of chromatin remodeling. The first step of pioneer action involves recruitment of the KDM1A (LSD1) H3K9me2 demethylase for removal of this repressive mark, as well as recruitment of the MLL complex for deposition of the activating H3K4me1 mark. Further progression of pioneer action requires passage through cell division, and this involves dissociation of pioneer targets from perinuclear lamin B. Only then are the SWI-SNF remodeling complex and the coactivator p300 recruited, leading to nucleosome displacement and enhancer activation. Thus, the unique features of pioneer actions are those occurring in the lamin-associated compartment of the nucleus. This model is consistent with previous work that showed a dependence on cell division for establishment of new cell fates.
    DOI:  https://doi.org/10.1038/s41594-023-01152-y
  21. Commun Biol. 2024 Jan 03. 7(1): 10
    STAT3 and SOX-5 induce BRG1-mediated chromatin remodeling of RORCE2 in Th17 cells.
    Xian Wang, Chao Han, Di Yang, Jian Zhou, Hui Dong, Zhiyuan Wei, Shuai Xu, Chen Xu, Yiwei Zhang, Yi Sun, Bing Ni, Sheng Guo, Jingbo Zhang, Tingting Zhao, Xiangmei Chen, Jie Luo, Yuzhang Wu, Yi Tian.
      Retinoid-related orphan receptor gamma t (RORγt) is the lineage-specific transcription factor for T helper 17 (Th17) cells. Our previous study demonstrated that STAT3 likely participates in the activation of RORCE2 (a novel enhancer of the RORγt gene) in Th17 cells. However, the detailed mechanism is still unclear. Here, we demonstrate that both STAT3 and SOX-5 mediate the enhancer activity of RORCE2 in vitro. Deletion of the STAT3 binding site (STAT3-BS) in RORCE2 impaired RORγt expression and Th17 differentiation, resulting in reduced severity of experimental autoimmune encephalomyelitis (EAE). Mechanistically, STAT3 and SOX-5 bind the RORCE2 region and recruit the chromatin remodeling factor BRG1 to remodel the nucleosomes positioned at this region. Collectively, our data suggest that STAT3 and SOX-5 mediate the differentiation of Th17 cells through the induction of BRG1-mediated chromatin remodeling of RORCE2 in Th17 cells.
    DOI:  https://doi.org/10.1038/s42003-023-05735-9
  22. Genome Res. 2024 Jan 03. pii: gr.278631.123. [Epub ahead of print]
    Power-law behavior of transcriptional bursting regulated by enhancer-promoter communication.
    Zihao Wang, Zhenquan Zhang, Songhao Luo, Tianshou Zhou, Jiajun Zhang.
      Revealing how transcriptional bursting kinetics is genomically encoded is challenging since genome structures are stochastic at the organization level and are suggestively linked to gene transcription. To address this challenge, we develop a generic theoretical framework that integrates chromatin dynamics, enhancer-promoter (E-P) communication and gene-state switching, to study transcriptional bursting. The theory predicts that power law can be a general rule to quantitatively describe bursting modulations by E-P spatial communication. Specifically, burst frequency and burst size are up-regulated by E-P communication strength, following power laws with positive exponents. Analysis of the scaling exponents further reveals that burst frequency is preferentially regulated. Bursting kinetics are down-regulated by E-P genomic distance with negative power-law exponents, and this negative modulation desensitizes at large distances. The mutual information between burst frequency (or burst size) and E-P spatial distance further reveals essential characteristics of the information transfer from E-P communication to transcriptional bursting kinetics. These findings, which are in agreement with experimental observations, not only reveal fundamental principles of E-P communication in transcriptional bursting but also are essential for understanding cellular decision-making.
    DOI:  https://doi.org/10.1101/gr.278631.123
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