bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2023–07–02
27 papers selected by
Connor Rogerson, University of Cambridge
  1. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53.
  2. Universal chromatin state annotation of the mouse genome.
  3. Transcription activator WCC recruits deacetylase HDA3 to control transcription dynamics and bursting in Neurospora.
  4. RAD21 is the core subunit of the cohesin complex involved in directing genome organization.
  5. MLL methyltransferases regulate H3K4 methylation to ensure CENP-A assembly at human centromeres.
  6. Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape.
  7. Carm1-arginine methylation of the transcription factor C/EBPα regulates transdifferentiation velocity.
  8. Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex function during cellular differentiation.
  9. Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells.
  10. ExplaiNN: interpretable and transparent neural networks for genomics.
  11. Integrative dissection of gene regulatory elements at base resolution.
  12. Structural insights into human co-transcriptional capping.
  13. A multi-omics atlas of the human retina at single-cell resolution.
  14. Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling.
  15. Early chromosome condensation by XIST builds A-repeat RNA density that facilitates gene silencing.
  16. Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity.
  17. The long non-coding RNA NEAT1 is a ΔNp63 target gene modulating epidermal differentiation.
  18. Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility.
  19. Etv5a suppresses neural progenitor cell proliferation by inhibiting sox2 transcription.
  20. The p23 co-chaperone is a succinate-activated COX-2 transcription factor in lung adenocarcinoma tumorigenesis.
  21. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.
  22. Molecular basis of RanGTP-activated release of Histones H2A-H2B from Importin-9.
  23. Major β cell-specific functions of NKX2.2 are mediated via the NK2-specific domain.
  24. Loss of Mettl3 enhances liver tumorigenesis by inducing hepatocyte dedifferentiation and hyperproliferation.
  25. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID.
  26. Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase.
  27. Nrf2 drives hepatocellular carcinoma progression through acetyl-CoA-mediated metabolic and epigenetic regulatory networks.
  1. Nat Struct Mol Biol. 2023 Jun 29.
    Readout of histone methylation by Trim24 locally restricts chromatin opening by p53.
    Luke Isbel, Murat Iskar, Sevi Durdu, Joscha Weiss, Ralph S Grand, Eric Hietter-Pfeiffer, Zuzanna Kozicka, Alicia K Michael, Lukas Burger, Nicolas H Thomä, Dirk Schübeler.
      The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are unusually diverse with regard to their chromatin features, including histone modifications, raising the possibility that the local chromatin environment can contextualize p53 regulation. Here, we show that epigenetic characteristics of closed chromatin, such as DNA methylation, do not influence the binding of p53 across the genome. Instead, the ability of p53 to open chromatin and activate its target genes is locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated histone 3 lysine 4 (H3K4), thereby preferentially localizing to those p53 sites that reside in closed chromatin, whereas it is deterred from accessible chromatin by H3K4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to affect gene expression as a function of the local chromatin state. These findings link H3K4 methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors that locally modulate TF function.
    DOI:  https://doi.org/10.1038/s41594-023-01021-8
  2. Genome Biol. 2023 Jun 27. 24(1): 153
    Universal chromatin state annotation of the mouse genome.
    Ha Vu, Jason Ernst.
      A large-scale application of the "stacked modeling" approach for chromatin state discovery previously provides a single "universal" chromatin state annotation of the human genome based jointly on data from many cell and tissue types. Here, we produce an analogous chromatin state annotation for mouse based on 901 datasets assaying 14 chromatin marks in 26 cell or tissue types. To characterize each chromatin state, we relate the states to external annotations and compare them to analogously defined human states. We expect the universal chromatin state annotation for mouse to be a useful resource for studying this key model organism's genome.
    DOI:  https://doi.org/10.1186/s13059-023-02994-x
  3. Sci Adv. 2023 Jun 30. 9(26): eadh0721
    Transcription activator WCC recruits deacetylase HDA3 to control transcription dynamics and bursting in Neurospora.
    Michael Oehler, Leonie Geisser, Axel C R Diernfellner, Michael Brunner.
      RNA polymerase II initiates transcription either randomly or in bursts. We examined the light-dependent transcriptional activator White Collar Complex (WCC) of Neurospora to characterize the transcriptional dynamics of the strong vivid (vvd) promoter and the weaker frequency (frq) promoter. We show that WCC is not only an activator but also represses transcription by recruiting histone deacetylase 3 (HDA3). Our data suggest that bursts of frq transcription are governed by a long-lived refractory state established and maintained by WCC and HDA3 at the core promoter, whereas transcription of vvd is determined by WCC binding dynamics at an upstream activating sequence. Thus, in addition to stochastic binding of transcription factors, transcription factor-mediated repression may also influence transcriptional bursting.
    DOI:  https://doi.org/10.1126/sciadv.adh0721
  4. Genome Biol. 2023 Jun 28. 24(1): 155
    RAD21 is the core subunit of the cohesin complex involved in directing genome organization.
    Yuao Sun, Xin Xu, Wenxue Zhao, Yu Zhang, Keyang Chen, Yongzheng Li, Xiaotian Wang, Mengling Zhang, Boxin Xue, Wanting Yu, Yingping Hou, Chaobin Wang, Wei Xie, Cheng Li, Daochun Kong, Shu Wang, Yujie Sun.
       BACKGROUND: The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesin and chromatin is poorly understood. In this study, we use super-resolution imaging to reveal the unique role of cohesin subunit RAD21 in cohesin loading and chromatin structure regulation.
    RESULTS: We directly visualize that up-regulation of RAD21 leads to excessive chromatin loop extrusion into a vermicelli-like morphology with RAD21 clustered into foci and excessively loaded cohesin bow-tying a TAD to form a beads-on-a-string-type pattern. In contrast, up-regulation of the other four cohesin subunits results in even distributions. Mechanistically, we identify that the essential role of RAD21 is attributed to the RAD21-loader interaction, which facilitates the cohesin loading process rather than increasing the abundance of cohesin complex upon up-regulation of RAD21. Furthermore, Hi-C and genomic analysis reveal how RAD21 up-regulation affects genome-wide higher-order chromatin structure. Accumulated contacts are shown at TAD corners while inter-TAD interactions increase after vermicelli formation. Importantly, we find that in breast cancer cells, the expression of RAD21 is aberrantly high with poor patient survival and RAD21 forms beads in the nucleus. Up-regulated RAD21 in HeLa cells leads to compartment switching and up-regulation of cancer-related genes.
    CONCLUSIONS: Our results provide key insights into the molecular mechanism by which RAD21 facilitates the cohesin loading process and provide an explanation to how cohesin and loader work cooperatively to promote chromatin extrusion, which has important implications in construction of three-dimensional genome organization.
    DOI:  https://doi.org/10.1186/s13059-023-02982-1
  5. PLoS Biol. 2023 Jun 28. 21(6): e3002161
    MLL methyltransferases regulate H3K4 methylation to ensure CENP-A assembly at human centromeres.
    Kausika Kumar Malik, Sreerama Chaitanya Sridhara, Kaisar Ahmad Lone, Payal Deepakbhai Katariya, Deepshika Pulimamidi, Shweta Tyagi.
      The active state of centromeres is epigenetically defined by the presence of CENP-A interspersed with histone H3 nucleosomes. While the importance of dimethylation of H3K4 for centromeric transcription has been highlighted in various studies, the identity of the enzyme(s) depositing these marks on the centromere is still unknown. The MLL (KMT2) family plays a crucial role in RNA polymerase II (Pol II)-mediated gene regulation by methylating H3K4. Here, we report that MLL methyltransferases regulate transcription of human centromeres. CRISPR-mediated down-regulation of MLL causes loss of H3K4me2, resulting in an altered epigenetic chromatin state of the centromeres. Intriguingly, our results reveal that loss of MLL, but not SETD1A, increases co-transcriptional R-loop formation, and Pol II accumulation at the centromeres. Finally, we report that the presence of MLL and SETD1A is crucial for kinetochore maintenance. Altogether, our data reveal a novel molecular framework where both the H3K4 methylation mark and the methyltransferases regulate stability and identity of the centromere.
    DOI:  https://doi.org/10.1371/journal.pbio.3002161
  6. Nat Commun. 2023 Jun 29. 14(1): 3844
    Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape.
    Nimrod Rappoport, Elad Chomsky, Takashi Nagano, Charlie Seibert, Yaniv Lubling, Yael Baran, Aviezer Lifshitz, Wing Leung, Zohar Mukamel, Ron Shamir, Peter Fraser, Amos Tanay.
      Embryonic development involves massive proliferation and differentiation of cell lineages. This must be supported by chromosome replication and epigenetic reprogramming, but how proliferation and cell fate acquisition are balanced in this process is not well understood. Here we use single cell Hi-C to map chromosomal conformations in post-gastrulation mouse embryo cells and study their distributions and correlations with matching embryonic transcriptional atlases. We find that embryonic chromosomes show a remarkably strong cell cycle signature. Despite that, replication timing, chromosome compartment structure, topological associated domains (TADs) and promoter-enhancer contacts are shown to be variable between distinct epigenetic states. About 10% of the nuclei are identified as primitive erythrocytes, showing exceptionally compact and organized compartment structure. The remaining cells are broadly associated with ectoderm and mesoderm identities, showing only mild differentiation of TADs and compartment structures, but more specific localized contacts in hundreds of ectoderm and mesoderm promoter-enhancer pairs. The data suggest that while fully committed embryonic lineages can rapidly acquire specific chromosomal conformations, most embryonic cells are showing plastic signatures driven by complex and intermixed enhancer landscapes.
    DOI:  https://doi.org/10.1038/s41467-023-39549-4
  7. Elife. 2023 06 27. pii: e83951. [Epub ahead of print]12
    Carm1-arginine methylation of the transcription factor C/EBPα regulates transdifferentiation velocity.
    Guillem Torcal Garcia, Elisabeth Kowenz-Leutz, Tian V Tian, Antonis Klonizakis, Jonathan Lerner, Luisa De Andres-Aguayo, Valeriia Sapozhnikova, Clara Berenguer, Marcos Plana Carmona, Maria Vila Casadesus, Romain Bulteau, Mirko Francesconi, Sandra Peiro, Philipp Mertins, Kenneth Zaret, Achim Leutz, Thomas Graf.
      Here, we describe how the speed of C/EBPα-induced B cell to macrophage transdifferentiation (BMT) can be regulated, using both mouse and human models. The identification of a mutant of C/EBPα (C/EBPαR35A) that greatly accelerates BMT helped to illuminate the mechanism. Thus, incoming C/EBPα binds to PU.1, an obligate partner expressed in B cells, leading to the release of PU.1 from B cell enhancers, chromatin closing and silencing of the B cell program. Released PU.1 redistributes to macrophage enhancers newly occupied by C/EBPα, causing chromatin opening and activation of macrophage genes. All these steps are accelerated by C/EBPαR35A, initiated by its increased affinity for PU.1. Wild-type C/EBPα is methylated by Carm1 at arginine 35 and the enzyme's perturbations modulate BMT velocity as predicted from the observations with the mutant. Increasing the proportion of unmethylated C/EBPα in granulocyte/macrophage progenitors by inhibiting Carm1 biases the cell's differentiation toward macrophages, suggesting that cell fate decision velocity and lineage directionality are closely linked processes.
    Keywords:  blood cell differentiation; cell fate; developmental biology; gene regulation; lineage choice; mouse; transcription factor; transdifferentiation
    DOI:  https://doi.org/10.7554/eLife.83951
  8. Nat Commun. 2023 Jun 29. 14(1): 3848
    Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex function during cellular differentiation.
    Nina Schmolka, Ino D Karemaker, Richard Cardoso da Silva, Davide C Recchia, Vincent Spegg, Jahnavi Bhaskaran, Michael Teske, Nathalie P de Wagenaar, Matthias Altmeyer, Tuncay Baubec.
      The Nucleosome Remodeling and Deacetylation (NuRD) complex is a crucial regulator of cellular differentiation. Two members of the Methyl-CpG-binding domain (MBD) protein family, MBD2 and MBD3, are known to be integral, but mutually exclusive subunits of the NuRD complex. Several MBD2 and MBD3 isoforms are present in mammalian cells, resulting in distinct MBD-NuRD complexes. Whether these different complexes serve distinct functional activities during differentiation is not fully explored. Based on the essential role of MBD3 in lineage commitment, we systematically investigated a diverse set of MBD2 and MBD3 variants for their potential to rescue the differentiation block observed for mouse embryonic stem cells (ESCs) lacking MBD3. While MBD3 is indeed crucial for ESC differentiation to neuronal cells, it functions independently of its MBD domain. We further identify that MBD2 isoforms can replace MBD3 during lineage commitment, however with different potential. Full-length MBD2a only partially rescues the differentiation block, while MBD2b, an isoform lacking an N-terminal GR-rich repeat, fully rescues the Mbd3 KO phenotype. In case of MBD2a, we further show that removing the methylated DNA binding capacity or the GR-rich repeat enables full redundancy to MBD3, highlighting the synergistic requirements for these domains in diversifying NuRD complex function.
    DOI:  https://doi.org/10.1038/s41467-023-39551-w
  9. Nat Commun. 2023 06 26. 14(1): 3791
    Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells.
    Marko Dunjić, Felix Jonas, Gilad Yaakov, Roye More, Yoav Mayshar, Yoach Rais, Ayelet-Hashahar Orenbuch, Saifeng Cheng, Naama Barkai, Yonatan Stelzer.
      Eviction of histones from nucleosomes and their exchange with newly synthesized or alternative variants is a central epigenetic determinant. Here, we define the genome-wide occupancy and exchange pattern of canonical and non-canonical histone variants in mouse embryonic stem cells by genetically encoded exchange sensors. While exchange of all measured variants scales with transcription, we describe variant-specific associations with transcription elongation and Polycomb binding. We found considerable exchange of H3.1 and H2B variants in heterochromatin and repeat elements, contrasting the occupancy and little exchange of H3.3 in these regions. This unexpected association between H3.3 occupancy and exchange of canonical variants is also evident in active promoters and enhancers, and further validated by reduced H3.1 dynamics following depletion of H3.3-specific chaperone, HIRA. Finally, analyzing transgenic mice harboring H3.1 or H3.3 sensors demonstrates the vast potential of this system for studying histone exchange and its impact on gene expression regulation in vivo.
    DOI:  https://doi.org/10.1038/s41467-023-39477-3
  10. Genome Biol. 2023 Jun 27. 24(1): 154
    ExplaiNN: interpretable and transparent neural networks for genomics.
    Gherman Novakovsky, Oriol Fornes, Manu Saraswat, Sara Mostafavi, Wyeth W Wasserman.
      Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of linear models. ExplaiNN can predict TF binding, chromatin accessibility, and de novo motifs, achieving performance comparable to state-of-the-art methods. Its predictions are transparent, providing global (cell state level) as well as local (individual sequence level) biological insights into the data. ExplaiNN can serve as a plug-and-play platform for pretrained models and annotated position weight matrices. ExplaiNN aims to accelerate the adoption of deep learning in genomic sequence analysis by domain experts.
    Keywords:  Deep learning; Explainable artificial intelligence; Gene regulation; Genomics; Model interpretation; Transcription factors
    DOI:  https://doi.org/10.1186/s13059-023-02985-y
  11. Cell Genom. 2023 Jun 14. 3(6): 100318
    Integrative dissection of gene regulatory elements at base resolution.
    Zeyu Chen, Nauman Javed, Molly Moore, Jingyi Wu, Gary Sun, Michael Vinyard, Alejandro Collins, Luca Pinello, Fadi J Najm, Bradley E Bernstein.
      Although vast numbers of putative gene regulatory elements have been cataloged, the sequence motifs and individual bases that underlie their functions remain largely unknown. Here, we combine epigenetic perturbations, base editing, and deep learning to dissect regulatory sequences within the exemplar immune locus encoding CD69. We converge on a ∼170 base interval within a differentially accessible and acetylated enhancer critical for CD69 induction in stimulated Jurkat T cells. Individual C-to-T base edits within the interval markedly reduce element accessibility and acetylation, with corresponding reduction of CD69 expression. The most potent base edits may be explained by their effect on regulatory interactions between the transcriptional activators GATA3 and TAL1 and the repressor BHLHE40. Systematic analysis suggests that the interplay between GATA3 and BHLHE40 plays a general role in rapid T cell transcriptional responses. Our study provides a framework for parsing regulatory elements in their endogenous chromatin contexts and identifying operative artificial variants.
    Keywords:  CRISPRi; base editing; immune response; regulatory elements; transcription factor
    DOI:  https://doi.org/10.1016/j.xgen.2023.100318
  12. Mol Cell. 2023 Jun 21. pii: S1097-2765(23)00424-0. [Epub ahead of print]
    Structural insights into human co-transcriptional capping.
    Gaurika Garg, Christian Dienemann, Lucas Farnung, Juliane Schwarz, Andreas Linden, Henning Urlaub, Patrick Cramer.
      Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryoelectron microscopy (cryo-EM) structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end. Addition of a GMP moiety can occur when the RNA is ∼22 nt long, sufficient to reach the active site of the guanylyltransferase. For subsequent cap(1) methylation, the methyltransferase CMTR1 binds the Pol II stalk and can receive RNA after it is grown to ∼29 nt in length. The observed rearrangements of capping factors on the Pol II surface may be triggered by the completion of catalytic reaction steps and are accommodated by domain movements in the elongation factor DRB sensitivity-inducing factor (DSIF).
    Keywords:  CMTR1; RNA Pol II; RNA polymerase II; RNGTT; capping; co-transcriptional capping; co-transcriptional processing; mRNA processing; transcription; transcription elongation
    DOI:  https://doi.org/10.1016/j.molcel.2023.06.002
  13. Cell Genom. 2023 Jun 14. 3(6): 100298
    A multi-omics atlas of the human retina at single-cell resolution.
    Qingnan Liang, Xuesen Cheng, Jun Wang, Leah Owen, Akbar Shakoor, John L Lillvis, Charles Zhang, Michael Farkas, Ivana K Kim, Yumei Li, Margaret DeAngelis, Rui Chen.
      Cell classes in the human retina are highly heterogeneous with their abundance varying by several orders of magnitude. Here, we generated and integrated a multi-omics single-cell atlas of the adult human retina, including more than 250,000 nuclei for single-nuclei RNA-seq and 137,000 nuclei for single-nuclei ATAC-seq. Cross-species comparison of the retina atlas among human, monkey, mice, and chicken revealed relatively conserved and non-conserved types. Interestingly, the overall cell heterogeneity in primate retina decreases compared with that of rodent and chicken retina. Through integrative analysis, we identified 35,000 distal cis-element-gene pairs, constructed transcription factor (TF)-target regulons for more than 200 TFs, and partitioned the TFs into distinct co-active modules. We also revealed the heterogeneity of the cis-element-gene relationships in different cell types, even from the same class. Taken together, we present a comprehensive single-cell multi-omics atlas of the human retina as a resource that enables systematic molecular characterization at individual cell-type resolution.
    Keywords:  cross-species analysis; gene regulation; human retina; single-cell multi-omics
    DOI:  https://doi.org/10.1016/j.xgen.2023.100298
  14. Science. 2023 Jun 29. eadf6287
    Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling.
    Min Zhang, Anna Jungblut, Franziska Kunert, Luis Hauptmann, Thomas Hoffmann, Olga Kolesnikova, Felix Metzner, Manuela Moldt, Felix Weis, Frank DiMaio, Karl-Peter Hopfner, Sebastian Eustermann.
      Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of non-canonical nucleosomal particles remains largely elusive. Here, we report the structural mechanism for ATP-dependent chromatin remodeling of hexasomes by the INO80 complex. We show how INO80 recognizes non-canonical DNA and histone features of hexasomes emerging from the loss of H2A-H2B. A large structural re-arrangement switches the catalytic core of INO80 into a distinct, spin-rotated mode of remodeling, while its nuclear actin module remains tethered to long stretches of unwrapped linker DNA. Direct sensing of an exposed H3-H4 histone interface activates INO80, independently of the H2A-H2B acidic patch. Our findings reveal how the loss of H2A-H2B grants remodelers access to a different, yet unexplored, layer of energy-driven chromatin regulation.
    DOI:  https://doi.org/10.1126/science.adf6287
  15. Cell Rep. 2023 Jun 28. pii: S2211-1247(23)00697-6. [Epub ahead of print]42(7): 112686
    Early chromosome condensation by XIST builds A-repeat RNA density that facilitates gene silencing.
    Melvys Valledor, Meg Byron, Brett Dumas, Dawn M Carone, Lisa L Hall, Jeanne B Lawrence.
      XIST RNA triggers chromosome-wide gene silencing and condenses an active chromosome into a Barr body. Here, we use inducible human XIST to examine early steps in the process, showing that XIST modifies cytoarchitecture before widespread gene silencing. In just 2-4 h, barely visible transcripts populate the large "sparse zone" surrounding the smaller "dense zone"; importantly, density zones exhibit different chromatin impacts. Sparse transcripts immediately trigger immunofluorescence for H2AK119ub and CIZ1, a matrix protein. H3K27me3 appears hours later in the dense zone, which enlarges with chromosome condensation. Genes examined are silenced after compaction of the RNA/DNA territory. Insights into this come from the findings that the A-repeat alone can silence genes and rapidly, but only where dense RNA supports sustained histone deacetylation. We propose that sparse XIST RNA quickly impacts architectural elements to condense the largely non-coding chromosome, coalescing RNA density that facilitates an unstable, A-repeat-dependent step required for gene silencing.
    Keywords:  A-Repeat; Barr body; CIZ1; CP: Molecular biology; CP: Stem cell research; H3K27; UbH2A; XIST; chromosome structure; epigenetics; heterochromatin; transcription
    DOI:  https://doi.org/10.1016/j.celrep.2023.112686
  16. BMC Biol. 2023 06 26. 21(1): 149
    Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity.
    Samuel N Bogan, Marie E Strader, Gretchen E Hofmann.
       BACKGROUND: Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing.
    RESULTS: Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state.
    CONCLUSIONS: DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.
    Keywords:  Chromatin; DNA Methylation; Environment; Epigenetics; Gene expression; Invertebrate
    DOI:  https://doi.org/10.1186/s12915-023-01645-8
  17. Nat Commun. 2023 06 26. 14(1): 3795
    The long non-coding RNA NEAT1 is a ΔNp63 target gene modulating epidermal differentiation.
    Claudia Fierro, Veronica Gatti, Veronica La Banca, Sara De Domenico, Stefano Scalera, Giacomo Corleone, Maurizio Fanciulli, Francesca De Nicola, Alessandro Mauriello, Manuela Montanaro, George A Calin, Gerry Melino, Angelo Peschiaroli.
      The transcription factor ΔNp63 regulates epithelial stem cell function and maintains the integrity of stratified epithelial tissues by acting as transcriptional repressor or activator towards a distinct subset of protein-coding genes and microRNAs. However, our knowledge of the functional link between ∆Np63 transcriptional activity and long non-coding RNAs (lncRNAs) expression is quite limited. Here, we show that in proliferating human keratinocytes ∆Np63 represses the expression of the lncRNA NEAT1 by recruiting the histone deacetylase HDAC1 to the proximal promoter of NEAT1 genomic locus. Upon induction of differentiation, ∆Np63 down-regulation is associated by a marked increase of NEAT1 RNA levels, resulting in an increased assembly of paraspeckles foci both in vitro and in human skin tissues. RNA-seq analysis associated with global DNA binding profile (ChIRP-seq) revealed that NEAT1 associates with the promoter of key epithelial transcription factors sustaining their expression during epidermal differentiation. These molecular events might explain the inability of NEAT1-depleted keratinocytes to undergo the proper formation of epidermal layers. Collectively, these data uncover the lncRNA NEAT1 as an additional player of the intricate network orchestrating epidermal morphogenesis.
    DOI:  https://doi.org/10.1038/s41467-023-39011-5
  18. Science. 2023 Jun 28.
    Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility.
    Hao Wu, Elise N Muñoz, Laura J Hsieh, Un Seng Chio, Muryam A Gourdet, Geeta J Narlikar, Yifan Cheng.
      Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of S. cerevisiae INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location (SHL)-2, across from SHL-6/-7 as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes, such that Ino80 is maximally active near SHL-2. The SHL-2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that sub-nucleosomal particles play considerable regulatory roles.
    DOI:  https://doi.org/10.1126/science.adf4197
  19. Stem Cells Dev. 2023 Jun 26.
    Etv5a suppresses neural progenitor cell proliferation by inhibiting sox2 transcription.
    Hung-Yu Shih, Hao-Yuan Chen, Yin-Cheng Huang, Tu-Hsueh Yeh, Yi-Chieh Chen, Yi-Chuan Cheng.
      Neural progenitor cells are self-renewable, proliferative, and multipotent cell populations that generate diverse types of neurons and glia to build the nervous system. Transcription factors play critical roles in regulating various cellular processes; however, the transcription factors that regulate the development of neural progenitors are yet to be identified. In the present study, we demonstrated that zebrafish etv5a is expressed in the neural progenitor cells of the neuroectoderm. Downregulation of endogenous Etv5a function by etv5a morpholino or an etv5a dominant-negative variant increased the proliferation of sox2-positive neural progenitor cells, accompanied by inhibition of neurogenesis and gliogenesis. These phenotypes in Etv5a-depleted embryos could be rescued by co-injection with etv5a cRNA. Etv5a overexpression reduced sox2 expression. Direct binding of Etv5a to the regulatory elements of sox2 was affirmed by chromatin immunoprecipitation. These data revealed that Etv5a directly suppressed sox2 expression to reduce the proliferation of neural progenitor cells. In addition, the expression of foxm1, a putative target gene of Etv5a and a direct upstream transcription factor of sox2, was upregulated in Etv5a-deficient embryos. Moreover, the suppression of Foxm1 function by the foxm1 dominant-negative construct nullified the phenotype of upregulated sox2 expression caused by Etv5a deficiency. Overall, our results indicated that Etv5a regulates the expression of sox2 via direct binding to the sox2 promoter and indirect regulation by inhibiting foxm1 expression. Hence, we revealed the role of Etv5a in the transcriptional hierarchy that regulates the proliferation of neural progenitor cells.
    DOI:  https://doi.org/10.1089/scd.2023.0005
  20. Sci Adv. 2023 Jun 30. 9(26): eade0387
    The p23 co-chaperone is a succinate-activated COX-2 transcription factor in lung adenocarcinoma tumorigenesis.
    Zhenlong Yu, Yulin Peng, Jian Gao, Meirong Zhou, Lei Shi, Feng Zhao, Chao Wang, Xiangge Tian, Lei Feng, Xiaokui Huo, Baojing Zhang, Min Liu, Deyu Fang, Xiaochi Ma.
      P23, historically known as a heat shock protein 90 (HSP90) co-chaperone, exerts some of its critical functions in an HSP90-independent manner, particularly when it translocates into the nucleus. The molecular nature underlying how this HSP90-independent p23 function is achieved remains as a biological mystery. Here, we found that p23 is a previously unidentified transcription factor of COX-2, and its nuclear localization predicts the poor clinical outcomes. Intratumor succinate promotes p23 succinylation at K7, K33, and K79, which drives its nuclear translocation for COX-2 transcription and consequently fascinates tumor growth. We then identified M16 as a potent p23 succinylation inhibitor from 1.6 million compounds through a combined virtual and biological screening. M16 inhibited p23 succinylation and nuclear translocation, attenuated COX-2 transcription in a p23-dependent manner, and markedly suppressed tumor growth. Therefore, our study defines p23 as a succinate-activated transcription factor in tumor progression and provides a rationale for inhibiting p23 succinylation as an anticancer chemotherapy.
    DOI:  https://doi.org/10.1126/sciadv.ade0387
  21. Science. 2023 Jun 30. 380(6652): 1357-1362
    Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.
    David B Brückner, Hongtao Chen, Lev Barinov, Benjamin Zoller, Thomas Gregor.
      Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.
    DOI:  https://doi.org/10.1126/science.adf5568
  22. Structure. 2023 Jun 19. pii: S0969-2126(23)00197-1. [Epub ahead of print]
    Molecular basis of RanGTP-activated release of Histones H2A-H2B from Importin-9.
    Joy M Shaffer, Jenny Jiou, Kiran Tripathi, Oladimeji S Olaluwoye, Ho Yee Joyce Fung, Yuh Min Chook, Sheena D'Arcy.
      Imp9 is the primary importin for shuttling H2A-H2B from the cytoplasm to the nucleus. It employs an unusual mechanism where the binding of RanGTP is insufficient to release H2A-H2B. The resulting stable RanGTP·Imp9·H2A-H2B complex gains nucleosome assembly activity with H2A-H2B able to be deposited into an assembling nucleosome in vitro. Using hydrogen-deuterium exchange coupled with mass spectrometry (HDX), we show that Imp9 stabilizes H2A-H2B beyond the direct-binding site, like other histone chaperones. HDX also shows that binding of RanGTP releases H2A-H2B contacts at Imp9 HEAT repeats 4-5, but not 18-19. DNA- and histone-binding surfaces of H2A-H2B are exposed in the ternary complex, facilitating nucleosome assembly. We also reveal that RanGTP has a weaker affinity for Imp9 when H2A-H2B is bound. Imp9 thus provides a connection between the nuclear import of H2A-H2B and its deposition into chromatin.
    Keywords:  HDX; Importin-9; Ran GTPase; histones; importin; mass spectrometry; nuclear import; nucleosome
    DOI:  https://doi.org/10.1016/j.str.2023.06.001
  23. Genes Dev. 2023 Jun 26.
    Major β cell-specific functions of NKX2.2 are mediated via the NK2-specific domain.
    Vladimir Abarinov, Joshua A Levine, Angela J Churchill, Bryce Hopwood, Cailin S Deiter, Michelle A Guney, Kristen L Wells, Jessica M Schrunk, Yuchun Guo, Jennifer Hammelman, David K Gifford, Mark A Magnuson, Hynek Wichterle, Lori Sussel.
      The consolidation of unambiguous cell fate commitment relies on the ability of transcription factors (TFs) to exert tissue-specific regulation of complex genetic networks. However, the mechanisms by which TFs establish such precise control over gene expression have remained elusive-especially in instances in which a single TF operates in two or more discrete cellular systems. In this study, we demonstrate that β cell-specific functions of NKX2.2 are driven by the highly conserved NK2-specific domain (SD). Mutation of the endogenous NKX2.2 SD prevents the developmental progression of β cell precursors into mature, insulin-expressing β cells, resulting in overt neonatal diabetes. Within the adult β cell, the SD stimulates β cell performance through the activation and repression of a subset of NKX2.2-regulated transcripts critical for β cell function. These irregularities in β cell gene expression may be mediated via SD-contingent interactions with components of chromatin remodelers and the nuclear pore complex. However, in stark contrast to these pancreatic phenotypes, the SD is entirely dispensable for the development of NKX2.2-dependent cell types within the CNS. Together, these results reveal a previously undetermined mechanism through which NKX2.2 directs disparate transcriptional programs in the pancreas versus neuroepithelium.
    Keywords:  NKX2.2; pancreatic islet; spinal cord; transcriptional regulation; β cells
    DOI:  https://doi.org/10.1101/gad.350569.123
  24. Cell Rep. 2023 Jun 27. pii: S2211-1247(23)00715-5. [Epub ahead of print]42(7): 112704
    Loss of Mettl3 enhances liver tumorigenesis by inducing hepatocyte dedifferentiation and hyperproliferation.
    Tao Wei, Jin Li, Jian Zhang, Qi Zhang, Xiaoyu Liu, Qi Chen, Liang Wen, Ke Ma, Wen Chen, Jianhui Zhao, Cheng Zhang, Jinyan Huang, Yali Xie, Hao Qin, Danfeng Qian, Tingbo Liang.
      While a few works have shown that Mettl3 plays oncogenic roles in hepatocellular carcinoma (HCC), its function in early HCC tumorigenesis remains unclear. In Mettl3flox/flox; Alb-Cre knockout mice, Mettl3 loss leads to aberrant hepatocyte homeostasis and liver damage. Importantly, Mettl3 deletion dramatically accelerates liver tumorigenesis in various HCC mouse models. Depletion of Mettl3 in adult Mettl3flox/flox mice through TBG-Cre administration also enhances liver tumor development, while overexpression of Mettl3 inhibits hepatocarcinogenesis. Mechanistically, aggravated tumorigenesis upon Mettl3 deletion is a consequence of hepatocyte dedifferentiation and hyperproliferation via m6A-mediated modulation on Hnf4α and cell cycle genes. In contrast, by using Mettl3flox/flox; Ubc-Cre mice, depletion of Mettl3 in established HCC ameliorates tumor progression. Additionally, Mettl3 is overexpressed in HCC tumors compared with adjacent non-tumor tissues. The present findings define a tumor-suppressive role of Mettl3 in liver tumorigenesis, indicating its potentially opposite stage-dependent functions in HCC initiation versus progression.
    Keywords:  CP: Cancer; CP: Molecular biology; Hnf4α; Mettl3; context-dependent function; liver cancer; liver damage; m6A modification; tumorigenesis
    DOI:  https://doi.org/10.1016/j.celrep.2023.112704
  25. Nat Struct Mol Biol. 2023 Jun 29.
    Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID.
    Andrea Bernardini, Pooja Mukherjee, Elisabeth Scheer, Ivanka Kamenova, Simona Antonova, Paulina Karen Mendoza Sanchez, Gizem Yayli, Bastien Morlet, H T Marc Timmers, László Tora.
      Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates the RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that human TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1-the largest protein in the complex-as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
    DOI:  https://doi.org/10.1038/s41594-023-01026-3
  26. EMBO J. 2023 Jun 26. e113475
    Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase.
    Paul Batty, Christoph Ch Langer, Zsuzsanna Takács, Wen Tang, Claudia Blaukopf, Jan-Michael Peters, Daniel W Gerlich.
      Genetic information is stored in linear DNA molecules, which are highly folded inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in an intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics presegregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin's looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.
    Keywords:  chromosomes; cohesin; condensin; mitosis; sister chromatid resolution
    DOI:  https://doi.org/10.15252/embj.2023113475
  27. Mol Cancer Res. 2023 Jun 26. pii: MCR-22-0935. [Epub ahead of print]
    Nrf2 drives hepatocellular carcinoma progression through acetyl-CoA-mediated metabolic and epigenetic regulatory networks.
    Caixia Xi, Junfeng Pang, Amanda Barrett, Anatolij Horuzsko, Satyanarayana Ande, Nahid F Mivechi, Xingguo Zhu.
      Correlations between the oxidative stress response and metabolic reprogramming have been observed during malignant tumor formation; however, the detailed mechanism remains elusive. The transcription factor Nrf2, a master regulator of the oxidative stress response, mediates metabolic reprogramming in multiple cancers. In a mouse model of hepatocellular carcinoma (HCC), through metabolic profiling, genome-wide gene expression, and chromatin structure analyses, we present new evidence showing that in addition to altering antioxidative stress response signaling, Nrf2 ablation impairs multiple metabolic pathways to reduce the generation of acetyl-CoA and suppress histone acetylation in tumors, but not in tumor-adjacent normal tissue. Nrf2 ablation and dysregulated histone acetylation impair transcription complex assembly on downstream target antioxidant and metabolic regulatory genes for expression regulation. Mechanistic studies indicate that the regulatory function of Nrf2 is low glucose dependent, the effect of which is demolished under energy refeeding. Together, our results implicate an unexpected effect of Nrf2 on acetyl-CoA generation, in addition to its classic antioxidative stress response regulatory activity, integrates metabolic and epigenetic programs to drive HCC progression. Implications: This study highlights that Nrf2 integrates metabolic and epigenetic regulatory networks to dictate tumor progression and that Nrf2 targeting is therapeutically exploitable in HCC treatment.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-22-0935
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