bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2023–09–17
27 papers selected by
Connor Rogerson, University of Cambridge
  1. Pioneer activity distinguishes activating from non-activating SOX2 binding sites.
  2. Activator-blocker model of transcriptional regulation by pioneer-like factors.
  3. Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation.
  4. Transposable elements are co-opted as oncogenic regulatory elements by lineage-specific transcription factors in prostate cancer.
  5. Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.
  6. NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development.
  7. Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler.
  8. Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma.
  9. Chemical-induced phase transition and global conformational reorganization of chromatin.
  10. CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin.
  11. Histone methylation regulates reproductive diapause in Drosophila melanogaster.
  12. Transcriptional repression upon S phase entry protects genome integrity in pluripotent cells.
  13. Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis.
  14. m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency.
  15. Interlocking of co-opted developmental gene networks in Drosophila and the evolution of pre-adaptive novelty.
  16. Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features.
  17. Serine starvation silences estrogen receptor signaling through histone hypoacetylation.
  18. SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells.
  19. Computational tools for inferring transcription factor activity.
  20. Cryo-ET study from in vitro to in vivo revealed a general folding mode of chromatin with two-start helical architecture.
  21. Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells.
  22. tgCRISPRi: efficient gene knock-down using truncated gRNAs and catalytically active Cas9.
  23. Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules.
  24. Nucleosome repositioning in chronic lymphocytic leukaemia.
  25. DUX4 expression in cancer induces a metastable early embryonic totipotent program.
  26. Modular pooled discovery of synthetic knockin sequences to program durable cell therapies.
  27. DELLA-mediated gene repression is maintained by chromatin modification in rice.
  1. EMBO J. 2023 Sep 11. e113150
    Pioneer activity distinguishes activating from non-activating SOX2 binding sites.
    Michela Maresca, Teun van den Brand, Hangpeng Li, Hans Teunissen, James Davies, Elzo de Wit.
      Genome-wide transcriptional activity involves the binding of many transcription factors (TFs) to thousands of sites in the genome. Pioneer TFs are a class of TFs that maintain open chromatin and allow non-pioneer TFs access to their target sites. Determining which TF binding sites directly drive transcription remains a challenge. Here, we use acute protein depletion of the pioneer TF SOX2 to establish its functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of the pioneer factor. To understand the relationship with transcription, we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to all other SOX2 binding sites. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted mainly at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.
    Keywords:  acute protein depletion; chromatin accessibility; gene regulation; pioneer activity; transcription factors
    DOI:  https://doi.org/10.15252/embj.2022113150
  2. Nat Commun. 2023 Sep 14. 14(1): 5677
    Activator-blocker model of transcriptional regulation by pioneer-like factors.
    Aileen Julia Riesle, Meijiang Gao, Marcus Rosenblatt, Jacques Hermes, Helge Hass, Anna Gebhard, Marina Veil, Björn Grüning, Jens Timmer, Daria Onichtchouk.
      Zygotic genome activation (ZGA) in the development of flies, fish, frogs and mammals depends on pioneer-like transcription factors (TFs). Those TFs create open chromatin regions, promote histone acetylation on enhancers, and activate transcription. Here, we use the panel of single, double and triple mutants for zebrafish genome activators Pou5f3, Sox19b and Nanog, multi-omics and mathematical modeling to investigate the combinatorial mechanisms of genome activation. We show that Pou5f3 and Nanog act differently on synergistic and antagonistic enhancer types. Pou5f3 and Nanog both bind as pioneer-like TFs on synergistic enhancers, promote histone acetylation and activate transcription. Antagonistic enhancers are activated by binding of one of these factors. The other TF binds as non-pioneer-like TF, competes with the activator and blocks all its effects, partially or completely. This activator-blocker mechanism mutually restricts widespread transcriptional activation by Pou5f3 and Nanog and prevents premature expression of late developmental regulators in the early embryo.
    DOI:  https://doi.org/10.1038/s41467-023-41507-z
  3. Nucleic Acids Res. 2023 Sep 13. pii: gkad741. [Epub ahead of print]
    Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation.
    Zeqian Gao, Alastair L Smith, James N F Scott, Sarah L Bevington, Joan Boyes.
      Transcription enhancers are essential activators of V(D)J recombination that orchestrate non-coding transcription through complementary, unrearranged gene segments. How transcription is coordinately increased at spatially distinct promoters, however, remains poorly understood. Using the murine immunoglobulin lambda (Igλ) locus as model, we find that three enhancer-like elements in the 3' Igλ domain, Eλ3-1, HSCλ1 and HSE-1, show strikingly similar transcription factor binding dynamics and close spatial proximity, suggesting that they form an active enhancer hub. Temporal analyses show coordinate recruitment of complementary V and J gene segments to this hub, with comparable transcription factor binding dynamics to that at enhancers. We find further that E2A, p300, Mediator and Integrator bind to enhancers as early events, whereas YY1 recruitment and eRNA synthesis occur later, corresponding to transcription activation. Remarkably, the interplay between sense and antisense enhancer RNA is central to both active enhancer hub formation and coordinate Igλ transcription: Antisense Eλ3-1 eRNA represses Igλ activation whereas temporal analyses demonstrate that accumulating levels of sense eRNA boost YY1 recruitment to stabilise enhancer hub/promoter interactions and lead to coordinate transcription activation. These studies therefore demonstrate for the first time a critical role for threshold levels of sense versus antisense eRNA in locus activation.
    DOI:  https://doi.org/10.1093/nar/gkad741
  4. Cancer Discov. 2023 Sep 11.
    Transposable elements are co-opted as oncogenic regulatory elements by lineage-specific transcription factors in prostate cancer.
    Giacomo Grillo, Tina Keshavarzian, Simon Linder, Christopher Arlidge, Lisanne Mout, Ankita Nand, Mona Teng, Aditi Qamra, Stanley Zhou, Ken J Kron, Alex Murison, James R Hawley, Michael Fraser, Theodorus H van der Kwast, Ganesh V Raj, Housheng Hansen He, Wilbert Zwart, Mathieu Lupien.
      Transposable elements hold regulatory functions that impact cell fate determination by controlling gene expression. However, little is known about the transcriptional machinery engaged at transposable elements in pluripotent and mature versus oncogenic cell states. Through positional analysis over repetitive DNA sequences of H3K27ac ChIP-seq data from 32 normal cell states, we report pluripotent/stem and mature cell state-specific "regulatory transposable elements". Pluripotent/stem elements are binding sites for pluripotency factors (e.g. NANOG, SOX2, OCT4). Mature cell elements are docking sites for lineage-specific transcription factors, including AR and FOXA1 in prostate epithelium. Expanding the analysis to prostate tumors, we identify a subset of regulatory transposable elements shared with pluripotent/stem cells, including Tigger3a. Using chromatin editing technology, we show how such elements promote prostate cancer growth by regulating AR transcriptional activity. Collectively, our results suggest that oncogenesis arises from lineage-specific transcription factors hijacking pluripotent/stem cell regulatory transposable elements.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-0331
  5. Nat Commun. 2023 Sep 12. 14(1): 5615
    Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.
    Li-Hsin Chang, Sourav Ghosh, Andrea Papale, Jennifer M Luppino, Mélanie Miranda, Vincent Piras, Jéril Degrouard, Joanne Edouard, Mallory Poncelet, Nathan Lecouvreur, Sébastien Bloyer, Amélie Leforestier, Eric F Joyce, David Holcman, Daan Noordermeer.
      Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.
    DOI:  https://doi.org/10.1038/s41467-023-41265-y
  6. Nat Commun. 2023 Sep 09. 14(1): 5554
    NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development.
    Romana Bohuslavova, Valeria Fabriciova, Ondrej Smolik, Laura Lebrón-Mora, Pavel Abaffy, Sarka Benesova, Daniel Zucha, Lukas Valihrach, Zuzana Berkova, Frantisek Saudek, Gabriela Pavlinkova.
      NEUROD1 is a transcription factor that helps maintain a mature phenotype of pancreatic β cells. Disruption of Neurod1 during pancreatic development causes severe neonatal diabetes; however, the exact role of NEUROD1 in the differentiation programs of endocrine cells is unknown. Here, we report a crucial role of the NEUROD1 regulatory network in endocrine lineage commitment and differentiation. Mechanistically, transcriptome and chromatin landscape analyses demonstrate that Neurod1 inactivation triggers a downregulation of endocrine differentiation transcription factors and upregulation of non-endocrine genes within the Neurod1-deficient endocrine cell population, disturbing endocrine identity acquisition. Neurod1 deficiency altered the H3K27me3 histone modification pattern in promoter regions of differentially expressed genes, which resulted in gene regulatory network changes in the differentiation pathway of endocrine cells, compromising endocrine cell potential, differentiation, and functional properties.
    DOI:  https://doi.org/10.1038/s41467-023-41306-6
  7. Nat Struct Mol Biol. 2023 Sep 11.
    Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler.
    Nour J Abdulhay, Laura J Hsieh, Colin P McNally, Megan S Ostrowski, Camille M Moore, Mythili Ketavarapu, Sivakanthan Kasinathan, Arjun S Nanda, Ke Wu, Un Seng Chio, Ziling Zhou, Hani Goodarzi, Geeta J Narlikar, Vijay Ramani.
      Nearly all essential nuclear processes act on DNA packaged into arrays of nucleosomes. However, our understanding of how these processes (for example, DNA replication, RNA transcription, chromatin extrusion and nucleosome remodeling) occur on individual chromatin arrays remains unresolved. Here, to address this deficit, we present SAMOSA-ChAAT: a massively multiplex single-molecule footprinting approach to map the primary structure of individual, reconstituted chromatin templates subject to virtually any chromatin-associated reaction. We apply this method to distinguish between competing models for chromatin remodeling by the essential imitation switch (ISWI) ATPase SNF2h: nucleosome-density-dependent spacing versus fixed-linker-length nucleosome clamping. First, we perform in vivo single-molecule nucleosome footprinting in murine embryonic stem cells, to discover that ISWI-catalyzed nucleosome spacing correlates with the underlying nucleosome density of specific epigenomic domains. To establish causality, we apply SAMOSA-ChAAT to quantify the activities of ISWI ATPase SNF2h and its parent complex ACF on reconstituted nucleosomal arrays of varying nucleosome density, at single-molecule resolution. We demonstrate that ISWI remodelers operate as density-dependent, length-sensing nucleosome sliders, whose ability to program DNA accessibility is dictated by single-molecule nucleosome density. We propose that the long-observed, context-specific regulatory effects of ISWI complexes can be explained in part by the sensing of nucleosome density within epigenomic domains. More generally, our approach promises molecule-precise views of the essential processes that shape nuclear physiology.
    DOI:  https://doi.org/10.1038/s41594-023-01093-6
  8. Cell Rep. 2023 Sep 13. pii: S2211-1247(23)01144-0. [Epub ahead of print]42(9): 113132
    Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma.
    David Gentien, Elnaz Saberi-Ansari, Nicolas Servant, Ariane Jolly, Pierre de la Grange, Fariba Némati, Géraldine Liot, Simon Saule, Aurélie Teissandier, Deborah Bourc'his, Elodie Girard, Jennifer Wong, Julien Masliah-Planchon, Erkan Narmanli, Yuanlong Liu, Emma Torun, Rebecca Goulancourt, Manuel Rodrigues, Laure Villoing Gaudé, Cécile Reyes, Matéo Bazire, Thomas Chenegros, Emilie Henry, Audrey Rapinat, Mylene Bohec, Sylvain Baulande, Radhia M'kacher, Eric Jeandidier, André Nicolas, Giovanni Ciriello, Raphael Margueron, Didier Decaudin, Nathalie Cassoux, Sophie Piperno-Neumann, Marc-Henri Stern, Johan Harmen Gibcus, Job Dekker, Edith Heard, Sergio Roman-Roman, Joshua J Waterfall.
      Uveal melanoma (UM) is a rare cancer resulting from the transformation of melanocytes in the uveal tract. Integrative analysis has identified four molecular and clinical subsets of UM. To improve our molecular understanding of UM, we performed extensive multi-omics characterization comparing two aggressive UM patient-derived xenograft models with normal choroidal melanocytes, including DNA optical mapping, specific histone modifications, and DNA topology analysis using Hi-C. Our gene expression and cytogenetic analyses suggest that genomic instability is a hallmark of UM. We also identified a recurrent deletion in the BAP1 promoter resulting in loss of expression and associated with high risk of metastases in UM patients. Hi-C revealed chromatin topology changes associated with the upregulation of PRAME, an independent prognostic biomarker in UM, and a potential therapeutic target. Our findings illustrate how multi-omics approaches can improve our understanding of tumorigenesis and reveal two distinct mechanisms of gene expression dysregulation in UM.
    Keywords:  BAP1; CP: Cancer; PRAME; genome instability; multi-omics; uveal melanoma
    DOI:  https://doi.org/10.1016/j.celrep.2023.113132
  9. Nat Commun. 2023 Sep 09. 14(1): 5556
    Chemical-induced phase transition and global conformational reorganization of chromatin.
    Tengfei Wang, Shuxiang Shi, Yuanyuan Shi, Peipei Jiang, Ganlu Hu, Qinying Ye, Zhan Shi, Kexin Yu, Chenguang Wang, Guoping Fan, Suwen Zhao, Hanhui Ma, Alex C Y Chang, Zhi Li, Qian Bian, Chao-Po Lin.
      Chemicals or drugs can accumulate within biomolecular condensates formed through phase separation in cells. Here, we use super-resolution imaging to search for chemicals that induce phase transition within chromatin at the microscale. This microscopic screening approach reveals that adriamycin (doxorubicin) - a widely used anticancer drug that is known to interact with chromatin - specifically induces visible local condensation and global conformational change of chromatin in cancer and primary cells. Hi-C and ATAC-seq experiments systematically and quantitatively demonstrate that adriamycin-induced chromatin condensation is accompanied by weakened chromatin interaction within topologically associated domains, compartment A/B switching, lower chromatin accessibility, and corresponding transcriptomic changes. Mechanistically, adriamycin complexes with histone H1 and induces phase transition of H1, forming fibrous aggregates in vitro. These results reveal a phase separation-driven mechanism for a chemotherapeutic drug.
    DOI:  https://doi.org/10.1038/s41467-023-41340-4
  10. Nucleic Acids Res. 2023 Sep 13. pii: gkad756. [Epub ahead of print]
    CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin.
    Janne J M van Schie, Klaas de Lint, Thom M Molenaar, Macarena Moronta Gines, Jesper A Balk, Martin A Rooimans, Khashayar Roohollahi, Govind M Pai, Lauri Borghuis, Anisha R Ramadhin, Francesco Corazza, Josephine C Dorsman, Kerstin S Wendt, Rob M F Wolthuis, Job de Lange.
      The cohesin complex regulates higher order chromosome architecture through maintaining sister chromatid cohesion and folding chromatin by DNA loop extrusion. Impaired cohesin function underlies a heterogeneous group of genetic syndromes and is associated with cancer. Here, we mapped the genetic dependencies of human cell lines defective of cohesion regulators DDX11 and ESCO2. The obtained synthetic lethality networks are strongly enriched for genes involved in DNA replication and mitosis and support the existence of parallel sister chromatid cohesion establishment pathways. Among the hits, we identify the chromatin binding, BRCT-domain containing protein PAXIP1 as a novel cohesin regulator. Depletion of PAXIP1 severely aggravates cohesion defects in ESCO2 mutant cells, leading to mitotic cell death. PAXIP1 promotes global chromatin association of cohesin, independent of DNA replication, a function that cannot be explained by indirect effects of PAXIP1 on transcription or DNA repair. Cohesin regulation by PAXIP1 requires its binding partner PAGR1 and a conserved FDF motif in PAGR1. PAXIP1 co-localizes with cohesin on multiple genomic loci, including active gene promoters and enhancers. Possibly, this newly identified role of PAXIP1-PAGR1 in regulating cohesin occupancy on chromatin is also relevant for previously described functions of PAXIP1 in transcription, immune cell maturation and DNA repair.
    DOI:  https://doi.org/10.1093/nar/gkad756
  11. PLoS Genet. 2023 Sep;19(9): e1010906
    Histone methylation regulates reproductive diapause in Drosophila melanogaster.
    Abigail DiVito Evans, Regina A Fairbanks, Paul Schmidt, Mia T Levine.
      Fluctuating environments threaten fertility and viability. To better match the immediate, local environment, many organisms adopt alternative phenotypic states, a phenomenon called "phenotypic plasticity." Natural populations that predictably encounter fluctuating environments tend to be more plastic than conspecific populations that encounter a constant environment, suggesting that phenotypic plasticity can be adaptive. Despite pervasive evidence of such "adaptive phenotypic plasticity," gene regulatory mechanisms underlying plasticity remains poorly understood. Here we test the hypothesis that environment-dependent phenotypic plasticity is mediated by epigenetic factors. To test this hypothesis, we exploit the adaptive reproductive arrest of Drosophila melanogaster females, called diapause. Using an inbred line from a natural population with high diapause plasticity, we demonstrate that diapause is determined epigenetically: only a subset of genetically identical individuals enter diapause and this diapause plasticity is epigenetically transmitted for at least three generations. Upon screening a suite of epigenetic marks, we discovered that the active histone marks H3K4me3 and H3K36me1 are depleted in diapausing ovaries. Using ovary-specific knockdown of histone mark writers and erasers, we demonstrate that H3K4me3 and H3K36me1 depletion promotes diapause. Given that diapause is highly polygenic, that is, distinct suites of alleles mediate diapause plasticity across distinct genotypes, we also investigated the potential for genetic variation in diapause-determining epigenetic marks. Specifically, we asked if these histone marks were similarly depleted in diapause of a genotypically distinct line. We found evidence of divergence in both the gene expression program and histone mark abundance. This study reveals chromatin determinants of phenotypic plasticity and suggests that these determinants may be genotype-dependent, offering new insight into how organisms may exploit and evolve epigenetic mechanisms to persist in fluctuating environments.
    DOI:  https://doi.org/10.1371/journal.pgen.1010906
  12. Nat Struct Mol Biol. 2023 Sep 11.
    Transcriptional repression upon S phase entry protects genome integrity in pluripotent cells.
    Deniz Gökbuget, Kayla Lenshoek, Ryan M Boileau, Jonathan Bayerl, Hector Huang, Arun P Wiita, Diana J Laird, Robert Blelloch.
      Coincident transcription and DNA replication causes replication stress and genome instability. Rapidly dividing mouse pluripotent stem cells are highly transcriptionally active and experience elevated replication stress, yet paradoxically maintain genome integrity. Here, we study FOXD3, a transcriptional repressor enriched in pluripotent stem cells, and show that its repression of transcription upon S phase entry is critical to minimizing replication stress and preserving genome integrity. Acutely deleting Foxd3 leads to immediate replication stress, G2/M phase arrest, genome instability and p53-dependent apoptosis. FOXD3 binds near highly transcribed genes during S phase entry, and its loss increases the expression of these genes. Transient inhibition of RNA polymerase II in S phase reduces observed replication stress and cell cycle defects. Loss of FOXD3-interacting histone deacetylases induces replication stress, while transient inhibition of histone acetylation opposes it. These results show how a transcriptional repressor can play a central role in maintaining genome integrity through the transient inhibition of transcription during S phase, enabling faithful DNA replication.
    DOI:  https://doi.org/10.1038/s41594-023-01092-7
  13. Genome Biol. 2023 09 11. 24(1): 206
    Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis.
    Sixian Zhou, Fengli Zhao, Danling Zhu, Qiqi Zhang, Ziwei Dai, Zhe Wu.
       BACKGROUND: In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive.
    RESULT: Here, we analyze Pol II dynamics at 3' ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated (Ser2P) Pol II positioning data specifically enriched at 3' ends and define a 3' end pause index (3'PI). The position but not the extent of the 3' end pause correlates with the termination window size. The 3'PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3' end pause is a regulatory step early during the termination and before XRN3-mediated RNA decay that releases Pol II. Unexpectedly, 3'PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3' end pauses and more efficient on-chromatin splicing than genes with fewer exons. Chemical inhibition of splicing strongly reduces the 3'PI and disrupts its correlation with exon numbers but does not globally impact 3' end readthrough levels. These results are further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics.
    CONCLUSION: Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at the 3' end of genes in plants.
    Keywords:  Co-transcriptional splicing; Exon numbers; Plants; Pol II transcription; Transcription termination
    DOI:  https://doi.org/10.1186/s13059-023-03050-4
  14. Nat Cell Biol. 2023 Sep;25(9): 1279-1289
    m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency.
    Evelyne Collignon, Brandon Cho, Giacomo Furlan, Julie Fothergill-Robinson, Sylvia-Bryn Martin, Sarah A McClymont, Robert L Ross, Patrick A Limbach, Miguel Ramalho-Santos.
      Embryos across metazoan lineages can enter reversible states of developmental pausing, or diapause, in response to adverse environmental conditions. The molecular mechanisms that underlie this remarkable dormant state remain largely unknown. Here we show that N6-methyladenosine (m6A) RNA methylation by Mettl3 is required for developmental pausing in mouse blastocysts and embryonic stem (ES) cells. Mettl3 enforces transcriptional dormancy through two interconnected mechanisms: (1) it promotes global mRNA destabilization and (2) it suppresses global nascent transcription by destabilizing the mRNA of the transcriptional amplifier and oncogene N-Myc, which we identify as a crucial anti-pausing factor. Knockdown of N-Myc rescues pausing in Mettl3-/- ES cells, and forced demethylation and stabilization of Mycn mRNA in paused wild-type ES cells largely recapitulates the transcriptional defects of Mettl3-/- ES cells. These findings uncover Mettl3 as a key orchestrator of the crosstalk between transcriptomic and epitranscriptomic regulation during developmental pausing, with implications for dormancy in adult stem cells and cancer.
    DOI:  https://doi.org/10.1038/s41556-023-01212-x
  15. Nat Commun. 2023 Sep 15. 14(1): 5730
    Interlocking of co-opted developmental gene networks in Drosophila and the evolution of pre-adaptive novelty.
    Sara Molina-Gil, Sol Sotillos, José Manuel Espinosa-Vázquez, Isabel Almudi, James C-G Hombría.
      The re-use of genes in new organs forms the base of many evolutionary novelties. A well-characterised case is the recruitment of the posterior spiracle gene network to the Drosophila male genitalia. Here we find that this network has also been co-opted to the testis mesoderm where is required for sperm liberation, providing an example of sequentially repeated developmental co-options. Associated to this co-option event, an evolutionary expression novelty appeared, the activation of the posterior segment determinant Engrailed to the anterior A8 segment controlled by common testis and spiracle regulatory elements. Enhancer deletion shows that A8 anterior Engrailed activation is not required for spiracle development but only necessary in the testis. Our study presents an example of pre-adaptive developmental novelty: the activation of the Engrailed transcription factor in the anterior compartment of the A8 segment where, despite having no specific function, opens the possibility of this developmental factor acquiring one. We propose that recently co-opted networks become interlocked, so that any change to the network because of its function in one organ, will be mirrored by other organs even if it provides no selective advantage to them.
    DOI:  https://doi.org/10.1038/s41467-023-41414-3
  16. Genome Res. 2023 Sep 12.
    Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features.
    Marielle L Bond, Eric S Davis, Ivana Y Quiroga, Anubha Dey, Manjari Kiran, Michael I Love, Hyejung Won, Douglas H Phanstiel.
      Three-dimensional (3D) chromatin structure has been shown to play a role in regulating gene transcription during biological transitions. Although our understanding of loop formation and maintenance is rapidly improving, much less is known about the mechanisms driving changes in looping and the impact of differential looping on gene transcription. One limitation has been a lack of well-powered differential looping data sets. To address this, we conducted a deeply sequenced Hi-C time course of megakaryocyte development comprising four biological replicates and 6 billion reads per time point. Statistical analysis revealed 1503 differential loops. Gained loop anchors were enriched for AP-1 occupancy and were characterized by large increases in histone H3K27ac (over 11-fold) but relatively small increases in CTCF and RAD21 binding (1.26- and 1.23-fold, respectively). Linear modeling revealed that changes in histone H3K27ac, chromatin accessibility, and JUN binding were better correlated with changes in looping than RAD21 and almost as well correlated as CTCF. Changes to epigenetic features between-rather than at-boundaries were highly predictive of changes in looping. Together these data suggest that although CTCF and RAD21 may be the core machinery dictating where loops form, other features (both at the anchors and within the loop boundaries) may play a larger role than previously anticipated in determining the relative loop strength across cell types and conditions.
    DOI:  https://doi.org/10.1101/gr.277397.122
  17. Proc Natl Acad Sci U S A. 2023 Sep 19. 120(38): e2302489120
    Serine starvation silences estrogen receptor signaling through histone hypoacetylation.
    Albert M Li, Bo He, Dimitris Karagiannis, Yang Li, Haowen Jiang, Preethi Srinivasan, Yaniel Ramirez, Meng-Ning Zhou, Christina Curtis, Joshua J Gruber, Chao Lu, Erinn B Rankin, Jiangbin Ye.
      Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.
    Keywords:  SLC25A1; breast cancer; estrogen receptor; histone acetylation; serine metabolism
    DOI:  https://doi.org/10.1073/pnas.2302489120
  18. Nat Commun. 2023 Sep 12. 14(1): 5616
    SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells.
    Meng Zhang, Mary Elisabeth Ehmann, Srija Matukumalli, Aashutosh Girish Boob, David M Gilbert, Huimin Zhao.
      Chromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less characterized in the non-coding genome, partially due to the lack of a platform to readily evaluate boundary-associated activities of putative DNA sequences. Here we report SHIELD (Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains), a platform tailored for the high-throughput screening of barrier-type DNA elements in human cells. SHIELD takes advantage of the high specificity of serine integrase at heterochromatin, and exploits the natural heterochromatin spreading inside lamina-associated domains (LADs) for the discovery of potent barrier elements. We adopt SHIELD to evaluate the barrier activity of 1000 DNA elements in a high-throughput manner and identify 8 candidates with barrier activities comparable to the core region of cHS4 element in human HCT116 cells. We anticipate SHIELD could facilitate the discovery of novel barrier DNA elements from the non-coding genome in human cells.
    DOI:  https://doi.org/10.1038/s41467-023-41468-3
  19. Proteomics. 2023 Sep 14. e2200462
    Computational tools for inferring transcription factor activity.
    Dennis Hecker, Michael Lauber, Fatemeh Behjati Ardakani, Shamim Ashrafiyan, Quirin Manz, Johannes Kersting, Markus Hoffmann, Marcel H Schulz, Markus List.
      Transcription factors (TFs) are essential players in orchestrating the regulatory landscape in cells. Still, their exact modes of action and dependencies on other regulatory aspects remain elusive. Since TFs act cell type-specific and each TF has its own characteristics, untangling their regulatory interactions from an experimental point of view is laborious and convoluted. Thus, there is an ongoing development of computational tools that estimate transcription factor activity (TFA) from a variety of data modalities, either based on a mapping of TFs to their putative target genes or in a genome-wide, gene-unspecific fashion. These tools can help to gain insights into TF regulation and to prioritize candidates for experimental validation. We want to give an overview of available computational tools that estimate TFA, illustrate examples of their application, debate common result validation strategies, and discuss assumptions and concomitant limitations.
    Keywords:  bioinformatic tools; gene regulation; gene regulatory networks; transcription factor activity
    DOI:  https://doi.org/10.1002/pmic.202200462
  20. Cell Rep. 2023 Sep 13. pii: S2211-1247(23)01146-4. [Epub ahead of print]42(9): 113134
    Cryo-ET study from in vitro to in vivo revealed a general folding mode of chromatin with two-start helical architecture.
    Yan Li, Haonan Zhang, Xiaomin Li, Wanyu Wu, Ping Zhu.
      The organization and dynamics of chromatin fiber play crucial roles in regulating DNA accessibility for gene expression. Here we combine cryoelectron tomography (cryo-ET), sub-volume averaging, and 3D segmentation to visualize the in vitro and in vivo chromatin fibers folding by linker histone. We discover that an increased nucleosome repeat length and prolonged fiber length do not change the two-start helical architecture in reconstituted chromatin of homogeneous composition. Additionally, an isolated chromatin fiber with heterogeneous composition was observed, which includes short-range regions compatible with two-start helix. In vivo, sub-volume averaging reveals similar subunits of two-start helical architecture in transcriptionally inactive chromatin in frog erythrocyte nuclei. Strikingly, unambiguous DNA trajectories that displayed a zigzag pattern universally between alternate N/N+2 nucleosomes were further determined by cryo-ET with voltage phase plate. Therefore, these structural similarities suggest a general folding mode of chromatin induced by linker histone, and heterogeneous compositions mainly affect local conformation rather than changing the overall architecture.
    Keywords:  CP: Molecular biology; DNA trajectory; chromatin fiber; chromatin mass; linker histone; sub-volume averaging; two-start helix; voltage phase plate; zigzag
    DOI:  https://doi.org/10.1016/j.celrep.2023.113134
  21. Nat Biotechnol. 2023 Sep 11.
    Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells.
    Heon Seok Kim, Susan M Grimes, Tianqi Chen, Anuja Sathe, Billy T Lau, Gue-Ho Hwang, Sangsu Bae, Hanlee P Ji.
      Genome sequencing studies have identified numerous cancer mutations across a wide spectrum of tumor types, but determining the phenotypic consequence of these mutations remains a challenge. Here, we developed a high-throughput, multiplexed single-cell technology called TISCC-seq to engineer predesignated mutations in cells using CRISPR base editors, directly delineate their genotype among individual cells and determine each mutation's transcriptional phenotype. Long-read sequencing of the target gene's transcript identifies the engineered mutations, and the transcriptome profile from the same set of cells is simultaneously analyzed by short-read sequencing. Through integration, we determine the mutations' genotype and expression phenotype at single-cell resolution. Using cell lines, we engineer and evaluate the impact of >100 TP53 mutations on gene expression. Based on the single-cell gene expression, we classify the mutations as having a functionally significant phenotype.
    DOI:  https://doi.org/10.1038/s41587-023-01949-8
  22. Nat Commun. 2023 Sep 11. 14(1): 5587
    tgCRISPRi: efficient gene knock-down using truncated gRNAs and catalytically active Cas9.
    Ankush Auradkar, Annabel Guichard, Saluja Kaduwal, Marketta Sneider, Ethan Bier.
      CRISPR-interference (CRISPRi), a highly effective method for silencing genes in mammalian cells, employs an enzymatically dead form of Cas9 (dCas9) complexed with one or more guide RNAs (gRNAs) with 20 nucleotides (nt) of complementarity to transcription initiation sites of target genes. Such gRNA/dCas9 complexes bind to DNA, impeding transcription of the targeted locus. Here, we present an alternative gene-suppression strategy using active Cas9 complexed with truncated gRNAs (tgRNAs). Cas9/tgRNA complexes bind to specific target sites without triggering DNA cleavage. When targeted near transcriptional start sites, these short 14-15 nts tgRNAs efficiently repress expression of several target genes throughout somatic tissues in Drosophila melanogaster without generating any detectable target site mutations. tgRNAs also can activate target gene expression when complexed with a Cas9-VPR fusion protein or modulate enhancer activity, and can be incorporated into a gene-drive, wherein a traditional gRNA sustains drive while a tgRNA inhibits target gene expression.
    DOI:  https://doi.org/10.1038/s41467-023-40836-3
  23. Nat Commun. 2023 Sep 13. 14(1): 5673
    Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules.
    Jingqiu Lan, Ning Wang, Yutao Wang, Yidan Jiang, Hao Yu, Xiaofeng Cao, Genji Qin.
      Abnormal high temperature (HT) caused by global warming threatens plant survival and food security, but the effects of HT on plant organ identity are elusive. Here, we show that Class II TEOSINTE BRANCHED 1/CYCLOIDEA/ PCF (TCP) transcription factors redundantly protect ovule identity under HT. The duodecuple tcp2/3/4/5/10/13/17/24/1/12/18/16 (tcpDUO) mutant displays HT-induced ovule conversion into carpelloid structures. Expression of TCP4 in tcpDUO complements the ovule identity conversion. TCP4 interacts with AGAMOUS (AG), SEPALLATA3 (SEP3), and the homeodomain transcription factor BELL1 (BEL1) to strengthen the association of BEL1 with AG-SEP3. The tcpDUO mutant synergistically interacts with bel1 and the ovule identity gene seedstick (STK) mutant stk in tcpDUO bel1 and tcpDUO stk. Our findings reveal the critical roles of Class II TCPs in maintaining ovule identity under HT and shed light on the molecular mechanisms by which ovule identity is determined by the integration of internal factors and environmental temperature.
    DOI:  https://doi.org/10.1038/s41467-023-41416-1
  24. Genome Res. 2023 Sep 12. pii: gr.277298.122. [Epub ahead of print]
    Nucleosome repositioning in chronic lymphocytic leukaemia.
    Kristan V Piroeva, Charlotte McDonald, Charalampos Xanthopoulos, Chelsea Fox, Christopher T Clarkson, Jan-Philipp Mallm, Yevhen Vainshtein, Luminita Ruje, Lara C Klett, Stephan Stilgenbauer, Daniel Mertens, Efterpi Kostareli, Karsten Rippe, Vladimir B Teif.
      The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral-blood B cells from patients with chronic lymphocytic leukaemia (CLL) and healthy individuals at single base pair resolution. Our investigation uncovered significant changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes - the nucleosome repeat length (NRL) - was shortened in CLL. This effect was stronger in the more aggressive IGHV-unmutated than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites were linked to active chromatin remodelling and reduced DNA methylation. Nucleosomes lost or gained in CLL marked differential binding of 3D chromatin organisers such as CTCF as well as immune response-related transcription factors and delineated mechanisms of epigenetic deregulation. The principal component analysis of nucleosome occupancy in cancer-specific regions allowed classification of samples between cancer subtypes and normal controls. Furthermore, patients could be better assigned to CLL subtypes according to differential nucleosome occupancy than based on DNA methylation or gene expression. Thus, nucleosome positioning constitutes a novel readout to dissect molecular mechanisms of disease progression and to stratify patients. Furthermore, we anticipate that the global nucleosome repositioning detected in our study, such as changes in the NRL, can be exploited for liquid biopsy applications based on cell-free DNA to stratify patients and monitor disease progression.
    DOI:  https://doi.org/10.1101/gr.277298.122
  25. Cell Rep. 2023 Sep 08. pii: S2211-1247(23)01125-7. [Epub ahead of print]42(9): 113114
    DUX4 expression in cancer induces a metastable early embryonic totipotent program.
    Andrew A Smith, Yee Nip, Sean R Bennett, Danielle C Hamm, Richard J L F Lemmers, Patrick J van der Vliet, Manu Setty, Silvère M van der Maarel, Stephen J Tapscott.
      The transcription factor DUX4 regulates a portion of the zygotic gene activation (ZGA) program in the early embryo. Many cancers express DUX4 but it is unknown whether this generates cells similar to early embryonic stem cells. Here we identified cancer cell lines that express DUX4 and showed that DUX4 is transiently expressed in a small subset of the cells. DUX4 expression activates the DUX4-regulated ZGA transcriptional program, the subsequent 8C-like program, and markers of early embryonic lineages, while suppressing steady-state and interferon-induced MHC class I expression. Although DUX4 was expressed in a small number of cells under standard culture conditions, DNA damage or changes in growth conditions increased the fraction of cells expressing DUX4 and its downstream programs. Our demonstration that transient expression of endogenous DUX4 in cancer cells induces a metastable early embryonic stem cell program and suppresses antigen presentation has implications for cancer growth, progression, and immune evasion.
    Keywords:  CP: Cancer; DUX4; Dux; HLA; MHC; cancer; stem cell; totipotent; zygotic gene activation
    DOI:  https://doi.org/10.1016/j.celrep.2023.113114
  26. Cell. 2023 Sep 14. pii: S0092-8674(23)00902-9. [Epub ahead of print]186(19): 4216-4234.e33
    Modular pooled discovery of synthetic knockin sequences to program durable cell therapies.
    Franziska Blaeschke, Yan Yi Chen, Ryan Apathy, Bence Daniel, Andy Y Chen, Peixin Amy Chen, Katalin Sandor, Wenxi Zhang, Zhongmei Li, Cody T Mowery, Tori N Yamamoto, William A Nyberg, Angela To, Ruby Yu, Raymund Bueno, Min Cheol Kim, Ralf Schmidt, Daniel B Goodman, Tobias Feuchtinger, Justin Eyquem, Chun Jimmie Ye, Julia Carnevale, Ansuman T Satpathy, Eric Shifrut, Theodore L Roth, Alexander Marson.
      Chronic stimulation can cause T cell dysfunction and limit the efficacy of cellular immunotherapies. Improved methods are required to compare large numbers of synthetic knockin (KI) sequences to reprogram cell functions. Here, we developed modular pooled KI screening (ModPoKI), an adaptable platform for modular construction of DNA KI libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors (SRs). Over 30 ModPoKI screens across human TCR- and CAR-T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct that enhanced fitness of chronically stimulated CAR-T cells and anti-cancer function in vitro and in vivo. ModPoKI's modularity allowed us to generate an ∼10,000-member library of TF combinations. Non-viral KI of a combined BATF-TFAP4 polycistronic construct enhanced fitness. Overexpressed BATF and TFAP4 co-occupy and regulate key gene targets to reprogram T cell function. ModPoKI facilitates the discovery of complex gene constructs to program cellular functions.
    Keywords:  CRISPR; chimeric antigen receptor; chronic stimulation; human T cells; immunotherapy; knockins; pooled screens; synthetic surface receptor; transcription factor
    DOI:  https://doi.org/10.1016/j.cell.2023.08.013
  27. EMBO J. 2023 Sep 11. e114220
    DELLA-mediated gene repression is maintained by chromatin modification in rice.
    Junjie Li, Qi Li, Wentao Wang, Xinran Zhang, Chen Chu, Xintian Tang, Bo Zhu, Lizhong Xiong, Yu Zhao, Dao-Xiu Zhou.
      DELLA proteins are master regulators of gibberellic acid (GA) signaling through their effects on gene expression. Enhanced DELLA accumulation in rice and wheat varieties has greatly contributed to grain yield increases during the green revolution. However, the molecular basis of DELLA-mediated gene repression remains elusive. In this work, we show that the rice DELLA protein SLENDER RICE1 (SLR1) forms a tripartite complex with Polycomb-repressive complex 2 (PRC2) and the histone deacetylase HDA702 to repress downstream genes by establishing a silent chromatin state. The slr1 mutation and GA signaling resulted in dissociation of PRC2 and HDA702 from GA-inducible genes. Loss-of-function or downregulation of the chromatin regulators impaired SLR1-dependent histone modification and gene repression. Time-resolved analysis of GA signaling revealed that GA-induced transcriptional activation was associated with a rapid increase of H3K9ac followed by H3K27me3 removal. Collectively, these results establish a general epigenetic mechanism for DELLA-mediated gene repression and reveal details of the chromatin dynamics during transcriptional activation stimulated by GA signaling.
    Keywords:  DELLA; HDA702; Polycomb-repressive complex 2 (PRC2); histone deacetylase; histone methylation
    DOI:  https://doi.org/10.15252/embj.2023114220
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