bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–05–08
twenty-one papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat.
  2. Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans.
  3. Transcriptional coupling of distant regulatory genes in living embryos.
  4. Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication.
  5. Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice.
  6. TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure.
  7. FTO mediates LINE1 m6A demethylation and chromatin regulation in mESCs and mouse development.
  8. Histone H3K4me3 breadth in hypoxia reveals endometrial core functions and stress adaptation linked to endometriosis.
  9. Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions.
  10. Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.
  11. A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation.
  12. NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells.
  13. ISL2 is a putative tumor suppressor whose epigenetic silencing reprograms the metabolism of pancreatic cancer.
  14. Enhancer selection dictates gene expression responses in remote organs during tissue regeneration.
  15. H3K4me3 recognition by the COMPASS complex facilitates the restoration of this histone mark following DNA replication.
  16. The Mettl3 epitranscriptomic writer amplifies p53 stress responses.
  17. The Chd4 subunit of the NuRD complex regulates Pdx1-controlled genes involved in β-cell function.
  18. A Runx1-enhancer Element eR1 Identified Lineage Restricted Mammary Luminal Stem Cells.
  19. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.
  20. Dnmt1a is essential for gene body methylation and the regulation of the zygotic genome in a wasp.
  21. Targeting CDCP1 gene transcription coactivated by BRD4 and CBP/p300 in castration-resistant prostate cancer.
  1. Genome Biol. 2022 Apr 30. 23(1): 109
    Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat.
    Yilin Xie, Yan Chen, Zijuan Li, Jiafu Zhu, Min Liu, Yijing Zhang, Zhicheng Dong.
      The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epigenome profiling, we detect active transcription of enhancers from the complex bread wheat genome. We find that genes associated with transcriptional enhancers are expressed at significantly higher levels, and enhancer RNA is more precise and robust in predicting enhancer activity compared to chromatin features. We demonstrate that sub-genome-biased enhancer transcription could drive sub-genome-biased gene expression. This study highlights enhancer transcription as a hallmark in regulating gene expression in wheat.
    Keywords:  Bread wheat; Enhancer; Nascent RNA; Subgenome-bias; eRNA
    DOI:  https://doi.org/10.1186/s13059-022-02675-1
  2. Cell Rep. 2022 05 03. pii: S2211-1247(22)00533-2. [Epub ahead of print]39(5): 110769
    Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans.
    Sarah E Gilbertson, Hannah C Walter, Katherine Gardner, Spencer N Wren, Golnaz Vahedi, Amy S Weinmann.
      Distinguishing between conserved and divergent regulatory mechanisms is essential for translating preclinical research from mice to humans, yet there is a lack of information about how evolutionary genome rearrangements affect the regulation of the immune response, a rapidly evolving system. The current model is topologically associating domains (TADs) are conserved between species, buffering evolutionary rearrangements and conserving long-range interactions within a TAD. However, we find that TADs frequently span evolutionary translocation and inversion breakpoints near genes with species-specific expression in immune cells, creating unique enhancer-promoter interactions exclusive to the mouse or human genomes. This includes TADs encompassing immune-related transcription factors, cytokines, and receptors. For example, we uncover an evolutionary rearrangement that created a shared LPS-inducible regulatory module between OASL and P2RX7 in human macrophages that is absent in mice. Therefore, evolutionary genome rearrangements disrupt TAD boundaries, enabling sequence-conserved enhancer elements from divergent genomic locations between species to create unique regulatory modules.
    Keywords:  B cells; CCR5; CD163; CP: Immunology; CXCL13; CXCR4; EOMES; IDO1; IL23R; IL6; IRF4; JUN; NAMPT; NOS2; P2RX7; T cells; TLR9; genome topology; genomic structural variation; iNOS; macrophages
    DOI:  https://doi.org/10.1016/j.celrep.2022.110769
  3. Nature. 2022 May 04.
    Transcriptional coupling of distant regulatory genes in living embryos.
    Michal Levo, João Raimundo, Xin Yang Bing, Zachary Sisco, Philippe J Batut, Sergey Ryabichko, Thomas Gregor, Michael S Levine.
      The prevailing view of metazoan gene regulation is that individual genes are independently regulated by their own dedicated sets of transcriptional enhancers. Past studies have reported long-range gene-gene associations1-3, but their functional importance in regulating transcription remains unclear. Here we used quantitative single-cell live imaging methods to provide a demonstration of co-dependent transcriptional dynamics of genes separated by large genomic distances in living Drosophila embryos. We find extensive physical and functional associations of distant paralogous genes, including co-regulation by shared enhancers and co-transcriptional initiation over distances of nearly 250 kilobases. Regulatory interconnectivity depends on promoter-proximal tethering elements, and perturbations in these elements uncouple transcription and alter the bursting dynamics of distant genes, suggesting a role of genome topology in the formation and stability of co-transcriptional hubs. Transcriptional coupling is detected throughout the fly genome and encompasses a broad spectrum of conserved developmental processes, suggesting a general strategy for long-range integration of gene activity.
    DOI:  https://doi.org/10.1038/s41586-022-04680-7
  4. Development. 2022 May 01. pii: dev200568. [Epub ahead of print]149(9):
    Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication.
    Rafael Galupa, Christel Picard, Nicolas Servant, Elphège P Nora, Yinxiu Zhan, Joke G van Bemmel, Fatima El Marjou, Colin Johanneau, Maud Borensztein, Katia Ancelin, Luca Giorgetti, Edith Heard.
      The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors (e.g. CTCF) underlying topologically associating domains (TADs) leads to modest alterations in gene expression, whereas genomic rearrangements involving TAD boundaries disrupt normal gene expression and can lead to pathological phenotypes. Here, we targeted the TAD neighboring that of the noncoding transcript Xist, which controls X-chromosome inactivation. Inverting 245 kb within the TAD led to expected rearrangement of CTCF-based contacts but revealed heterogeneity in the 'contact' potential of different CTCF sites. Expression of most genes therein remained unaffected in mouse embryonic stem cells and during differentiation. Interestingly, expression of Xist was ectopically upregulated. The same inversion in mouse embryos led to biased Xist expression. Smaller inversions and deletions of CTCF clusters led to similar results: rearrangement of contacts and limited changes in local gene expression, but significant changes in Xist expression in embryos. Our study suggests that the wiring of regulatory interactions within a TAD can influence the expression of genes in neighboring TADs, highlighting the existence of mechanisms of inter-TAD communication.
    Keywords:  Gene expression; Genomic engineering; TADs; X-inactivation; Xist
    DOI:  https://doi.org/10.1242/dev.200568
  5. Nat Commun. 2022 May 05. 13(1): 2464
    Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice.
    Mathew Van de Pette, Andrew Dimond, António M Galvão, Steven J Millership, Wilson To, Chiara Prodani, Gráinne McNamara, Ludovica Bruno, Alessandro Sardini, Zoe Webster, James McGinty, Paul M W French, Anthony G Uren, Juan Castillo-Fernandez, William Watkinson, Anne C Ferguson-Smith, Matthias Merkenschlager, Rosalind M John, Gavin Kelsey, Amanda G Fisher.
      Transmission of epigenetic information between generations occurs in nematodes, flies and plants, mediated by specialised small RNA pathways, modified histones and DNA methylation. Similar processes in mammals can also affect phenotype through intergenerational or trans-generational mechanisms. Here we generate a luciferase knock-in reporter mouse for the imprinted Dlk1 locus to visualise and track epigenetic fidelity across generations. Exposure to high-fat diet in pregnancy provokes sustained re-expression of the normally silent maternal Dlk1 in offspring (loss of imprinting) and increased DNA methylation at the somatic differentially methylated region (sDMR). In the next generation heterogeneous Dlk1 mis-expression is seen exclusively among animals born to F1-exposed females. Oocytes from these females show altered gene and microRNA expression without changes in DNA methylation, and correct imprinting is restored in subsequent generations. Our results illustrate how diet impacts the foetal epigenome, disturbing canonical and non-canonical imprinting mechanisms to modulate the properties of successive generations of offspring.
    DOI:  https://doi.org/10.1038/s41467-022-30022-2
  6. Nucleic Acids Res. 2022 May 07. pii: gkac318. [Epub ahead of print]
    TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure.
    Barbara Poszewiecka, Victor Murcia Pienkowski, Karol Nowosad, Jérôme D Robin, Krzysztof Gogolewski, Anna Gambin.
      In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement's breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl.
    DOI:  https://doi.org/10.1093/nar/gkac318
  7. Science. 2022 May 05. eabe9582
    FTO mediates LINE1 m6A demethylation and chromatin regulation in mESCs and mouse development.
    Jiangbo Wei, Xianbin Yu, Lei Yang, Xuelian Liu, Boyang Gao, Boxian Huang, Xiaoyang Dou, Jun Liu, Zhongyu Zou, Xiao-Long Cui, Li-Sheng Zhang, Xingsen Zhao, Qinzhe Liu, P Cody He, Caraline Sepich-Poore, Nicole Zhong, Wenqiang Liu, Yanhe Li, Xiaochen Kou, Yanhong Zhao, You Wu, Xuejun Cheng, Chuan Chen, Yiming An, Xueyang Dong, Huanyu Wang, Qiang Shu, Ziyang Hao, Tao Duan, Yu-Ying He, Xuekun Li, Shaorong Gao, Yawei Gao, Chuan He.
      N6-methyladenosine (m6A) is the most abundant internal modification on mammalian messenger RNA (mRNA). It is installed by a writer complex and can be reversed by erasers such as the fat mass and obesity-associated protein (FTO). Despite extensive research, the primary physiological substrates of FTO in mammalian tissues and development remain elusive. Here, we show that FTO mediates m6A demethylation of long-interspersed element-1 (LINE1) RNA in mouse embryonic stem cells (mESCs), regulating LINE1 RNA abundance and the local chromatin state, which in turn modulates transcription of LINE1-containing genes. FTO-mediated LINE1 RNA m6A demethylation also plays regulatory roles in shaping chromatin state and gene expression during mouse oocyte and embryonic development. Our results suggest broad effects of LINE1 RNA m6A demethylation by FTO in mammals.
    DOI:  https://doi.org/10.1126/science.abe9582
  8. iScience. 2022 May 20. 25(5): 104235
    Histone H3K4me3 breadth in hypoxia reveals endometrial core functions and stress adaptation linked to endometriosis.
    Kalle T Rytkönen, Thomas Faux, Mehrad Mahmoudian, Taija Heinosalo, Mauris C Nnamani, Antti Perheentupa, Matti Poutanen, Laura L Elo, Günter P Wagner.
      Trimethylation of histone H3 at lysine 4 (H3K4me3) is a marker of active promoters. Broad H3K4me3 promoter domains have been associated with cell type identity, but H3K4me3 dynamics upon cellular stress have not been well characterized. We assessed this by exposing endometrial stromal cells to hypoxia, which is a major cellular stress condition. We observed that hypoxia modifies the existing H3K4me3 marks and that promoter H3K4me3 breadth rather than height correlates with transcription. Broad H3K4me3 domains mark genes for endometrial core functions and are maintained or selectively extended upon hypoxia. Hypoxic extension of H3K4me3 breadth associates with stress adaptation genes relevant for the survival of endometrial cells including transcription factor KLF4, for which we found increased protein expression in the stroma of endometriosis lesions. These results substantiate the view on broad H3K4me3 as a marker of cell identity genes and reveal participation of H3K4me3 extension in cellular stress adaptation.
    Keywords:  Biological sciences; Cell biology; Epigenetics; Functional aspects of cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2022.104235
  9. Nat Commun. 2022 May 06. 13(1): 2514
    Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions.
    Xiaowei Xu, Shoufu Duan, Xu Hua, Zhiming Li, Richard He, Zhiguo Zhaang.
      Newly synthesized H3.1 and H3.3 histones are assembled into nucleosomes by different histone chaperones in replication-coupled and replication-independent pathways, respectively. However, it is not clear how parental H3.3 molecules are transferred following DNA replication, especially when compared to H3.1. Here, by monitoring parental H3.1- and H3.3-SNAP signals, we show that parental H3.3, like H3.1, are stably transferred into daughter cells. Moreover, Mcm2-Pola1 and Pole3-Pole4, two pathways involved in parental histone transfer based upon the analysis of modifications on parental histones, participate in the transfer of both H3.1 and H3.3 following DNA replication. Lastly, we found that Mcm2, Pole3 and Pole4 mutants defective in parental histone transfer show defects in chromosome segregation. These results indicate that in contrast to deposition of newly synthesized H3.1 and H3.3, transfer of parental H3.1 and H3.3 is mediated by these shared mechanisms, which contributes to epigenetic memory of gene expression and maintenance of genome stability.
    DOI:  https://doi.org/10.1038/s41467-022-30298-4
  10. Nat Commun. 2022 May 04. 13(1): 2429
    Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.
    Vladyslava Gorbovytska, Seung-Kyoon Kim, Filiz Kuybu, Michael Götze, Dahun Um, Keunsoo Kang, Andreas Pittroff, Theresia Brennecke, Lisa-Marie Schneider, Alexander Leitner, Tae-Kyung Kim, Claus-D Kuhn.
      Enhancer RNAs (eRNAs) are long non-coding RNAs that originate from enhancers. Although eRNA transcription is a canonical feature of activated enhancers, the molecular features required for eRNA function and the mechanism of how eRNAs impinge on target gene transcription have not been established. Thus, using eRNA-dependent RNA polymerase II (Pol II) pause release as a model, we here investigate the requirement of sequence, structure and length of eRNAs for their ability to stimulate Pol II pause release by detaching NELF from paused Pol II. We find eRNAs not to exert their function through common structural or sequence motifs. Instead, eRNAs that exhibit a length >200 nucleotides and that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release. By revealing the molecular determinants of eRNA function, our study establishes eRNAs as an important player in Pol II pause release, and it provides new insight into the regulation of metazoan transcription.
    DOI:  https://doi.org/10.1038/s41467-022-29934-w
  11. Nucleic Acids Res. 2022 May 03. pii: gkac256. [Epub ahead of print]
    A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation.
    Ankitha Shetty, Subhash Kumar Tripathi, Sini Junttila, Tanja Buchacher, Rahul Biradar, Santosh D Bhosale, Tapio Envall, Asta Laiho, Robert Moulder, Omid Rasool, Sanjeev Galande, Laura L Elo, Riitta Lahesmaa.
      Th17 cells are essential for protection against extracellular pathogens, but their aberrant activity can cause autoimmunity. Molecular mechanisms that dictate Th17 cell-differentiation have been extensively studied using mouse models. However, species-specific differences underscore the need to validate these findings in human. Here, we characterized the human-specific roles of three AP-1 transcription factors, FOSL1, FOSL2 and BATF, during early stages of Th17 differentiation. Our results demonstrate that FOSL1 and FOSL2 co-repress Th17 fate-specification, whereas BATF promotes the Th17 lineage. Strikingly, FOSL1 was found to play different roles in human and mouse. Genome-wide binding analysis indicated that FOSL1, FOSL2 and BATF share occupancy over regulatory regions of genes involved in Th17 lineage commitment. These AP-1 factors also share their protein interacting partners, which suggests mechanisms for their functional interplay. Our study further reveals that the genomic binding sites of FOSL1, FOSL2 and BATF harbour hundreds of autoimmune disease-linked SNPs. We show that many of these SNPs alter the ability of these transcription factors to bind DNA. Our findings thus provide critical insights into AP-1-mediated regulation of human Th17-fate and associated pathologies.
    DOI:  https://doi.org/10.1093/nar/gkac256
  12. Nat Methods. 2022 May 02.
    NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells.
    Amy F Chen, Benjamin Parks, Arwa S Kathiria, Benjamin Ober-Reynolds, Jorg J Goronzy, William J Greenleaf.
      In this work, we describe NEAT-seq (sequencing of nuclear protein epitope abundance, chromatin accessibility and the transcriptome in single cells), enabling interrogation of regulatory mechanisms spanning the central dogma. We apply this technique to profile CD4 memory T cells using a panel of master transcription factors (TFs) that drive T cell subsets and identify examples of TFs with regulatory activity gated by transcription, translation and regulation of chromatin binding. We also link a noncoding genome-wide association study single-nucleotide polymorphism (SNP) within a GATA motif to a putative target gene, using NEAT-seq data to internally validate SNP impact on GATA3 regulation.
    DOI:  https://doi.org/10.1038/s41592-022-01461-y
  13. Dev Cell. 2022 Apr 22. pii: S1534-5807(22)00254-4. [Epub ahead of print]
    ISL2 is a putative tumor suppressor whose epigenetic silencing reprograms the metabolism of pancreatic cancer.
    Harun Ozturk, Harun Cingoz, Turan Tufan, Jiekun Yang, Sara J Adair, Krishna Seshu Tummala, Cem Kuscu, Meric Kinali, Gamze Comertpay, Sarbajeet Nagdas, Bernadette J Goudreau, Husnu Umit Luleyap, Yagmur Bingul, Timothy B Ware, Wiliam L Hwang, Ku-Lung Hsu, David F Kashatus, David T Ting, Navdeep S Chandel, Nabeel Bardeesy, Todd W Bauer, Mazhar Adli.
      Pancreatic ductal adenocarcinoma (PDA) cells reprogram their transcriptional and metabolic programs to survive the nutrient-poor tumor microenvironment. Through in vivo CRISPR screening, we discovered islet-2 (ISL2) as a candidate tumor suppressor that modulates aggressive PDA growth. Notably, ISL2, a nuclear and chromatin-associated transcription factor, is epigenetically silenced in PDA tumors and high promoter DNA methylation or its reduced expression correlates with poor patient survival. The exogenous ISL2 expression or CRISPR-mediated upregulation of the endogenous loci reduces cell proliferation. Mechanistically, ISL2 regulates the expression of metabolic genes, and its depletion increases oxidative phosphorylation (OXPHOS). As such, ISL2-depleted human PDA cells are sensitive to the inhibitors of mitochondrial complex I in vitro and in vivo. Spatial transcriptomic analysis shows heterogeneous intratumoral ISL2 expression, which correlates with the expression of critical metabolic genes. These findings nominate ISL2 as a putative tumor suppressor whose inactivation leads to increased mitochondrial metabolism that may be exploitable therapeutically.
    Keywords:  CRISPR; ISL2; pancreatic cancer; tumor suppressor
    DOI:  https://doi.org/10.1016/j.devcel.2022.04.014
  14. Nat Cell Biol. 2022 May 05.
    Enhancer selection dictates gene expression responses in remote organs during tissue regeneration.
    Fei Sun, Jianhong Ou, Adam R Shoffner, Yu Luan, Hongbo Yang, Lingyun Song, Alexias Safi, Jingli Cao, Feng Yue, Gregory E Crawford, Kenneth D Poss.
      Acute trauma stimulates local repair mechanisms but can also impact structures distant from the injury, for example through the activity of circulating factors. To study the responses of remote tissues during tissue regeneration, we profiled transcriptomes of zebrafish brains after experimental cardiac damage. We found that the transcription factor gene cebpd was upregulated remotely in brain ependymal cells as well as kidney tubular cells, in addition to its local induction in epicardial cells. cebpd mutations altered both local and distant cardiac injury responses, altering the cycling of epicardial cells as well as exchange between distant fluid compartments. Genome-wide profiling and transgenesis identified a hormone-responsive enhancer near cebpd that exists in a permissive state, enabling rapid gene expression in heart, brain and kidney after cardiac injury. Deletion of this sequence selectively abolished cebpd induction in remote tissues and disrupted fluid regulation after injury, without affecting its local cardiac expression response. Our findings suggest a model to broaden gene function during regeneration in which enhancer regulatory elements define short- and long-range expression responses to injury.
    DOI:  https://doi.org/10.1038/s41556-022-00906-y
  15. Sci Adv. 2022 May 06. 8(18): eabm6246
    H3K4me3 recognition by the COMPASS complex facilitates the restoration of this histone mark following DNA replication.
    Albert Serra-Cardona, Shoufu Duan, Chuanhe Yu, Zhiguo Zhang.
      During DNA replication, parental H3-H4 marked by H3K4me3 are transferred almost equally onto leading and lagging strands of DNA replication forks. Mutations in replicative helicase subunit, Mcm2 (Mcm2-3A), and leading strand DNA polymerase subunit, Dpb3 (dpb3∆), result in asymmetric distributions of H3K4me3 at replicating DNA strands immediately following DNA replication. Here, we show that mcm2-3A and dpb3∆ mutant cells markedly reduce the asymmetric distribution of H3K4me3 during cell cycle progression before mitosis. Furthermore, the restoration of a more symmetric distribution of H3K4me3 at replicating DNA strands in these mutant cells is driven by methylating nucleosomes without H3K4me3 by the H3K4 methyltransferase complex, COMPASS. Last, both gene transcription machinery and the binding of parental H3K4me3 by Spp1 subunit of the COMPASS complex help recruit the enzyme to chromatin for the restoration of the H3K4me3-marked state following DNA replication, shedding light on inheritance of this mark following DNA replication.
    DOI:  https://doi.org/10.1126/sciadv.abm6246
  16. Mol Cell. 2022 Apr 27. pii: S1097-2765(22)00321-5. [Epub ahead of print]
    The Mettl3 epitranscriptomic writer amplifies p53 stress responses.
    Nitin Raj, Mengxiong Wang, Jose A Seoane, Richard L Zhao, Alyssa M Kaiser, Nancie A Moonie, Janos Demeter, Anthony M Boutelle, Craig H Kerr, Abigail S Mulligan, Clare Moffatt, Shelya X Zeng, Hua Lu, Maria Barna, Christina Curtis, Howard Y Chang, Peter K Jackson, Laura D Attardi.
      The p53 transcription factor drives anti-proliferative gene expression programs in response to diverse stressors, including DNA damage and oncogenic signaling. Here, we seek to uncover new mechanisms through which p53 regulates gene expression using tandem affinity purification/mass spectrometry to identify p53-interacting proteins. This approach identified METTL3, an m6A RNA-methyltransferase complex (MTC) constituent, as a p53 interactor. We find that METTL3 promotes p53 protein stabilization and target gene expression in response to DNA damage and oncogenic signals, by both catalytic activity-dependent and independent mechanisms. METTL3 also enhances p53 tumor suppressor activity in in vivo mouse cancer models and human cancer cells. Notably, METTL3 only promotes tumor suppression in the context of intact p53. Analysis of human cancer genome data further supports the notion that the MTC reinforces p53 function in human cancer. Together, these studies reveal a fundamental role for METTL3 in amplifying p53 signaling in response to cellular stress.
    Keywords:  DNA damage; METTL14; METTL3; N(6)-methyladenosine (m6A) modification; epitranscriptomics; lung cancer; mass spectrometry; methyltransferase complex; p53; tumor suppressor
    DOI:  https://doi.org/10.1016/j.molcel.2022.04.010
  17. J Mol Endocrinol. 2022 May 01. pii: JME-22-0011. [Epub ahead of print]
    The Chd4 subunit of the NuRD complex regulates Pdx1-controlled genes involved in β-cell function.
    Rebecca K Davidson, Staci A Weaver, Nolan Casey, Sukrati Kanojia, Elise Hogarth, Rebecca Schneider Aguirre, Emily K Sims, Carmella Evans-Molina, Jason M Spaeth.
      Type 2 diabetes (T2D) is associated with loss of transcription factors (TFs) from a subset of failing β-cells. Among these TFs is Pdx1, which controls the expression of numerous genes involved in maintaining β-cell function and identity. Pdx1 activity is modulated by transcriptional coregulators and has recently been shown, through an unbiased screen, to interact with the Chd4 ATPase subunit of the Nucleosome Remodeling and Deacetylase complex. Chd4 contributes to the maintenance of cellular identity and functional status of numerous different cell types. Here, we demonstrate Pdx1 dynamically interacts with Chd4 under physiological and stimulatory conditions within islet β-cells. We establish a fundamental role for Chd4 in regulating insulin secretion and modulating numerous Pdx1 bound genes in vitro, including the MafA TF, where we discovered Chd4 is bound at the MafA Region 3 enhancer. Furthermore, we found that Pdx1:Chd4 interactions are significantly compromised in islet β-cells under metabolically-induced stress in vivo and in human donor tissues with T2D. Our findings establish a fundamental role for Chd4 in regulating insulin secretion and modulating Pdx1-bound genes in vitro, and disruption of Pdx1:Chd4 interactions coincides with β-cell dysfunction associated with T2D.
    DOI:  https://doi.org/10.1530/JME-22-0011
  18. Stem Cells. 2022 Mar 03. 40(1): 112-122
    A Runx1-enhancer Element eR1 Identified Lineage Restricted Mammary Luminal Stem Cells.
    Junichi Matsuo, Naing Naing Mon, Daisuke Douchi, Akihiro Yamamura, Madhura Kulkarni, Dede Liana Heng, Sabirah Chen, Napat Nuttonmanit, Ying Li, Henry Yang, May Yin Lee, Wai Leong Tam, Motomi Osato, Linda Shyue Huey Chuang, Yoshiaki Ito.
      Mammary gland homeostasis is maintained by adult tissue stem-progenitor cells residing within the luminal and basal epithelia. Dysregulation of mammary stem cells is a key mechanism for cancer development. However, stem cell characterization is challenging because reporter models using cell-specific promoters do not fully recapitulate the mammary stem cell populations. We previously found that a 270-basepair Runx1 enhancer element, named eR1, marked stem cells in the blood and stomach. Here, we identified eR1 activity in a rare subpopulation of the ERα-negative luminal epithelium in mouse mammary glands. Lineage-tracing using an eR1-CreERT2 mouse model revealed that eR1+ luminal cells generated the entire luminal lineage and milk-secreting alveoli-eR1 therefore specifically marks lineage-restricted luminal stem cells. eR1-targeted-conditional knockout of Runx1 led to the expansion of luminal epithelial cells, accompanied by elevated ERα expression. Our findings demonstrate a definitive role for Runx1 in the regulation of the eR1-positive luminal stem cell proliferation during mammary homeostasis. Our findings identify a mechanistic link for Runx1 in stem cell proliferation and its dysregulation in breast cancer. Runx1 inactivation is therefore likely to be an early hit in the cell-of-origin of ERα+ luminal type breast cancer.
    Keywords:  ERα; Runx1; eR1; enhancer; mammary gland; stem cell
    DOI:  https://doi.org/10.1093/stmcls/sxab009
  19. Cell. 2022 Apr 28. pii: S0092-8674(22)00462-7. [Epub ahead of print]
    Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.
    Dian Yang, Matthew G Jones, Santiago Naranjo, William M Rideout, Kyung Hoi Joseph Min, Raymond Ho, Wei Wu, Joseph M Replogle, Jennifer L Page, Jeffrey J Quinn, Felix Horns, Xiaojie Qiu, Michael Z Chen, William A Freed-Pastor, Christopher S McGinnis, David M Patterson, Zev J Gartner, Eric D Chow, Trever G Bivona, Michelle M Chan, Nir Yosef, Tyler Jacks, Jonathan S Weissman.
      Tumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth and expansion to neighboring and distal tissues. The study of phylogenetic relationships between cancer cells provides key insights into these processes. Here, we introduced an evolving lineage-tracing system with a single-cell RNA-seq readout into a mouse model of Kras;Trp53(KP)-driven lung adenocarcinoma and tracked tumor evolution from single-transformed cells to metastatic tumors at unprecedented resolution. We found that the loss of the initial, stable alveolar-type2-like state was accompanied by a transient increase in plasticity. This was followed by the adoption of distinct transcriptional programs that enable rapid expansion and, ultimately, clonal sweep of stable subclones capable of metastasizing. Finally, tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates progression by creating novel trajectories. Our study elucidates the hierarchical nature of tumor evolution and, more broadly, enables in-depth studies of tumor progression.
    Keywords:  fitness; genetically engineered mouse model; lineage tracing; lung cancer; phylogenetics; plasticity; single cell; transcriptome heterogeneity; tumor evolution
    DOI:  https://doi.org/10.1016/j.cell.2022.04.015
  20. PLoS Genet. 2022 May;18(5): e1010181
    Dnmt1a is essential for gene body methylation and the regulation of the zygotic genome in a wasp.
    Deanna Arsala, Xin Wu, Soojin V Yi, Jeremy A Lynch.
      Gene body methylation (GBM) is an ancestral mode of DNA methylation whose role in development has been obscured by the more prominent roles of promoter and CpG island methylation. The wasp Nasonia vitripennis has little promoter and CpG island methylation, yet retains strong GBM, making it an excellent model for elucidating the roles of GBM. Here we show that N. vitripennis DNA methyltransferase 1a (Nv-Dnmt1a) knockdown leads to failures in cellularization and gastrulation of the embryo. Both of these disrupted events are hallmarks of the maternal-zygotic transition (MZT) in insects. Analysis of the embryonic transcriptome and methylome revealed strong reduction of GBM and widespread disruption of gene expression during embryogenesis after Nv-Dnmt1a knockdown. Strikingly, there was a strong correlation between loss of GBM and reduced gene expression in thousands of methylated loci, consistent with the hypothesis that GBM directly facilitates high levels of transcription. We propose that lower expression levels of methylated genes due to reduced GBM is the crucial direct effect of Nv-Dnmt1 knockdown. Subsequently, the disruption of methylated genes leads to downstream dysregulation of the MZT, culminating in developmental failure at gastrulation.
    DOI:  https://doi.org/10.1371/journal.pgen.1010181
  21. Oncogene. 2022 May 05.
    Targeting CDCP1 gene transcription coactivated by BRD4 and CBP/p300 in castration-resistant prostate cancer.
    Donglei Ji, Guanglei Shang, Enwei Wei, Yanjie Jia, Chunyu Wang, Qiang Zhang, Lei Zeng.
      CUB domain-containing protein 1 (CDCP1), a transmembrane protein with tumor pro-metastatic activity, is highly expressed in late-stage and castrate-resistant prostate cancer (CRPC). However, the molecular mechanism driving CDCP1 overexpression in CRPC progress remains elusive. Here we report that transcription cofactors BRD4 and CBP/p300 co-regulate transcriptional expression of CDCP1 in CRPC tumorigenesis. In contrast to androgen receptor (AR) in CRPC, increased expression of BRD4 and CBP/p300 is strongly correlated with CDCP1 gene amplification. Combined knockdown or dual-inhibition of BRD4 and CBP/p300 down-regulated CDCP1 transcription and downstream PI3K/AKT and/or SRC/MAPK signaling pathways in CRPC cells much more so than single-protein perturbation. Our biochemical and structural analyses further showed that NEO2734, a dual-inhibitor targeting BRD4 and p300 bromodomains exhibits greater efficacy than single inhibitors for BRD4 or CBP/p300 in suppressing CDCP1 transcriptional expression and its downstream signaling pathways in CRPC cell proliferation and metastasis. Our study illustrates that targeting CDCP1 through dual-inhibition of BRD4 and CBP/p300 represents a synergistic therapeutic strategy for new treatment of CRPC.
    DOI:  https://doi.org/10.1038/s41388-022-02327-5
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