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Kucinski J, Tallan A, Taslim C, Wang M, Cannon MV, Silvius KM, Stanton BZ, Kendall GC. Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603270. [PMID: 39071299 PMCID: PMC11275748 DOI: 10.1101/2024.07.12.603270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Fusion-positive rhabdomyosarcoma is an aggressive pediatric cancer molecularly characterized by arrested myogenesis. The defining genetic driver, PAX3::FOXO1, functions as a chimeric gain-of-function transcription factor. An incomplete understanding of PAX3::FOXO1's in vivo epigenetic mechanisms has hindered therapeutic development. Here, we establish a PAX3::FOXO1 zebrafish injection model and semi-automated ChIP-seq normalization strategy to evaluate how PAX3::FOXO1 initially interfaces with chromatin in a developmental context. We investigated PAX3::FOXO1's recognition of chromatin and subsequent transcriptional consequences. We find that PAX3::FOXO1 interacts with inaccessible chromatin through partial/homeobox motif recognition consistent with pioneering activity. However, PAX3::FOXO1-genome binding through a composite paired-box/homeobox motif alters chromatin accessibility and redistributes H3K27ac to activate neural transcriptional programs. We uncover neural signatures that are highly representative of clinical rhabdomyosarcoma gene expression programs that are enriched following chemotherapy. Overall, we identify partial/homeobox motif recognition as a new mode for PAX3::FOXO1 pioneer function and identify neural signatures as a potentially critical PAX3::FOXO1 tumor initiation event.
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2
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D'Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. Nat Commun 2024; 15:5859. [PMID: 38997286 PMCID: PMC11245487 DOI: 10.1038/s41467-024-49905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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3
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Freund MM, Harrison MM, Torres-Zelada EF. Exploring the reciprocity between pioneer factors and development. Development 2024; 151:dev201921. [PMID: 38958075 PMCID: PMC11266817 DOI: 10.1242/dev.201921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Development is regulated by coordinated changes in gene expression. Control of these changes in expression is largely governed by the binding of transcription factors to specific regulatory elements. However, the packaging of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because of these properties, pioneer factors act at the top of gene-regulatory networks and drive developmental transitions. Despite the ability to bind target motifs in closed chromatin, pioneer factors have cell type-specific chromatin occupancy and activity. Thus, developmental context clearly shapes pioneer-factor function. Here, we discuss this reciprocal interplay between pioneer factors and development: how pioneer factors control changes in cell fate and how cellular environment influences pioneer-factor binding and activity.
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Affiliation(s)
- Meghan M. Freund
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Eliana F. Torres-Zelada
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
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4
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Fang F, Chen D, Basharat AR, Poulos W, Wang Q, Cibelli JB, Liu X, Sun L. Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during the maternal-to-zygotic transition. iScience 2024; 27:109944. [PMID: 38784018 PMCID: PMC11111832 DOI: 10.1016/j.isci.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/23/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Maternal-to-zygotic transition (MZT) is central to early embryogenesis. However, its underlying molecular mechanisms are still not well described. Here, we revealed the expression dynamics of 5,000 proteins across four stages of zebrafish embryos during MZT, representing one of the most systematic surveys of proteome landscape of the zebrafish embryos during MZT. Nearly 700 proteins were differentially expressed and were divided into six clusters according to their expression patterns. The proteome expression profiles accurately reflect the main events that happen during the MZT, i.e., zygotic genome activation (ZGA), clearance of maternal mRNAs, and initiation of cellular differentiation and organogenesis. MZT is modulated by many proteins at multiple levels in a collaborative fashion, i.e., transcription factors, histones, histone-modifying enzymes, RNA helicases, and P-body proteins. Significant discrepancies were discovered between zebrafish proteome and transcriptome profiles during the MZT. The proteome dynamics database will be a valuable resource for bettering our understanding of MZT.
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Affiliation(s)
- Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - William Poulos
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Jose B. Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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5
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Maekawa M, Saito S, Isobe D, Takemoto K, Miura Y, Dobashi Y, Yamasu K. The Oct4-related PouV gene, pou5f3, mediates isthmus development in zebrafish by directly and dynamically regulating pax2a. Cells Dev 2024:203933. [PMID: 38908828 DOI: 10.1016/j.cdev.2024.203933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Using a transgenic zebrafish line harboring a heat-inducible dominant-interference pou5f3 gene (en-pou5f3), we reported that this PouV gene is involved in isthmus development at the midbrain-hindbrain boundary (MHB), which patterns the midbrain and cerebellum. Importantly, the functions of pou5f3 reportedly differ before and after the end of gastrulation. In the present study, we examined in detail the effects of en-pou5f3 induction on isthmus development during embryogenesis. When en-pou5f3 was induced around the end of gastrulation (bud stage), the isthmus was abrogated or deformed by the end of somitogenesis (24 hours post-fertilization). At this stage, the expression of MHB markers -- such as pax2a, fgf8a, wnt1, and gbx2 -- was absent in embryos lacking the isthmus structure, whereas it was present, although severely distorted, in embryos with a deformed isthmus. We further found that, after en-pou5f3 induction at late gastrulation, pax2a, fgf8a, and wnt1 were immediately and irreversibly downregulated, whereas the expression of en2a and gbx2 was reduced only weakly and slowly. Induction of en-pou5f3 at early somite stages also immediately downregulated MHB genes, particularly pax2a, but their expression was restored later. Overall, the data suggested that pou5f3 directly upregulates at least pax2a and possibly fgf8a and wnt1, which function in parallel in establishing the MHB, and that the role of pou5f3 dynamically changes around the end of gastrulation. We next examined the transcriptional regulation of pax2a using both in vitro and in vivo reporter analyses; the results showed that two upstream 1.0-kb regions with sequences conserved among vertebrates specifically drove transcription at the MHB. These reporter analyses confirmed that development of the isthmic organizer is regulated by PouV through direct regulation of pax2/pax2a in vertebrate embryos.
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Affiliation(s)
- Masato Maekawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Shinji Saito
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Institute for Vaccine Research and Development, Hokkaido University, N21, W11, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Daiki Isobe
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kazumasa Takemoto
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Road, U3156, Storrs, CT 06269, USA
| | - Yuhei Miura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Yurie Dobashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
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Hernandez-Huertas L, Moreno-Sanchez I, Crespo-Cuadrado J, Vargas-Baco A, da Silva Pescador G, Santos-Pereira JM, Bazzini AA, Moreno-Mateos MA. CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595167. [PMID: 38826327 PMCID: PMC11142190 DOI: 10.1101/2024.05.22.595167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10/Baf45a, a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects observed after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation.
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Affiliation(s)
- Luis Hernandez-Huertas
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ismael Moreno-Sanchez
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Jesús Crespo-Cuadrado
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ana Vargas-Baco
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | | | - José M. Santos-Pereira
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ariel A. Bazzini
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Miguel A. Moreno-Mateos
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
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Youlten SE, Miao L, Hoppe C, Boswell CW, Musaev D, Abdelmessih M, Krishnaswamy S, Tornini VA, Giraldez AJ. Novel cell states arise in embryonic cells devoid of key reprogramming factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593729. [PMID: 38798464 PMCID: PMC11118305 DOI: 10.1101/2024.05.13.593729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The capacity for embryonic cells to differentiate relies on a large-scale reprogramming of the oocyte and sperm nucleus into a transient totipotent state. In zebrafish, this reprogramming step is achieved by the pioneer factors Nanog, Pou5f3, and Sox19b (NPS). Yet, it remains unclear whether cells lacking this reprogramming step are directed towards wild type states or towards novel developmental canals in the Waddington landscape of embryonic development. Here we investigate the developmental fate of embryonic cells mutant for NPS by analyzing their single-cell gene expression profiles. We find that cells lacking the first developmental reprogramming steps can acquire distinct cell states. These states are manifested by gene expression modules that result from a failure of nuclear reprogramming, the persistence of the maternal program, and the activation of somatic compensatory programs. As a result, most mutant cells follow new developmental canals and acquire new mixed cell states in development. In contrast, a group of mutant cells acquire primordial germ cell-like states, suggesting that NPS-dependent reprogramming is dispensable for these cell states. Together, these results demonstrate that developmental reprogramming after fertilization is required to differentiate most canonical developmental programs, and loss of the transient totipotent state canalizes embryonic cells into new developmental states in vivo.
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Affiliation(s)
- Scott E. Youlten
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Caroline Hoppe
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Curtis W. Boswell
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mario Abdelmessih
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Current Address: AstraZeneca, Waltham, MA 02451, USA
| | - Smita Krishnaswamy
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Computer Science, Yale University, New Haven, CT 06510, USA
| | - Valerie A. Tornini
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA
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8
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D’Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592422. [PMID: 38746145 PMCID: PMC11092767 DOI: 10.1101/2024.05.05.592422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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9
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Ertl HA, Bayala EX, Siddiq MA, Wittkopp PJ. Divergence of Grainy head affects chromatin accessibility, gene expression, and embryonic viability in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588430. [PMID: 38645200 PMCID: PMC11030446 DOI: 10.1101/2024.04.07.588430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pioneer factors are critical for gene regulation and development because they bind chromatin and make DNA more accessible for binding by other transcription factors. The pioneer factor Grainy head (Grh) is present across metazoans and has been shown to retain a role in epithelium development in fruit flies, nematodes, and mice despite extensive divergence in both amino acid sequence and length. Here, we investigate the evolution of Grh function by comparing the effects of the fly ( Drosophila melanogaster ) and worm ( Caenorhabditis elegans ) Grh orthologs on chromatin accessibility, gene expression, embryonic development, and viability in transgenic D. melanogaster . We found that the Caenorhabditis elegans ortholog rescued cuticle development but not full embryonic viability in Drosophila melanogaster grh null mutants. At the molecular level, the C. elegans ortholog only partially rescued chromatin accessibility and gene expression. Divergence in the disordered N-terminus of the Grh protein contributes to these differences in embryonic viability and molecular phenotypes. These data show how pioneer factors can diverge in sequence and function at the molecular level while retaining conserved developmental functions at the organismal level. SUMMARY STATEMENT Despite divergence in a disordered region that affects function at both molecular and organismal levels, the Caenorhabditis elegans Grainy head (Grh) protein rescued cuticle morphology in D. melanogaster embryos.
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10
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Ugolini M, Kerlin MA, Kuznetsova K, Oda H, Kimura H, Vastenhouw NL. Transcription bodies regulate gene expression by sequestering CDK9. Nat Cell Biol 2024; 26:604-612. [PMID: 38589534 PMCID: PMC11021188 DOI: 10.1038/s41556-024-01389-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. It remains unclear, however, if and how transcription bodies affect gene expression. Here we disrupted the formation of two prominent endogenous transcription bodies that mark the onset of zygotic transcription in zebrafish embryos and analysed the effect on gene expression using enriched SLAM-seq and live-cell imaging. We find that the disruption of transcription bodies results in the misregulation of hundreds of genes. Here we focus on genes that are upregulated. These genes have accessible chromatin and are poised to be transcribed in the presence of the two transcription bodies, but they do not go into elongation. Live-cell imaging shows that disruption of the two large transcription bodies enables these poised genes to be transcribed in ectopic transcription bodies, suggesting that the large transcription bodies sequester a pause release factor. Supporting this hypothesis, we find that CDK9-the kinase that releases paused polymerase II-is highly enriched in the two large transcription bodies. Overexpression of CDK9 in wild-type embryos results in the formation of ectopic transcription bodies and thus phenocopies the removal of the two large transcription bodies. Taken together, our results show that transcription bodies regulate transcription by sequestering machinery, thereby preventing genes elsewhere in the nucleus from being transcribed.
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Affiliation(s)
- Martino Ugolini
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Maciej A Kerlin
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ksenia Kuznetsova
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Institute of Human Genetics, CNRS, Montpellier, France
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Nadine L Vastenhouw
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland.
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
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11
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Ling Z, Li J, Jiang T, Zhang Z, Zhu Y, Zhou Z, Yang J, Tong X, Yang B, Huang L. Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits. Commun Biol 2024; 7:381. [PMID: 38553586 PMCID: PMC10980749 DOI: 10.1038/s42003-024-06050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
Genetic variants can influence complex traits by altering gene expression through changes to regulatory elements. However, the genetic variants that affect the activity of regulatory elements in pigs are largely unknown, and the extent to which these variants influence gene expression and contribute to the understanding of complex phenotypes remains unclear. Here, we annotate 90,991 high-quality regulatory elements using acetylation of histone H3 on lysine 27 (H3K27ac) ChIP-seq of 292 pig livers. Combined with genome resequencing and RNA-seq data, we identify 28,425 H3K27ac quantitative trait loci (acQTLs) and 12,250 expression quantitative trait loci (eQTLs). Through the allelic imbalance analysis, we validate two causative acQTL variants in independent datasets. We observe substantial sharing of genetic controls between gene expression and H3K27ac, particularly within promoters. We infer that 46% of H3K27ac exhibit a concomitant rather than causative relationship with gene expression. By integrating GWAS, eQTLs, acQTLs, and transcription factor binding prediction, we further demonstrate their application, through metabolites dulcitol, phosphatidylcholine (PC) (16:0/16:0) and published phenotypes, in identifying likely causal variants and genes, and discovering sub-threshold GWAS loci. We provide insight into the relationship between regulatory elements and gene expression, and the genetic foundation for dissecting the molecular mechanism of phenotypes.
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Affiliation(s)
- Ziqi Ling
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
| | - Jing Li
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Tao Jiang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Zhen Zhang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Yaling Zhu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Zhimin Zhou
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Jiawen Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Xinkai Tong
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Bin Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
| | - Lusheng Huang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
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12
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Baia Amaral D, Egidy R, Perera A, Bazzini AA. miR-430 regulates zygotic mRNA during zebrafish embryogenesis. Genome Biol 2024; 25:74. [PMID: 38504288 PMCID: PMC10949700 DOI: 10.1186/s13059-024-03197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. RESULTS By employing SLAM-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional activation events and follow nascent mRNA trajectories, finding that most de novo transcriptional events are stable throughout this period. Additionally, by blocking microRNA-430 function, a key post transcriptional regulator during zebrafish embryogenesis, we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal-zygotic genes. This unveils a novel miR-430 function during embryogenesis, fine-tuning zygotic gene expression. CONCLUSION These insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post-transcriptional regulators in zygotic genome activation. The findings pave the way for future investigations into the coordinated interplay between transcriptional and post-transcriptional landscapes required for the establishment of animal cell identities and functions.
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Affiliation(s)
- Danielson Baia Amaral
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Rhonda Egidy
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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13
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Gibson TJ, Larson ED, Harrison MM. Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function. Nat Struct Mol Biol 2024; 31:548-558. [PMID: 38365978 PMCID: PMC11261375 DOI: 10.1038/s41594-024-01231-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Chromatin is a barrier to the binding of many transcription factors. By contrast, pioneer factors access nucleosomal targets and promote chromatin opening. Despite binding to target motifs in closed chromatin, many pioneer factors display cell-type-specific binding and activity. The mechanisms governing pioneer factor occupancy and the relationship between chromatin occupancy and opening remain unclear. We studied three Drosophila transcription factors with distinct DNA-binding domains and biological functions: Zelda, Grainy head and Twist. We demonstrated that the level of chromatin occupancy is a key determinant of pioneering activity. Multiple factors regulate occupancy, including motif content, local chromatin and protein concentration. Regions outside the DNA-binding domain are required for binding and chromatin opening. Our results show that pioneering activity is not a binary feature intrinsic to a protein but occurs on a spectrum and is regulated by a variety of protein-intrinsic and cell-type-specific features.
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Affiliation(s)
- Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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14
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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15
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Zhu W, Bu G, Hu R, Zhang J, Qiao L, Zhou K, Wang T, Li Q, Zhang J, Wu L, Xie Y, Hu T, Yang S, Guan J, Chu X, Shi J, Zhang X, Lu F, Liu X, Miao YL. KLF4 facilitates chromatin accessibility remodeling in porcine early embryos. SCIENCE CHINA. LIFE SCIENCES 2024; 67:96-112. [PMID: 37698691 DOI: 10.1007/s11427-022-2349-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/20/2023] [Indexed: 09/13/2023]
Abstract
Chromatin accessibility remodeling driven by pioneer factors is critical for the development of early embryos. Current studies have illustrated several pioneer factors as being important for agricultural animals, but what are the pioneer factors and how the pioneer factors remodel the chromatin accessibility in porcine early embryos is not clear. By employing low-input DNase-seq (liDNase-seq), we profiled the landscapes of chromatin accessibility in porcine early embryos and uncovered a unique chromatin accessibility reprogramming pattern during porcine preimplantation development. Our data revealed that KLF4 played critical roles in remodeling chromatin accessibility in porcine early embryos. Knocking down of KLF4 led to the reduction of chromatin accessibility in early embryos, whereas KLF4 overexpression promoted the chromatin openness in porcine blastocysts. Furthermore, KLF4 deficiency resulted in mitochondrial dysfunction and developmental failure of porcine embryos. In addition, we found that overexpression of KLF4 in blastocysts promoted lipid droplet accumulation, whereas knockdown of KLF4 disrupted this process. Taken together, our study revealed the chromatin accessibility dynamics and identified KLF4 as a key regulator in chromatin accessibility and cellular metabolism during porcine preimplantation embryo development.
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Affiliation(s)
- Wei Zhu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Guowei Bu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Ruifeng Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jixiang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lianyong Qiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kai Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Tingting Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Qiao Li
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Yali Xie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taotao Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Shichun Yang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jiaqi Guan
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Xiaoyu Chu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Juanjuan Shi
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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16
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Maresca M, van den Brand T, Li H, Teunissen H, Davies J, de Wit E. Pioneer activity distinguishes activating from non-activating SOX2 binding sites. EMBO J 2023; 42:e113150. [PMID: 37691488 PMCID: PMC10577566 DOI: 10.15252/embj.2022113150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 09/12/2023] Open
Abstract
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.
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Affiliation(s)
- Michela Maresca
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Teun van den Brand
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Hangpeng Li
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Hans Teunissen
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - James Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Elzo de Wit
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
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17
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Phelps WA, Hurton MD, Ayers TN, Carlson AE, Rosenbaum JC, Lee MT. Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis. eLife 2023; 12:e83952. [PMID: 37787392 PMCID: PMC10569791 DOI: 10.7554/elife.83952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/02/2023] [Indexed: 10/04/2023] Open
Abstract
After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency to give rise to embryonic stem cells, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that pervasive regulatory remodeling has shaped the earliest stages of development. Here, we show that maternal homologs of mammalian pluripotency reprogramming factors OCT4 and SOX2 divergently activate the two subgenomes of Xenopus laevis, an allotetraploid that arose from hybridization of two diploid species ~18 million years ago. Although most genes have been retained as two homeologous copies, we find that a majority of them undergo asymmetric activation in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in predicted enhancer architecture between the subgenomes, which likely arose through genomic disruptions as a consequence of allotetraploidy. However, comparison with diploid X. tropicalis and zebrafish shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the core vertebrate pluripotency transcriptional program, amid genomic instability following hybridization.
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Affiliation(s)
- Wesley A Phelps
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Matthew D Hurton
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Taylor N Ayers
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Anne E Carlson
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Joel C Rosenbaum
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
| | - Miler T Lee
- Department of Biological Sciences, University of PittsburghPittsburghUnited States
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18
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Riesle AJ, Gao M, Rosenblatt M, Hermes J, Hass H, Gebhard A, Veil M, Grüning B, Timmer J, Onichtchouk D. Activator-blocker model of transcriptional regulation by pioneer-like factors. Nat Commun 2023; 14:5677. [PMID: 37709752 PMCID: PMC10502082 DOI: 10.1038/s41467-023-41507-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
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.
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Affiliation(s)
- Aileen Julia Riesle
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, EMBL Rome, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015, Monterotondo, RM, Italy
| | - Meijiang Gao
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Signalling Research centers BIOSS and CIBSS, 79104, Freiburg, Germany
| | - Marcus Rosenblatt
- Institute of Physics, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling (FDM), 79104, Freiburg, Germany
| | - Jacques Hermes
- Institute of Physics, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling (FDM), 79104, Freiburg, Germany
| | - Helge Hass
- Institute of Physics, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling (FDM), 79104, Freiburg, Germany
| | - Anna Gebhard
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Marina Veil
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Björn Grüning
- Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
- Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104, Freiburg, Germany
| | - Jens Timmer
- Signalling Research centers BIOSS and CIBSS, 79104, Freiburg, Germany.
- Institute of Physics, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany.
- Freiburg Center for Data Analysis and Modelling (FDM), 79104, Freiburg, Germany.
| | - Daria Onichtchouk
- Department of Developmental Biology, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany.
- Signalling Research centers BIOSS and CIBSS, 79104, Freiburg, Germany.
- Institute of Developmental Biology RAS, 119991, Moscow, Russia.
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19
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Cho CY, O'Farrell PH. Stepwise modifications of transcriptional hubs link pioneer factor activity to a burst of transcription. Nat Commun 2023; 14:4848. [PMID: 37563108 PMCID: PMC10415302 DOI: 10.1038/s41467-023-40485-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/29/2023] [Indexed: 08/12/2023] Open
Abstract
Binding of transcription factors (TFs) promotes the subsequent recruitment of coactivators and preinitiation complexes to initiate eukaryotic transcription, but this time course is usually not visualized. It is commonly assumed that recruited factors eventually co-reside in a higher-order structure, allowing distantly bound TFs to activate transcription at core promoters. We use live imaging of endogenously tagged proteins, including the pioneer TF Zelda, the coactivator dBrd4, and RNA polymerase II (RNAPII), to define a cascade of events upstream of transcriptional initiation in early Drosophila embryos. These factors are sequentially and transiently recruited to discrete clusters during activation of non-histone genes. Zelda and the acetyltransferase dCBP nucleate dBrd4 clusters, which then trigger pre-transcriptional clustering of RNAPII. Subsequent transcriptional elongation disperses clusters of dBrd4 and RNAPII. Our results suggest that activation of transcription by eukaryotic TFs involves a succession of distinct biomolecular condensates that culminates in a self-limiting burst of transcription.
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Affiliation(s)
- Chun-Yi Cho
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Patrick H O'Farrell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA.
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20
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Zhou CY, Heald R. Principles of genome activation in the early embryo. Curr Opin Genet Dev 2023; 81:102062. [PMID: 37339553 DOI: 10.1016/j.gde.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/22/2023]
Abstract
A major hurdle in an embryo's life is the initiation of its own transcriptional program, a process termed Zygotic Genome Activation (ZGA). In many species, ZGA is intricately timed, with bulk transcription initiating at the end of a series of reductive cell divisions when cell cycle duration increases. At the same time, major changes in genome architecture give rise to chromatin states that are permissive to RNA polymerase II activity. Yet, we still do not understand the series of events that trigger gene expression at the right time and in the correct sequence. Here we discuss new discoveries that deepen our understanding of how zygotic genes are primed for transcription, and how these events are regulated by the cell cycle and nuclear import. Finally, we speculate on the evolutionary basis of ZGA timing as an exciting future direction for the field.
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Affiliation(s)
- Coral Y Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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21
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Ji S, Chen F, Stein P, Wang J, Zhou Z, Wang L, Zhao Q, Lin Z, Liu B, Xu K, Lai F, Xiong Z, Hu X, Kong T, Kong F, Huang B, Wang Q, Xu Q, Fan Q, Liu L, Williams CJ, Schultz RM, Xie W. OBOX regulates mouse zygotic genome activation and early development. Nature 2023; 620:1047-1053. [PMID: 37459895 PMCID: PMC10528489 DOI: 10.1038/s41586-023-06428-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 07/12/2023] [Indexed: 08/25/2023]
Abstract
Zygotic genome activation (ZGA) activates the quiescent genome to enable the maternal-to-zygotic transition1,2. However, the identity of transcription factors that underlie mammalian ZGA in vivo remains elusive. Here we show that OBOX, a PRD-like homeobox domain transcription factor family (OBOX1-OBOX8)3-5, are key regulators of mouse ZGA. Mice deficient for maternally transcribed Obox1/2/5/7 and zygotically expressed Obox3/4 had a two-cell to four-cell arrest, accompanied by impaired ZGA. The Obox knockout defects could be rescued by restoring either maternal and zygotic OBOX, which suggests that maternal and zygotic OBOX redundantly support embryonic development. Chromatin-binding analysis showed that Obox knockout preferentially affected OBOX-binding targets. Mechanistically, OBOX facilitated the 'preconfiguration' of RNA polymerase II, as the polymerase relocated from the initial one-cell binding targets to ZGA gene promoters and distal enhancers. Impaired polymerase II preconfiguration in Obox mutants was accompanied by defective ZGA and chromatin accessibility transition, as well as aberrant activation of one-cell polymerase II targets. Finally, ectopic expression of OBOX activated ZGA genes and MERVL repeats in mouse embryonic stem cells. These data thus demonstrate that OBOX regulates mouse ZGA and early embryogenesis.
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Affiliation(s)
- Shuyan Ji
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Fengling Chen
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Paula Stein
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiacheng Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ziming Zhou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qing Zhao
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- College of Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiaoyu Hu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Tianxiang Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bo Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qianhua Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Anatomy, Physiology and Cell Biology School of Veterinary Medicine University of California, Davis, Davis, CA, USA.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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22
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Lerner J, Katznelson A, Zhang J, Zaret KS. Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2. Cell Rep 2023; 42:112748. [PMID: 37405916 PMCID: PMC10529229 DOI: 10.1016/j.celrep.2023.112748] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription factors, the nucleosome-binding properties of pioneer factors enable them to initiate zygotic genome activation, embryonic development, and cellular reprogramming. To better understand nucleosome targeting in vivo, we assess whether pioneer factors FoxA1 and Sox2 target stable or unstable nucleosomes and find that they target DNase-resistant, stable nucleosomes, whereas HNF4A, a non-nucleosome binding factor, targets open, DNase-sensitive chromatin. Despite FOXA1 and SOX2 targeting similar proportions of DNase-resistant chromatin, using single-molecule tracking, we find that FOXA1 uses lower nucleoplasmic diffusion and longer residence times while SOX2 uses higher nucleoplasmic diffusion and shorter residence times to scan compact chromatin, while HNF4 scans compact chromatin much less efficiently. Thus, pioneer factors target compact chromatin through distinct processes.
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Affiliation(s)
- Jonathan Lerner
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Andrew Katznelson
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA.
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23
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Galitsyna A, Ulianov SV, Bykov NS, Veil M, Gao M, Perevoschikova K, Gelfand M, Razin SV, Mirny L, Onichtchouk D. Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.15.549120. [PMID: 37503128 PMCID: PMC10370019 DOI: 10.1101/2023.07.15.549120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The first activation of gene expression during development (zygotic genome activation, ZGA) is accompanied by massive changes in chromosome organization. The connection between these two processes remains unknown. Using Hi-C for zebrafish embryos, we found that chromosome folding starts by establishing "fountains", novel elements of chromosome organization, emerging selectively at enhancers upon ZGA. Using polymer simulations, we demonstrate that fountains can emerge as sites of targeted cohesin loading and require two-sided, yet desynchronized, loop extrusion. Specific loss of fountains upon loss of pioneer transcription factors that drive ZGA reveals a causal connection between enhancer activity and fountain formation. Finally, we show that fountains emerge in early Medaka and Xenopus embryos; moreover, we found cohesin-dependent fountain pattern on enhancers of mouse embryonic stem cells. Taken together, fountains are the first enhancer-specific elements of chromosome organization; they constitute starting points of chromosome folding during early development, likely serving as sites of targeted cohesin loading.
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Affiliation(s)
- Aleksandra Galitsyna
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergey V. Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Nikolai S. Bykov
- Institute for Information Transmission Problems (the Kharkevich Institute), Russian Academy of Sciences, Moscow, 127051, Russia
- Centro Nacional de Análisis Genómico (CNAG), Baldiri Reixac 4, Barcelona, 08028 Spain
| | - Marina Veil
- Department of Developmental Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Meijiang Gao
- Department of Developmental Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, Freiburg, 79104, Germany
| | - Kristina Perevoschikova
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Mikhail Gelfand
- Institute for Information Transmission Problems (the Kharkevich Institute), Russian Academy of Sciences, Moscow, 127051, Russia
| | - Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Daria Onichtchouk
- Department of Developmental Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, Freiburg, 79104, Germany
- Koltzov Institute of Developmental Biology RAS, Moscow, 119991, Russia
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24
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Pownall ME, Miao L, Vejnar CE, M’Saad O, Sherrard A, Frederick MA, Benitez MD, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023; 381:92-100. [PMID: 37410825 PMCID: PMC10372697 DOI: 10.1126/science.ade5308] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer-promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.
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Affiliation(s)
- Mark E. Pownall
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Charles E. Vejnar
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Ons M’Saad
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
| | - Alice Sherrard
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Megan A. Frederick
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria D.J. Benitez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Curtis W. Boswell
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
- Department of Physics, Yale University; New Haven, CT 06510, USA
- Nanobiology Institute, Yale University; West Haven, CT 06477, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Cancer Center, Yale University School of Medicine; New Haven, CT 06510, USA
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25
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. PLoS Genet 2023; 19:e1010845. [PMID: 37440598 PMCID: PMC10368294 DOI: 10.1371/journal.pgen.1010845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus. Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities similar to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far particular to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
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26
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Shi Z, Liu G, Jiang H, Shi S, Zhang X, Deng Y, Chen Y. Activation of P53 pathway contributes to Xenopus hybrid inviability. Proc Natl Acad Sci U S A 2023; 120:e2303698120. [PMID: 37186864 PMCID: PMC10214167 DOI: 10.1073/pnas.2303698120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Hybrid incompatibility as a kind of reproductive isolation contributes to speciation. The nucleocytoplasmic incompatibility between Xenopus tropicalis eggs and Xenopus laevis sperm (te×ls) leads to specific loss of paternal chromosomes 3L and 4L. The hybrids die before gastrulation, of which the lethal causes remain largely unclear. Here, we show that the activation of the tumor suppressor protein P53 at late blastula stage contributes to this early lethality. We find that in stage 9 embryos, P53-binding motif is the most enriched one in the up-regulated Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) peaks between te×ls and wild-type X. tropicalis controls, which correlates with an abrupt stabilization of P53 protein in te×ls hybrids at stage 9. Inhibition of P53 activity via either tp53 knockout or overexpression of a dominant-negative P53 mutant or Murine double minute 2 proto-oncogene (Mdm2), a negative regulator of P53, by mRNA injection can rescue the te×ls early lethality. Our results suggest a causal function of P53 on hybrid lethality prior to gastrulation.
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Affiliation(s)
- Zhaoying Shi
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Guanghui Liu
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Hao Jiang
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Songyuan Shi
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Xuan Zhang
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Yi Deng
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Yonglong Chen
- Department of Chemical Biology, School of Life Sciences, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, 518055 Shenzhen, China
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27
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Tornini VA, Miao L, Lee HJ, Gerson T, Dube SE, Schmidt V, Kroll F, Tang Y, Du K, Kuchroo M, Vejnar CE, Bazzini AA, Krishnaswamy S, Rihel J, Giraldez AJ. linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells. eLife 2023; 12:e82249. [PMID: 37191016 PMCID: PMC10188112 DOI: 10.7554/elife.82249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open-reading frames and are speculated to encode micropeptides. However, systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here, we show that two putative lincRNAs (linc-mipep, also called lnc-rps25, and linc-wrb) encode micropeptides with homology to the vertebrate-specific chromatin architectural protein, Hmgn1, and demonstrate that they are required for development of vertebrate-specific brain cell types. Specifically, we show that NMDA receptor-mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes - evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions, with implications for neurodevelopmental disorders and disease.
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Affiliation(s)
| | - Liyun Miao
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Ho-Joon Lee
- Department of Genetics, Yale UniversityNew HavenUnited States
- Yale Center for Genome Analysis, Yale UniversityNew HavenUnited States
| | - Timothy Gerson
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Sarah E Dube
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Valeria Schmidt
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - François Kroll
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Yin Tang
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Katherine Du
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | - Manik Kuchroo
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | | | - Ariel Alejandro Bazzini
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular & Integrative Physiology, University of Kansas School of MedicineKansas CityUnited States
| | - Smita Krishnaswamy
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Antonio J Giraldez
- Department of Genetics, Yale UniversityNew HavenUnited States
- Yale Stem Cell Center, Yale University School of MedicineNew HavenUnited States
- Yale Cancer Center, Yale University School of MedicineNew HavenUnited States
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28
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540083. [PMID: 37214839 PMCID: PMC10197650 DOI: 10.1101/2023.05.09.540083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus . Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities analogous to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far unique to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261 U.S.A
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
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29
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Ciabrelli F, Rabbani L, Cardamone F, Zenk F, Löser E, Schächtle MA, Mazina M, Loubiere V, Iovino N. CBP and Gcn5 drive zygotic genome activation independently of their catalytic activity. SCIENCE ADVANCES 2023; 9:eadf2687. [PMID: 37083536 PMCID: PMC10121174 DOI: 10.1126/sciadv.adf2687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Zygotic genome activation (ZGA) is a crucial step of embryonic development. So far, little is known about the role of chromatin factors during this process. Here, we used an in vivo RNA interference reverse genetic screen to identify chromatin factors necessary for embryonic development in Drosophila melanogaster. Our screen reveals that histone acetyltransferases (HATs) and histone deacetylases are crucial ZGA regulators. We demonstrate that Nejire (CBP/EP300 ortholog) is essential for the acetylation of histone H3 lysine-18 and lysine-27, whereas Gcn5 (GCN5/PCAF ortholog) for lysine-9 of H3 at ZGA, with these marks being enriched at all actively transcribed genes. Nonetheless, these HATs activate distinct sets of genes. Unexpectedly, individual catalytic dead mutants of either Nejire or Gcn5 can activate zygotic transcription (ZGA) and transactivate a reporter gene in vitro. Together, our data identify Nejire and Gcn5 as key regulators of ZGA.
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Affiliation(s)
- Filippo Ciabrelli
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Leily Rabbani
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Francesco Cardamone
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- University of Freiburg, Faculty of Biology, Freiburg im Breisgau, Germany
| | - Fides Zenk
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Eva Löser
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Melanie A. Schächtle
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Marina Mazina
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | - Nicola Iovino
- Department of Chromatin Regulation, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
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30
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Fukushima HS, Takeda H, Nakamura R. Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development. Genome Res 2023; 33:572-586. [PMID: 37117034 PMCID: PMC10234297 DOI: 10.1101/gr.277577.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/29/2023] [Indexed: 04/30/2023]
Abstract
Epigenetic modifications undergo drastic erasure and reestablishment after fertilization. This reprogramming is required for proper embryonic development and cell differentiation. In mammals, some histone modifications are not completely reprogrammed and play critical roles in later development. In contrast, in nonmammalian vertebrates, most histone modifications are thought to be more intensively erased and reestablished by the stage of zygotic genome activation (ZGA). However, histone modifications that escape reprogramming in nonmammalian vertebrates and their potential functional roles remain unknown. Here, we quantitatively and comprehensively analyzed histone modification dynamics during epigenetic reprogramming in Japanese killifish, medaka (Oryzias latipes) embryos. Our data revealed that H3K27ac, H3K27me3, and H3K9me3 escape complete reprogramming, whereas H3K4 methylation is completely erased during cleavage stage. Furthermore, we experimentally showed the functional roles of such retained modifications at early stages: (i) H3K27ac premarks promoters during the cleavage stage, and inhibition of histone acetyltransferases disrupts proper patterning of H3K4 and H3K27 methylation at CpG-dense promoters, but does not affect chromatin accessibility after ZGA; (ii) H3K9me3 is globally erased but specifically retained at telomeric regions, which is required for maintenance of genomic stability during the cleavage stage. These results expand the understanding of diversity and conservation of reprogramming in vertebrates, and unveil previously uncharacterized functions of histone modifications retained during epigenetic reprogramming.
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Affiliation(s)
- Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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31
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Bhat P, Cabrera-Quio LE, Herzog VA, Fasching N, Pauli A, Ameres SL. SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis. Cell Rep 2023; 42:112070. [PMID: 36757845 DOI: 10.1016/j.celrep.2023.112070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/27/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
The maternal-to-zygotic transition (MZT) is a key developmental process in metazoan embryos that involves the activation of zygotic transcription (ZGA) and degradation of maternal transcripts. We employed metabolic mRNA sequencing (SLAMseq) to deconvolute the compound embryonic transcriptome in zebrafish. While mitochondrial zygotic transcripts prevail prior to MZT, we uncover the spurious transcription of hundreds of short and intron-poor genes as early as the 2-cell stage. Upon ZGA, most zygotic transcripts originate from thousands of maternal-zygotic (MZ) genes that are transcribed at rates comparable to those of hundreds of purely zygotic genes and replenish maternal mRNAs at distinct timescales. Rapid replacement of MZ transcripts involves transcript decay features unrelated to major maternal degradation pathways and promotes de novo synthesis of the core gene expression machinery by increasing poly(A)-tail length and translation efficiency. SLAMseq hence provides insights into the timescales, molecular features, and regulation of MZT during zebrafish embryogenesis.
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Affiliation(s)
- Pooja Bhat
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Luis E Cabrera-Quio
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Veronika A Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Nina Fasching
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Stefan L Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria.
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32
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Hadzhiev Y, Wheatley L, Cooper L, Ansaloni F, Whalley C, Chen Z, Finaurini S, Gustincich S, Sanges R, Burgess S, Beggs A, Müller F. The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation. Dev Cell 2023; 58:155-170.e8. [PMID: 36693321 PMCID: PMC9904021 DOI: 10.1016/j.devcel.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/10/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023]
Abstract
In anamniote embryos, the major wave of zygotic genome activation starts during the mid-blastula transition. However, some genes escape global genome repression, are activated substantially earlier, and contribute to the minor wave of genome activation. The mechanisms underlying the minor wave of genome activation are little understood. We explored the genomic organization and cis-regulatory mechanisms of a transcription body, in which the minor wave of genome activation is first detected in zebrafish. We identified the miR-430 cluster as having excessive copy number and the highest density of Pol-II-transcribed promoters in the genome, and this is required for forming the transcription body. However, this transcription body is not essential for, nor does it encompasse, minor wave transcription globally. Instead, distinct minor-wave-specific promoter architecture suggests that promoter-autonomous mechanisms regulate the minor wave of genome activation. The minor-wave-specific features also suggest distinct transcription initiation mechanisms between the minor and major waves of genome activation.
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Affiliation(s)
- Yavor Hadzhiev
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Lucy Wheatley
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ledean Cooper
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Federico Ansaloni
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy; Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Celina Whalley
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Zhelin Chen
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Sara Finaurini
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy; Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Shawn Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Andrew Beggs
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ferenc Müller
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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Zaret KS. Two ways to skin a new cell fate. Dev Cell 2023; 58:1-2. [PMID: 36626868 PMCID: PMC9979843 DOI: 10.1016/j.devcel.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
To induce cell fate changes, do transcription factors engage open domains of chromatin or elicit chromatin opening in a pioneering fashion? In this issue of Developmental Cell, Delás et al. show that the same sonic hedgehog (Shh) inducing signal can yield different neural tube fates by either modality.
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Affiliation(s)
- Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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34
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Shen W, Gong B, Xing C, Zhang L, Sun J, Chen Y, Yang C, Yan L, Chen L, Yao L, Li G, Deng H, Wu X, Meng A. Comprehensive maturity of nuclear pore complexes regulates zygotic genome activation. Cell 2022; 185:4954-4970.e20. [PMID: 36493774 DOI: 10.1016/j.cell.2022.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/23/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Nuclear pore complexes (NPCs) are channels for nucleocytoplasmic transport of proteins and RNAs. However, it remains unclear whether composition, structure, and permeability of NPCs dynamically change during the cleavage period of vertebrate embryos and affect embryonic development. Here, we report that the comprehensive NPC maturity (CNM) controls the onset of zygotic genome activation (ZGA) during zebrafish early embryogenesis. We show that more nucleoporin proteins are recruited to and assembled into NPCs with development, resulting in progressive increase of NPCs in size and complexity. Maternal transcription factors (TFs) transport into nuclei more efficiently with increasing CNM. Deficiency or dysfunction of Nup133 or Ahctf1/Elys impairs NPC assembly, maternal TFs nuclear transport, and ZGA onset, while nup133 overexpression promotes these processes. Therefore, CNM may act as a molecular timer for ZGA by controlling nuclear transport of maternal TFs that reach nuclear concentration thresholds at a given time to initiate ZGA.
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Affiliation(s)
- Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Gong
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Cencan Xing
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lin Zhang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Sun
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Changmei Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lu Yan
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Luxi Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Likun Yao
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangyuan Li
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaotong Wu
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Developmental Diseases and Cancer Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Laboratory of Stem Cell Regulation, Guangzhou Laboratory, Guangzhou 510320, China.
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35
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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36
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Wang M, Chen Z, Zhang Y. CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. EMBO J 2022; 41:e112012. [PMID: 36215692 PMCID: PMC9670200 DOI: 10.15252/embj.2022112012] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 01/13/2023] Open
Abstract
Epigenome reprogramming after fertilization enables transcriptionally quiescent maternal and paternal chromatin to acquire a permissive state for subsequent zygotic genome activation (ZGA). H3K27 acetylation (H3K27ac) is a well-established chromatin marker of active enhancers and promoters. However, reprogramming dynamics of H3K27ac during maternal-to-zygotic transition (MZT) in mammalian embryos are not well-studied. By profiling the allelic landscape of H3K27ac during mouse MZT, we show that H3K27ac undergoes three waves of rapid global transitions between oocyte stage and 2-cell stage. Notably, germinal vesicle oocyte and zygote chromatin are globally hyperacetylated, with noncanonical, broad H3K27ac domains that correlate with broad H3K4 trimethylation (H3K4me3) and open chromatin. H3K27ac marks genomic regions primed for activation including ZGA genes, retrotransposons, and active alleles of imprinted genes. We show that CBP/p300 and HDAC activities play important roles in regulating H3K27ac dynamics and are essential for preimplantation development. Specifically, CBP/p300 acetyltransferase broadly deposits H3K27ac in zygotes to induce the opening of condensed chromatin at putative enhancers and ensure proper ZGA. On the contrary, HDACs revert broad H3K27ac domains to canonical domains and safeguard ZGA by preventing premature expression of developmental genes. In conclusion, coordinated activities of CBP/p300 and HDACs during mouse MZT are essential for ZGA and preimplantation development.
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Affiliation(s)
- Meng Wang
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA,Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA,Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA
| | - Zhiyuan Chen
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA,Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA,Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA
| | - Yi Zhang
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA,Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA,Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA,Department of GeneticsHarvard Medical SchoolBostonMAUSA,Harvard Stem Cell InstituteBostonMAUSA
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37
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Abstract
Enhancers confer precise spatiotemporal patterns of gene expression in response to developmental and environmental stimuli. Over the last decade, the transcription of enhancer RNAs (eRNAs) – nascent RNAs transcribed from active enhancers – has emerged as a key factor regulating enhancer activity. eRNAs are relatively short-lived RNA species that are transcribed at very high rates but also quickly degraded. Nevertheless, eRNAs are deeply intertwined within enhancer regulatory networks and are implicated in a number of transcriptional control mechanisms. Enhancers show changes in function and sequence over evolutionary time, raising questions about the relationship between enhancer sequences and eRNA function. Moreover, the vast majority of single nucleotide polymorphisms associated with human complex diseases map to the non-coding genome, with causal disease variants enriched within enhancers. In this Primer, we survey the diverse roles played by eRNAs in enhancer-dependent gene expression, evaluating different models for eRNA function. We also explore questions surrounding the genetic conservation of enhancers and how this relates to eRNA function and dysfunction. Summary: This Primer evaluates the ideas that underpin developing models for eRNA function, exploring cases in which perturbed eRNA function contributes to disease.
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Affiliation(s)
- Laura J. Harrison
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
| | - Daniel Bose
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
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