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Saredi G, Carelli FN, Rolland SGM, Furlan G, Piquet S, Appert A, Sanchez-Pulido L, Price JL, Alcon P, Lampersberger L, Déclais AC, Ramakrishna NB, Toth R, Macartney T, Alabert C, Ponting CP, Polo SE, Miska EA, Gartner A, Ahringer J, Rouse J. The histone chaperone SPT2 regulates chromatin structure and function in Metazoa. Nat Struct Mol Biol 2024; 31:523-535. [PMID: 38238586 PMCID: PMC7615752 DOI: 10.1038/s41594-023-01204-3] [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: 02/13/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024]
Abstract
Histone chaperones control nucleosome density and chromatin structure. In yeast, the H3-H4 chaperone Spt2 controls histone deposition at active genes but its roles in metazoan chromatin structure and organismal physiology are not known. Here we identify the Caenorhabditis elegans ortholog of SPT2 (CeSPT-2) and show that its ability to bind histones H3-H4 is important for germline development and transgenerational epigenetic gene silencing, and that spt-2 null mutants display signatures of a global stress response. Genome-wide profiling showed that CeSPT-2 binds to a range of highly expressed genes, and we find that spt-2 mutants have increased chromatin accessibility at a subset of these loci. We also show that SPT2 influences chromatin structure and controls the levels of soluble and chromatin-bound H3.3 in human cells. Our work reveals roles for SPT2 in controlling chromatin structure and function in Metazoa.
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Affiliation(s)
- Giulia Saredi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Francesco N Carelli
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Stéphane G M Rolland
- IBS Centre for Genomic Integrity at Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Giulia Furlan
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Transine Therapeutics, Babraham Hall, Cambridge, UK
| | - Sandra Piquet
- Laboratory of Epigenome Integrity, Epigenetics and Cell Fate Centre, UMR 7216 CNRS - Université Paris Cité, Paris, France
| | - Alex Appert
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Jonathan L Price
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pablo Alcon
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Lisa Lampersberger
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Maxion Therapeutics, Unity Campus, Cambridge, UK
| | - Anne-Cécile Déclais
- Molecular Cell and Developmental Biology Division, School of Life Sciences, University of Dundee, Dundee, UK
| | - Navin B Ramakrishna
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Constance Alabert
- Molecular Cell and Developmental Biology Division, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sophie E Polo
- Laboratory of Epigenome Integrity, Epigenetics and Cell Fate Centre, UMR 7216 CNRS - Université Paris Cité, Paris, France
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Anton Gartner
- IBS Centre for Genomic Integrity at Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Julie Ahringer
- Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
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Poulet A, Rousselot E, Téletchéa S, Noirot C, Jacob Y, van Wolfswinkel J, Thiriet C, Duc C. The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum. Int J Mol Sci 2023; 24:1051. [PMID: 36674565 PMCID: PMC9864664 DOI: 10.3390/ijms24021051] [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: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. Physarum polycephalum is a Mycetozoan, a clade located at the crown of the eukaryotic tree. We previously found that histones, which are highly conserved between plants and animals, are also highly conserved in Physarum. However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in Physarum and their evolution relative to animal and plants. Most of the known histone chaperones and their functional domains are conserved as well as key residues required for histone and chaperone interactions. Physarum is divergent from yeast, plants and animals, but PpHIRA, PpCABIN1 and PpSPT6 are similar in structure to plant orthologues. PpFACT is closely related to the yeast complex, and the Physarum genome encodes the animal-specific APFL chaperone. Furthermore, we performed RNA sequencing to monitor chaperone expression during the cell cycle and uncovered two distinct patterns during S-phase. In summary, our study demonstrates the conserved role of histone chaperones in handling histones in an early-branching eukaryote.
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Affiliation(s)
- Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Ellyn Rousselot
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Stéphane Téletchéa
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Céline Noirot
- INRAE, UR 875 Unité de Mathématique et Informatique Appliquées, Genotoul Bioinfo Auzeville, 31326 Castanet-Tolosan, France
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Josien van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Christophe Thiriet
- Université Rennes 1, CNRS, IGDR (Institut de Génétique et Développement de Rennes)—UMR 6290, 35043 Rennes, France
| | - Céline Duc
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
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Cabin1 domain-containing gene picd-1 interacts with pry-1/Axin to regulate multiple processes in Caenorhabditis elegans. Sci Rep 2022; 12:12029. [PMID: 35835800 PMCID: PMC9283418 DOI: 10.1038/s41598-022-15873-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/30/2022] [Indexed: 11/08/2022] Open
Abstract
The Axin family of scaffolding proteins control diverse processes, such as facilitating the interactions between cellular components and providing specificity to signaling pathways. While several Axin family members have been discovered in metazoans and shown to play crucial roles, their mechanism of action are not well understood. The Caenorhabditis elegans Axin homolog, pry-1, is a powerful tool for identifying interacting genes and downstream effectors that function in a conserved manner to regulate Axin-mediated signaling. Our lab and others have established pry-1's essential role in developmental processes that affect the reproductive system, seam cells, and a posterior P lineage cell, P11.p. Additionally, pry-1 is crucial for lipid metabolism, stress responses, and aging. In this study, we expanded on our previous work on pry-1 by reporting a novel interacting gene named picd-1 (pry-1-interacting and Cabin1 domain-containing). PICD-1 protein shares sequence conservation with CABIN1, a component of the HUCA complex. Our findings have revealed that PICD-1 is involved in several pry-1-mediated processes, including stress response and lifespan maintenance. picd-1's expression overlapped with that of pry-1 in multiple tissues throughout the lifespan. Furthermore, PRY-1 and PICD-1 inhibited CREB-regulated transcriptional coactivator homolog CRTC-1, which promotes longevity in a calcineurin-dependent manner. Overall, our study has demonstrated that picd-1 is necessary for mediating pry-1 function and provides the basis to investigate whether Cabin-1 domain-containing protein plays a similar role in Axin signaling in other systems.
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Bogoch Y, Jamieson-Lucy A, Vejnar CE, Levy K, Giraldez AJ, Mullins MC, Elkouby YM. Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis. Front Cell Dev Biol 2022; 10:826892. [PMID: 35733854 PMCID: PMC9207522 DOI: 10.3389/fcell.2022.826892] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/11/2022] [Indexed: 01/21/2023] Open
Abstract
Oogenesis produces functional eggs and is essential for fertility, embryonic development, and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates, and recent studies have identified multiple regulators in oocyte development through forward genetic screens, as well as reverse genetics by CRISPR mutagenesis. However, many developmental steps in oogenesis, in zebrafish and other species, remain poorly understood, and their underlying mechanisms are unknown. Here, we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis, from the onset of oocyte differentiation through Stage III, which precedes oocyte maturation. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis, as well as their expression in pair-wise comparisons between stages. We determined their functionally enriched terms, identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish, which we deposit online as a resource for the community. Further, the presence of multiple gene paralogs in zebrafish, and the exclusive curation by many bioinformatic tools of the single paralogs present in humans, challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether, our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.
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Affiliation(s)
- Yoel Bogoch
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem Faculty of Medicine, Jerusalem, Israel
- Institute for Biomedical Research, Israel-Canada, Jerusalem, Israel
| | - Allison Jamieson-Lucy
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | | | - Karine Levy
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem Faculty of Medicine, Jerusalem, Israel
- Institute for Biomedical Research, Israel-Canada, Jerusalem, Israel
| | | | - Mary C. Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Yaniv M. Elkouby
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem Faculty of Medicine, Jerusalem, Israel
- Institute for Biomedical Research, Israel-Canada, Jerusalem, Israel
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Özdemir I, Steiner FA. Transmission of chromatin states across generations in C. elegans. Semin Cell Dev Biol 2021; 127:133-141. [PMID: 34823984 DOI: 10.1016/j.semcdb.2021.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022]
Abstract
Epigenetic inheritance refers to the transmission of phenotypes across generations without affecting the genomic DNA sequence. Even though it has been documented in many species in fungi, animals and plants, the mechanisms underlying epigenetic inheritance are not fully uncovered. Epialleles, the heritable units of epigenetic information, can take the form of several biomolecules, including histones and their post-translational modifications (PTMs). Here, we review the recent advances in the understanding of the transmission of histone variants and histone PTM patterns across generations in C. elegans. We provide a general overview of the intergenerational and transgenerational inheritance of histone PTMs and their modifiers and discuss the interplay among different histone PTMs. We also evaluate soma-germ line communication and its impact on the inheritance of epigenetic traits.
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Affiliation(s)
- Isa Özdemir
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland.
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Prosée RF, Wenda JM, Özdemir I, Gabus C, Delaney K, Schwager F, Gotta M, Steiner FA. Transgenerational inheritance of centromere identity requires the CENP-A N-terminal tail in the C. elegans maternal germ line. PLoS Biol 2021; 19:e3000968. [PMID: 34228701 PMCID: PMC8259991 DOI: 10.1371/journal.pbio.3000968] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
Centromere protein A (CENP-A) is a histone H3 variant that defines centromeric chromatin and is essential for centromere function. In most eukaryotes, CENP-A-containing chromatin is epigenetically maintained, and centromere identity is inherited from one cell cycle to the next. In the germ line of the holocentric nematode Caenorhabditis elegans, this inheritance cycle is disrupted. CENP-A is removed at the mitosis-to-meiosis transition and is reestablished on chromatin during diplotene of meiosis I. Here, we show that the N-terminal tail of CENP-A is required for the de novo establishment of centromeres, but then its presence becomes dispensable for centromere maintenance during development. Worms homozygous for a CENP-A tail deletion maintain functional centromeres during development but give rise to inviable offspring because they fail to reestablish centromeres in the maternal germ line. We identify the N-terminal tail of CENP-A as a critical domain for the interaction with the conserved kinetochore protein KNL-2 and argue that this interaction plays an important role in setting centromere identity in the germ line. We conclude that centromere establishment and maintenance are functionally distinct in C. elegans.
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Affiliation(s)
- Reinier F. Prosée
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Joanna M. Wenda
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Isa Özdemir
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Caroline Gabus
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Kamila Delaney
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Francoise Schwager
- Department of Cell Physiology and Metabolism and Institute of Genetics and Genomics in Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Monica Gotta
- Department of Cell Physiology and Metabolism and Institute of Genetics and Genomics in Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Florian A. Steiner
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
- * E-mail:
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