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Dedukh D, Krasikova A. Delete and survive: strategies of programmed genetic material elimination in eukaryotes. Biol Rev Camb Philos Soc 2021; 97:195-216. [PMID: 34542224 PMCID: PMC9292451 DOI: 10.1111/brv.12796] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023]
Abstract
Genome stability is a crucial feature of eukaryotic organisms because its alteration drastically affects the normal development and survival of cells and the organism as a whole. Nevertheless, some organisms can selectively eliminate part of their genomes from certain cell types during specific stages of ontogenesis. This review aims to describe the phenomenon of programmed DNA elimination, which includes chromatin diminution (together with programmed genome rearrangement or DNA rearrangements), B and sex chromosome elimination, paternal genome elimination, parasitically induced genome elimination, and genome elimination in animal and plant hybrids. During programmed DNA elimination, individual chromosomal fragments, whole chromosomes, and even entire parental genomes can be selectively removed. Programmed DNA elimination occurs independently in different organisms, ranging from ciliate protozoa to mammals. Depending on the sequences destined for exclusion, programmed DNA elimination may serve as a radical mechanism of dosage compensation and inactivation of unnecessary or dangerous genetic entities. In hybrids, genome elimination results from competition between parental genomes. Despite the different consequences of DNA elimination, all genetic material destined for elimination must be first recognised, epigenetically marked, separated, and then removed and degraded.
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Affiliation(s)
- Dmitrij Dedukh
- Saint-Petersburg State University, 7/9 Universitetskaya Embankment, Saint-Petersburg, 199034, Russia
| | - Alla Krasikova
- Saint-Petersburg State University, 7/9 Universitetskaya Embankment, Saint-Petersburg, 199034, Russia
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Smith R, Pickering SJ, Kopakaki A, Thong KJ, Anderson RA, Lin CJ. HIRA contributes to zygote formation in mice and is implicated in human 1PN zygote phenotype. Reproduction 2021; 161:697-707. [PMID: 33835048 PMCID: PMC8188263 DOI: 10.1530/rep-20-0636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/08/2021] [Indexed: 11/08/2022]
Abstract
Elucidating the mechanisms underpinning fertilisation is essential to optimising IVF procedures. One of the critical steps involves paternal chromatin reprogramming, in which compacted sperm chromatin packed by protamines is removed by oocyte factors and new histones, including histone H3.3, are incorporated. HIRA is the main H3.3 chaperone governing this protamine-to-histone exchange. Failure of this step results in abnormally fertilised zygotes containing only one pronucleus (1PN), in contrast to normal two-pronuclei (2PN) zygotes. 1PN zygotes are frequently observed in IVF treatments, but the genotype-phenotype correlation remains elusive. We investigated the maternal functions of two other molecules of the HIRA complex, Cabin1 and Ubn1, in mouse. Loss-of-function Cabin1 and Ubn1 mouse models were developed: their zygotes displayed an abnormal 1PN zygote phenotype. We then studied human 1PN zygotes and found that the HIRA complex was absent in 1PN zygotes that lacked the male pronucleus. This shows that the role of the HIRA complex in male pronucleus formation potentially has coherence from mice to humans. Furthermore, rescue experiments in mouse showed that the abnormal 1PN phenotype derived from Hira mutants could be resolved by overexpression of HIRA. We have demonstrated that HIRA complex regulates male pronucleus formation in mice and is implicated in humans, that both CABIN1 and UBN1 components of the HIRA complex are equally essential for male pronucleus formation, and that rescue is feasible.
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Affiliation(s)
- Rowena Smith
- MRC Centre for Reproductive Health, University of Edinburgh, Queen’s Medical Research Institute, Edinburgh Bioquarter, Edinburgh, UK
| | - Sue J Pickering
- Edinburgh Fertility and Reproductive Endocrine Centre, Simpson’s Centre for Reproductive Health, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Anna Kopakaki
- Edinburgh Fertility and Reproductive Endocrine Centre, Simpson’s Centre for Reproductive Health, Edinburgh Royal Infirmary, Edinburgh, UK
| | - K J Thong
- Edinburgh Fertility and Reproductive Endocrine Centre, Simpson’s Centre for Reproductive Health, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Queen’s Medical Research Institute, Edinburgh Bioquarter, Edinburgh, UK
- Edinburgh Fertility and Reproductive Endocrine Centre, Simpson’s Centre for Reproductive Health, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Chih-Jen Lin
- MRC Centre for Reproductive Health, University of Edinburgh, Queen’s Medical Research Institute, Edinburgh Bioquarter, Edinburgh, UK
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Abstract
Nucleosome dynamics and properties are central to all forms of genomic activities. Among the core histones, H3 variants play a pivotal role in modulating nucleosome structure and function. Here, we focus on the impact of H3 variants on various facets of development. The deposition of the replicative H3 variant following DNA replication is essential for the transmission of the epigenomic information encoded in posttranscriptional modifications. Through this process, replicative H3 maintains cell fate while, in contrast, the replacement H3.3 variant opposes cell differentiation during early embryogenesis. In later steps of development, H3.3 and specialized H3 variants are emerging as new, important regulators of terminal cell differentiation, including neurons and gametes. The specific pathways that regulate the dynamics of the deposition of H3.3 are paramount during reprogramming events that drive zygotic activation and the initiation of a new cycle of development.
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Affiliation(s)
- Benjamin Loppin
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007 Lyon, France;
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria;
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4
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Wu CH, Zong Q, Du AL, Zhang W, Yao HC, Yu XQ, Wang YF. Knockdown of Dynamitin in testes significantly decreased male fertility in Drosophila melanogaster. Dev Biol 2016; 420:79-89. [DOI: 10.1016/j.ydbio.2016.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 10/09/2016] [Accepted: 10/09/2016] [Indexed: 10/20/2022]
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Liu Z, Zhang XJ, Wang W, Zhang J, Li Z, Gui JF. Molecular characterization and expression of an oocyte-specific histone stem-loop binding protein in Carassius gibelio. Comp Biochem Physiol B Biochem Mol Biol 2015; 190:46-53. [DOI: 10.1016/j.cbpb.2015.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/30/2015] [Accepted: 08/25/2015] [Indexed: 11/25/2022]
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O'Farrell PH. Growing an Embryo from a Single Cell: A Hurdle in Animal Life. Cold Spring Harb Perspect Biol 2015; 7:cshperspect.a019042. [PMID: 26254311 DOI: 10.1101/cshperspect.a019042] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A requirement that an animal be able to feed to grow constrains how a cell can grow into an animal, and it forces an alternation between growth (increase in mass) and proliferation (increase in cell number). A growth-only phase that transforms a stem cell of ordinary proportions into a huge cell, the oocyte, requires dramatic adaptations to help a nucleus direct a 10(5)-fold expansion of cytoplasmic volume. Proliferation without growth transforms the huge egg into an embryo while still accommodating an impotent nucleus overwhelmed by the voluminous cytoplasm. This growth program characterizes animals that deposit their eggs externally, but it is changed in mammals and in endoparasites. In these organisms, development in a nutritive environment releases the growth constraint, but growth of cells before gastrulation requires a new program to sustain pluripotency during this growth.
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Affiliation(s)
- Patrick H O'Farrell
- Department of Biochemistry, University of California San Francisco, San Francisco, California 94158
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7
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Horard B, Loppin B. Histone storage and deposition in the early Drosophila embryo. Chromosoma 2015; 124:163-75. [PMID: 25563491 DOI: 10.1007/s00412-014-0504-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Drosophila development initiates with the formation of a diploid zygote followed by the rapid division of embryonic nuclei. This syncytial phase of development occurs almost entirely under maternal control and ends when the blastoderm embryo cellularizes and activates its zygotic genome. The biosynthesis and storage of histones in quantity sufficient for chromatin assembly of several thousands of genome copies represent a unique challenge for the developing embryo. In this article, we have reviewed our current understanding of the mechanisms involved in the production, storage, and deposition of histones in the fertilized egg and during the exponential amplification of cleavage nuclei.
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Affiliation(s)
- Béatrice Horard
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire-CNRS UMR5534, Université Claude Bernard Lyon 1, University of Lyon, 69100, Villeurbanne, France
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Filipescu D, Müller S, Almouzni G. Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control. Annu Rev Cell Dev Biol 2014; 30:615-46. [DOI: 10.1146/annurev-cellbio-100913-013311] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Filipescu
- Institut Curie, Centre de Recherche, Paris, F-75248 France; , ,
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Amin AD, Vishnoi N, Prochasson P. A global requirement for the HIR complex in the assembly of chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1819:264-276. [PMID: 24459729 DOI: 10.1016/j.bbagrm.2011.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Due to its extensive length, DNA is packaged into a protective chromatin structure known as the nucleosome. In order to carry out various cellular functions, nucleosomes must be disassembled, allowing access to the underlying DNA, and subsequently reassembled on completion of these processes. The assembly and disassembly of nucleosomes is dependent on the function of histone modifiers, chromatin remodelers and histone chaperones. In this review, we discuss the roles of an evolutionarily conserved histone chaperone known as the HIR/HIRA complex. In S. cerevisiae, the HIR complex is made up of the proteins Hir1, Hir2, Hir3 and Hpc2, which collectively act in transcriptional regulation, elongation, gene silencing, cellular senescence and even aging. This review presents an overview of the role of the HIR complex, in yeast as well as other organisms, in each of these processes, in order to give a better understanding of how nucleosome assembly is imperative for cellular homeostasis and genomic integrity. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.
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Wang MY, Guo QH, Du XZ, Zhou L, Luo Q, Zeng QH, Wang JL, Zhao HB, Wang YF. HIRA is essential for the development of gibel carp. FISH PHYSIOLOGY AND BIOCHEMISTRY 2014; 40:235-244. [PMID: 23912483 DOI: 10.1007/s10695-013-9839-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/27/2013] [Indexed: 06/02/2023]
Abstract
HIRA is one of the chaperones of histone H3.3. Mutation of Hira results in embryonic lethality in mice, suggesting a critical role in embryogenesis. However, Hira-mutated Drosophila may survive to adults, indicating that it is dispensable in Drosophila development. The role of Hira in fish development is unknown. In this study we first investigated the expression of Hira during embryogenesis of gibel carp (Carassius auratus gibelio) by whole-mount in situ hybridization. We found that Hira signal appeared ubiquitously in the early embryos. After gastrulation, it appeared mainly along the anterior-posterior axis, including the tail bud. In hatching period, the signal was detected in head, heart, and the endoderm region on the back of yolk. Then by microinjection with morpholino-HIRA at the beginning of development, we observed delayed gastrulation and abnormal somitogenesis in gibel carp embryos. The HIRA morphants exhibited short trunk, limited yolk extension, and twisted tail. Most of the mutants died during embryogenesis or shortly after hatching. The rest of the HIRA morphants could survive to larvae but with severe defects in organogenesis. These data suggest that HIRA may be essential for the development of gibel carp, and this function is conserved in vertebrates.
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Affiliation(s)
- Meng-Yu Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan, 430079, People's Republic of China
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Filipescu D, Szenker E, Almouzni G. Developmental roles of histone H3 variants and their chaperones. Trends Genet 2013; 29:630-40. [PMID: 23830582 DOI: 10.1016/j.tig.2013.06.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/14/2013] [Accepted: 06/03/2013] [Indexed: 11/27/2022]
Abstract
Animal development and lifetime potential exploit a balance between the stability and plasticity of cellular identity. Within the nucleus, this is controlled by an interplay involving lineage-specific transcription factors and chromatin dynamics. Histone H3 variants contribute to chromatin dynamics through the timing and sites of their incorporation, promoted by dedicated histone chaperones. Moreover, their individual modifications and binding partners provide distinct features at defined genomic loci. We highlight here the importance of the H3.3 replacement variant for the nuclear reprogramming that occurs during gametogenesis, fertilization, and germline establishment. Furthermore, we describe how the recently characterized H3.3 dynamics associated with gastrulation, myogenesis, or neurogenesis underline the role of chromatin changes in cell differentiation. Finally, we discuss the challenges of maintaining centromeric identity through propagation of the centromeric CenH3 variant in different cell types. Future challenges will be to gain a comprehensive picture of H3 variants and their chaperones during development and differentiation.
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Affiliation(s)
- Dan Filipescu
- Institut Curie, Centre de Recherche, Paris F-75248 Cedex 05, France; CNRS, UMR218, Paris F-75248 Cedex 05, France
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12
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Orsi GA, Algazeery A, Meyer RE, Capri M, Sapey-Triomphe LM, Horard B, Gruffat H, Couble P, Aït-Ahmed O, Loppin B. Drosophila Yemanuclein and HIRA cooperate for de novo assembly of H3.3-containing nucleosomes in the male pronucleus. PLoS Genet 2013; 9:e1003285. [PMID: 23408912 PMCID: PMC3567178 DOI: 10.1371/journal.pgen.1003285] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 12/14/2012] [Indexed: 01/13/2023] Open
Abstract
The differentiation of post-meiotic spermatids in animals is characterized by a unique reorganization of their nuclear architecture and chromatin composition. In many species, the formation of sperm nuclei involves the massive replacement of nucleosomes with protamines, followed by a phase of extreme nuclear compaction. At fertilization, the reconstitution of a nucleosome-based paternal chromatin after the removal of protamines requires the deposition of maternally provided histones before the first round of DNA replication. This process exclusively uses the histone H3 variant H3.3 and constitutes a unique case of genome-wide replication-independent (RI) de novo chromatin assembly. We had previously shown that the histone H3.3 chaperone HIRA plays a central role for paternal chromatin assembly in Drosophila. Although several conserved HIRA-interacting proteins have been identified from yeast to human, their conservation in Drosophila, as well as their actual implication in this highly peculiar RI nucleosome assembly process, is an open question. Here, we show that Yemanuclein (YEM), the Drosophila member of the Hpc2/Ubinuclein family, is essential for histone deposition in the male pronucleus. yem loss of function alleles affect male pronucleus formation in a way remarkably similar to Hira mutants and abolish RI paternal chromatin assembly. In addition, we demonstrate that HIRA and YEM proteins interact and are mutually dependent for their targeting to the decondensing male pronucleus. Finally, we show that the alternative ATRX/XNP-dependent H3.3 deposition pathway is not involved in paternal chromatin assembly, thus underlining the specific implication of the HIRA/YEM complex for this essential step of zygote formation. Chromosome organization relies on a basic functional unit called the nucleosome, in which DNA is wrapped around a core of histone proteins. However, during male gamete formation, the majority of histones are replaced by sperm-specific proteins that are adapted to sexual reproduction but incompatible with the formation of the first zygotic nucleus. These proteins must therefore be replaced by histones upon fertilization, in a replication-independent chromatin assembly process that requires the histone deposition factor HIRA. In this study, we identified the protein Yemanuclein (YEM) as a new partner of HIRA at fertilization. We show that, in eggs laid by yem mutant females, the male pronucleus fails to assemble its nucleosomes, resulting in the loss of paternal chromosomes at the first zygotic division. In addition, we found that YEM and HIRA are mutually dependent to perform chromatin assembly at fertilization, demonstrating that they tightly cooperate in vivo. Finally, we demonstrate that the replication-independent chromatin assembly factor ATRX/XNP is not involved in the assembly of paternal nucleosomes. In conclusion, our results shed new light into critical mechanisms controlling paternal chromosome formation at fertilization.
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Affiliation(s)
- Guillermo A. Orsi
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Ahmed Algazeery
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier, France
| | - Régis E. Meyer
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier, France
| | - Michèle Capri
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier, France
| | - Laure M. Sapey-Triomphe
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Béatrice Horard
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Henri Gruffat
- Laboratoire de Biologie Moléculaire des Herpesvirus, INSERM U758, Ecole Normale Supérieure de Lyon, France
| | - Pierre Couble
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Ounissa Aït-Ahmed
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier, France
- * E-mail: (OA-A); (BL)
| | - Benjamin Loppin
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, Villeurbanne, France
- * E-mail: (OA-A); (BL)
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Vishnoi N, Flaherty K, Hancock LC, Ferreira ME, Amin AD, Prochasson P. Separation-of-function mutation in HPC2, a member of the HIR complex in S. cerevisiae, results in derepression of the histone genes but does not confer cryptic TATA phenotypes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:557-66. [PMID: 21782987 DOI: 10.1016/j.bbagrm.2011.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 07/02/2011] [Accepted: 07/06/2011] [Indexed: 12/29/2022]
Abstract
The HIR complex, which is comprised of the four proteins Hir1, Hir2, Hir3 and Hpc2, was first characterized as a repressor of three of the four histone gene loci in Saccharomyces cerevisiae. Using a bioinformatical approach, previous studies have identified a region of Hpc2 that is conserved in Schizosaccharomyces pombe and humans. Using a similar approach, we identified two additional domains, CDI and CDII, of the Hpc2 protein that are conserved among yeast species related to S. cerevisiae. We showed that the N terminal CDI domain (spanning amino acids 63-79) is dispensable for HIR complex assembly, but plays an essential role in the repression of the histone genes by recruiting the HIR complex to the HIR-dependent histone gene loci. The second conserved domain, CDII (spanning amino acids 452-480), is required for the stability of the Hpc2 protein itself as well as for the assembly of the HIR complex. In addition, we report a novel separation-of-function mutation within CDI of Hpc2, which causes derepression of the histone genes but does not confer other reported hir/hpc- phenotypes (such as Spt phenotypes, heterochromatin silencing defects and repression of cryptic promoters). This is the first direct demonstration that a separation-of-function mutation exists within the HIR complex.
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Affiliation(s)
- Nidhi Vishnoi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
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