1
|
Lismer A, Kimmins S. Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development. Nat Commun 2023; 14:2142. [PMID: 37059740 PMCID: PMC10104880 DOI: 10.1038/s41467-023-37820-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Although more studies are demonstrating that a father's environment can influence child health and disease, the molecular mechanisms underlying non-genetic inheritance remain unclear. It was previously thought that sperm exclusively contributed its genome to the egg. More recently, association studies have shown that various environmental exposures including poor diet, toxicants, and stress, perturbed epigenetic marks in sperm at important reproductive and developmental loci that were associated with offspring phenotypes. The molecular and cellular routes that underlie how epigenetic marks are transmitted at fertilization, to resist epigenetic reprogramming in the embryo, and drive phenotypic changes are only now beginning to be unraveled. Here, we provide an overview of the state of the field of intergenerational paternal epigenetic inheritance in mammals and present new insights into the relationship between embryo development and the three pillars of epigenetic inheritance: chromatin, DNA methylation, and non-coding RNAs. We evaluate compelling evidence of sperm-mediated transmission and retention of paternal epigenetic marks in the embryo. Using landmark examples, we discuss how sperm-inherited regions may escape reprogramming to impact development via mechanisms that implicate transcription factors, chromatin organization, and transposable elements. Finally, we link paternally transmitted epigenetic marks to functional changes in the pre- and post-implantation embryo. Understanding how sperm-inherited epigenetic factors influence embryo development will permit a greater understanding related to the developmental origins of health and disease.
Collapse
Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal Hospital Research Centre, Montreal, QC, H2X 0A9, Canada.
| |
Collapse
|
2
|
de la Iglesia A, Jodar M, Oliva R, Castillo J. Insights into the sperm chromatin and implications for male infertility from a protein perspective. WIREs Mech Dis 2023; 15:e1588. [PMID: 36181449 DOI: 10.1002/wsbm.1588] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
Male germ cells undergo an extreme but fascinating process of chromatin remodeling that begins in the testis during the last phase of spermatogenesis and continues through epididymal sperm maturation. Most of the histones are replaced by small proteins named protamines, whose high basicity leads to a tight genomic compaction. This process is epigenetically regulated at many levels, not only by posttranslational modifications, but also by readers, writers, and erasers, in a context of a highly coordinated postmeiotic gene expression program. Protamines are key proteins for acquiring this highly specialized chromatin conformation, needed for sperm functionality. Interestingly, and contrary to what could be inferred from its very specific DNA-packaging function across protamine-containing species, human sperm chromatin contains a wide spectrum of protamine proteoforms, including truncated and posttranslationally modified proteoforms. The generation of protamine knock-out models revealed not only chromatin compaction defects, but also collateral sperm alterations contributing to infertile phenotypes, evidencing the importance of sperm chromatin protamination toward the generation of a new individual. The unique features of sperm chromatin have motivated its study, applying from conventional to the most ground-breaking techniques to disentangle its peculiarities and the cellular mechanisms governing its successful conferment, especially relevant from the protein point of view due to the important epigenetic role of sperm nuclear proteins. Gathering and contextualizing the most striking discoveries will provide a global understanding of the importance and complexity of achieving a proper chromatin compaction and exploring its implications on postfertilization events and beyond. This article is categorized under: Reproductive System Diseases > Genetics/Genomics/Epigenetics Reproductive System Diseases > Molecular and Cellular Physiology.
Collapse
Affiliation(s)
- Alberto de la Iglesia
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain
| | - Meritxell Jodar
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
| | - Judit Castillo
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain
| |
Collapse
|
3
|
Joseph FM, Young NL. Histone variant-specific post-translational modifications. Semin Cell Dev Biol 2023; 135:73-84. [PMID: 35277331 PMCID: PMC9458767 DOI: 10.1016/j.semcdb.2022.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 01/12/2023]
Abstract
Post-translational modifications (PTMs) of histones play a key role in DNA-based processes and contribute to cell differentiation and gene function by adding an extra layer of regulation. Variations in histone sequences within each family of histones expands the chromatin repertoire and provide further mechanisms for regulation and signaling. While variants are known to be present in certain genomic loci and carry out important functions, much remains unknown about variant-specific PTMs and their role in regulating chromatin. This ambiguity is in part due to the limited technologies and appropriate reagents to identify and quantitate variant-specific PTMs. Nonetheless, histone variants are an integral portion of the chromatin system and the understanding of their modifications and resolving how PTMs function differently on specific variants is paramount to the advancement of the field. Here we review the current knowledge on post-translational modifications specific to histone variants, with an emphasis on well-characterized PTMs of known function. While not every possible PTM is addressed, we present key variant-specific PTMs and what is known about their function and mechanisms in convenient reference tables.
Collapse
Affiliation(s)
- Faith M Joseph
- Translational Biology and Molecular Medicine Graduate Program, USA
| | - Nicolas L Young
- Translational Biology and Molecular Medicine Graduate Program, USA; Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
4
|
Raman P, Rominger MC, Young JM, Molaro A, Tsukiyama T, Malik HS. Novel classes and evolutionary turnover of histone H2B variants in the mammalian germline. Mol Biol Evol 2022; 39:6517784. [PMID: 35099534 PMCID: PMC8857922 DOI: 10.1093/molbev/msac019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Histones and their posttranslational modifications facilitate diverse chromatin functions in eukaryotes. Core histones (H2A, H2B, H3, and H4) package genomes after DNA replication. In contrast, variant histones promote specialized chromatin functions, including DNA repair, genome stability, and epigenetic inheritance. Previous studies have identified only a few H2B variants in animals; their roles and evolutionary origins remain largely unknown. Here, using phylogenomic analyses, we reveal the presence of five H2B variants broadly present in mammalian genomes. Three of these variants have been previously described: H2B.1, H2B.L (also called subH2B), and H2B.W. In addition, we identify and describe two new variants: H2B.K and H2B.N. Four of these variants originated in mammals, whereas H2B.K arose prior to the last common ancestor of bony vertebrates. We find that though H2B variants are subject to high gene turnover, most are broadly retained in mammals, including humans. Despite an overall signature of purifying selection, H2B variants evolve more rapidly than core H2B with considerable divergence in sequence and length. All five H2B variants are expressed in the germline. H2B.K and H2B.N are predominantly expressed in oocytes, an atypical expression site for mammalian histone variants. Our findings suggest that H2B variants likely encode potentially redundant but vital functions via unusual chromatin packaging or nonchromatin functions in mammalian germline cells. Our discovery of novel histone variants highlights the advantages of comprehensive phylogenomic analyses and provides unique opportunities to study how innovations in chromatin function evolve.
Collapse
Affiliation(s)
- Pravrutha Raman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Mary C Rominger
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Whitman College, Walla Walla, Washington, 99362, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Antoine Molaro
- Genetics, Reproduction and Development (GReD) Institute, CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Toshio Tsukiyama
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| |
Collapse
|
5
|
Moritz L, Hammoud SS. The Art of Packaging the Sperm Genome: Molecular and Structural Basis of the Histone-To-Protamine Exchange. Front Endocrinol (Lausanne) 2022; 13:895502. [PMID: 35813619 PMCID: PMC9258737 DOI: 10.3389/fendo.2022.895502] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/02/2022] [Indexed: 01/18/2023] Open
Abstract
Male fertility throughout life hinges on the successful production of motile sperm, a developmental process that involves three coordinated transitions: mitosis, meiosis, and spermiogenesis. Germ cells undergo both mitosis and meiosis to generate haploid round spermatids, in which histones bound to the male genome are replaced with small nuclear proteins known as protamines. During this transformation, the chromatin undergoes extensive remodeling to become highly compacted in the sperm head. Despite its central role in spermiogenesis and fertility, we lack a comprehensive understanding of the molecular mechanisms underlying the remodeling process, including which remodelers/chaperones are involved, and whether intermediate chromatin proteins function as discrete steps, or unite simultaneously to drive successful exchange. Furthermore, it remains largely unknown whether more nuanced interactions instructed by protamine post-translational modifications affect chromatin dynamics or gene expression in the early embryo. Here, we bring together past and more recent work to explore these topics and suggest future studies that will elevate our understanding of the molecular basis of the histone-to-protamine exchange and the underlying etiology of idiopathic male infertility.
Collapse
Affiliation(s)
- Lindsay Moritz
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Lindsay Moritz, ; Saher Sue Hammoud,
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, United States
- Department of Urology, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Lindsay Moritz, ; Saher Sue Hammoud,
| |
Collapse
|
6
|
Mahadevan IA, Pentakota S, Roy R, Bhaduri U, Satyanarayana Rao MR. TH2BS11ph histone mark is enriched in the unsynapsed axes of the XY body and predominantly associates with H3K4me3-containing genomic regions in mammalian spermatocytes. Epigenetics Chromatin 2019; 12:53. [PMID: 31493790 PMCID: PMC6731575 DOI: 10.1186/s13072-019-0300-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023] Open
Abstract
Background TH2B is a major histone variant that replaces about 80–85% of somatic H2B in mammalian spermatocytes and spermatids. The post-translational modifications (PTMs) on TH2B have been well characterised in spermatocytes and spermatids. However, the biological function(s) of these PTMs on TH2B have not been deciphered in great detail. In our attempt to decipher the unique function(s) of histone variant TH2B, we detected the modification in the N-terminal tail, Serine 11 phosphorylation on TH2B (TH2BS11ph) in spermatocytes. Results The current study is aimed at understanding the function of the TH2BS11ph modification in the context of processes that occur during meiotic prophase I. Immunofluorescence studies with the highly specific antibodies revealed that TH2BS11ph histone mark is enriched in the unsynapsed axes of the sex body and is associated with XY body-associated proteins like Scp3, γH2AX, pATM, ATR, etc. Genome-wide occupancy studies as determined by ChIP sequencing experiments in P20 C57BL6 mouse testicular cells revealed that TH2BS11ph is enriched in X and Y chromosomes confirming the immunofluorescence staining pattern in the pachytene spermatocytes. Apart from the localisation of this modification in the XY body, TH2BS11ph is majorly associated with H3K4me3-containing genomic regions like gene promoters, etc. These data were also found to corroborate with the ChIP sequencing data of TH2BS11ph histone mark carried out in P12 C57BL6 mouse testicular cells, wherein we found the predominant localisation of this modification at H3K4me3-containing genomic regions. Mass spectrometry analysis of proteins that associate with TH2BS11ph-containing mononucleosomes revealed key proteins linked with the functions of XY body, pericentric heterochromatin and transcription. Conclusions TH2BS11ph modification is densely localised in the unsynapsed axes of the XY body of the pachytene spermatocyte. By ChIP sequencing studies in mouse P12 and P20 testicular cells, we demonstrate that TH2BS11ph is predominantly associated with H3K4me3 positive genomic regions like gene promoters, etc. We propose that TH2BS11ph modification could act alone or in concert with other histone modifications to recruit the appropriate transcription or XY body recombination protein machinery at specific genomic loci.
Collapse
Affiliation(s)
- Iyer Aditya Mahadevan
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO., Bangalore, 560064, India
| | - Satyakrishna Pentakota
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Raktim Roy
- The Graduate School of the Stowers Institute for Medical Research, 1000E. 50th St., Kansas City, MO, 64110, USA
| | - Utsa Bhaduri
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO., Bangalore, 560064, India
| | - Manchanahalli R Satyanarayana Rao
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur PO., Bangalore, 560064, India.
| |
Collapse
|
7
|
The dynamics and regulation of chromatin remodeling during spermiogenesis. Gene 2019; 706:201-210. [DOI: 10.1016/j.gene.2019.05.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/06/2023]
|
8
|
Beedle MT, Topping T, Hogarth C, Griswold M. Differential localization of histone variant TH2B during the first round compared with subsequent rounds of spermatogenesis. Dev Dyn 2019; 248:488-500. [PMID: 30939211 PMCID: PMC6545161 DOI: 10.1002/dvdy.33] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 03/20/2019] [Accepted: 03/29/2019] [Indexed: 02/02/2023] Open
Abstract
Background Male germ cells are unique because they express a substantial number of variants of the general DNA binding proteins, known as histones, yet the biological significance of these variants is still unknown. In the present study, we aimed to address the expression pattern of the testis‐specific histone H2B variant (TH2B) and the testis‐specific histone H2A variant (TH2A) within the neonatal mouse testis. Results We demonstrate that TH2B and TH2A are present in a testis‐enriched for undifferentiated spermatogonia. Co‐localization studies with an undifferentiated marker, ZBTB16, revealed that TH2B and ZBTB16 co‐localize in the neonatal testis. Upon the appearance of the primary spermatocytes, TH2B no longer co‐localized with the ZBTB16 positive spermatogonia but were instead detected within the differentiating spermatogonia. This pattern of expression where TH2B and ZBTB16 no longer co‐localize was maintained in the adult testis. Conclusion These findings are in contrast to previous studies, which demonstrated that TH2B and TH2A were found only in adult spermatocytes. Our data are in support of a switch in the expression of these variants following the first round of spermatogonial differentiation. These studies reinforce current understandings that spermatogonia within the neonatal mouse testis are inherently different from those residing within the adult testis. Contrary to previous beliefs, testis specific histone variants TH2B and TH2A are also expressed expressed in undifferentiated spermatogonia in the neonatal mouse testis. Upon the appearance of the primary spermatocytes, TH2B switches its expression from spermatogonia to the spermatocyte population. This study reinforces the idea that spermatogonia in the neonatal mouse testis is inherently different than those residing within the adult.
Collapse
Affiliation(s)
- My-Thanh Beedle
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington
| | - Traci Topping
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington
| | - Cathryn Hogarth
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington
| | - Michael Griswold
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington
| |
Collapse
|
9
|
El-Gammal Z, AlOkda A, El-Badri N. Role of human oocyte-enriched factors in somatic cell reprograming. Mech Ageing Dev 2018; 175:88-99. [PMID: 29890177 DOI: 10.1016/j.mad.2018.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 12/20/2022]
Abstract
Cellular reprograming paves the way for creating functional patient-specific tissues to eliminate immune rejection responses by applying the same genetic profile. However, the epigenetic memory of a cell remains a challenge facing the current reprograming methods and does not allow transcription factors to bind properly. Because somatic cells can be reprogramed by transferring their nuclear contents into oocytes, introducing specific oocyte factors into differentiated cells is considered a promising approach for mimicking the reprograming process that occurs during fertilization. Mammalian metaphase II oocyte possesses a superior capacity to epigenetically reprogram somatic cell nuclei towards an embryonic stem cell-like state than the current factor-based reprograming approaches. This may be due to the presence of specific factors that are lacking in the current factor-based reprograming approaches. In this review, we focus on studies identifying human oocyte-enriched factors aiming to understand the molecular mechanisms mediating cellular reprograming. We describe the role of oocyte-enriched factors in metabolic switch, chromatin remodelling, and global epigenetic transformation. This is critical for improving the quality of resulting reprogramed cells, which is crucial for therapeutic applications.
Collapse
Affiliation(s)
- Zaynab El-Gammal
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Egypt
| | - Abdelrahman AlOkda
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Egypt.
| |
Collapse
|
10
|
García-Rodríguez A, de la Casa M, Peinado H, Gosálvez J, Roy R. Human prostasomes from normozoospermic and non-normozoospermic men show a differential protein expression pattern. Andrology 2018; 6:585-596. [DOI: 10.1111/andr.12496] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - H. Peinado
- Microenvironment and Metastasis Group; Molecular Oncology Program; Spanish National Cancer Research Centre (CNIO); Madrid Spain
| | - J. Gosálvez
- Biology Department; University Autónoma of Madrid; Madrid Spain
| | - R. Roy
- Biology Department; University Autónoma of Madrid; Madrid Spain
| |
Collapse
|
11
|
Hoghoughi N, Barral S, Vargas A, Rousseaux S, Khochbin S. Histone variants: essential actors in male genome programming. J Biochem 2018; 163:97-103. [PMID: 29165574 DOI: 10.1093/jb/mvx079] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/13/2017] [Indexed: 02/03/2023] Open
Abstract
Prior to its transmission to the offspring, the male genome has to be tightly compacted. A genome-scale histone eviction and the subsequent repackaging of DNA by protamines (Prms) direct this essential genome condensation step. The requirement for male germ cells to undergo such a dramatic and unique genome reorganization explains why these cells express the largest number of histone variants, including many testis-specific ones. Indeed, an open chromatin, nucleosome instability and a facilitated process of histone disassembly are direct consequences of the presence of these histone variants in the chromatin of male germ cells. These histone-induced changes in chromatin first control a stage-specific gene expression program and then directly mediate the histone-to-Prm transition process. This review aims at summarizing and discussing a series of recent functional studies of male germ cell histone variants with a focus on their impact on the process of histone eviction and male genome compaction.
Collapse
Affiliation(s)
- Naghmeh Hoghoughi
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| | - Sophie Barral
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| | - Alexandra Vargas
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| | - Sophie Rousseaux
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| | - Saadi Khochbin
- CNRS UMR 5309, Inserm, U1209, Université Grenoble Alpes, Institut Albert Bonniot, Grenoble F-38700, France
| |
Collapse
|
12
|
Rafatmanesh A, Nikzad H, Ebrahimi A, Karimian M, Zamani T. Association of the c.-9C>T and c.368A>G transitions in H2BFWT
gene with male infertility in an Iranian population. Andrologia 2017; 50. [DOI: 10.1111/and.12805] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2017] [Indexed: 01/05/2023] Open
Affiliation(s)
- A. Rafatmanesh
- Gametogenesis Research Center; Kashan University of Medical Sciences; Kashan Iran
| | - H. Nikzad
- Gametogenesis Research Center; Kashan University of Medical Sciences; Kashan Iran
- Anatomical Sciences Research Center; Kashan University of Medical Sciences; Kashan Iran
| | - A. Ebrahimi
- Gametogenesis Research Center; Kashan University of Medical Sciences; Kashan Iran
| | - M. Karimian
- Gametogenesis Research Center; Kashan University of Medical Sciences; Kashan Iran
| | - T. Zamani
- Gametogenesis Research Center; Kashan University of Medical Sciences; Kashan Iran
| |
Collapse
|
13
|
Bagheri-Sereshki N, Hales BF, Robaire B. The Effects of Chemotherapeutic Agents, Bleomycin, Etoposide, and Cisplatin, on Chromatin Remodeling in Male Rat Germ Cells. Biol Reprod 2016; 94:81. [PMID: 26911428 PMCID: PMC4861167 DOI: 10.1095/biolreprod.115.137802] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/03/2016] [Accepted: 02/11/2016] [Indexed: 11/30/2022] Open
Abstract
The coadministration of bleomycin, etoposide, and cisplatin (BEP) has increased the survival rate of testicular cancer patients to over 90%. Previous studies have demonstrated that BEP induces germ cell damage during the final stages of spermatogenesis, when major chromatin remodeling occurs. Chromatin remodeling permits histone-protamine exchange, resulting in sperm head chromatin compaction. This process involves different epigenetic modifications of the core histones. The objective of these studies was to investigate the effects of BEP on epigenetic modifications to histones involved in chromatin remodeling. Brown Norway rats were treated with BEP, and their testes were removed to isolate pachytene spermatocytes and round spermatids by unit gravity sedimentation. Western blot analyses were conducted on extracted proteins to detect the expression of key modified histones. In a second cohort testes were prepared for immunohistochemical analysis. The stage-specific expression of each modified histone mark in rat spermatogenesis suggests the involvement of these modifications in chromatin remodeling. BEP treatment significantly increased expression of H3K9m and decreased that of tH2B (or Hist1h2ba) in pachytene spermatocytes, suggesting that nucleosomes were not destabilized to allow for transcription of genes involved in chromatin remodeling. Moreover, BEP treatment altered the expression of H4K8ac in round and elongating spermatids, suggesting that histone eviction was compromised, leading to a looser chromatin structure in mature spermatozoa. Less-compacted sperm chromatin, with alterations to the sperm epigenome, may have an adverse effect on male fertility.
Collapse
Affiliation(s)
- Negar Bagheri-Sereshki
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Barbara F Hales
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
| | - Bernard Robaire
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada Department of Obstetrics and Gynecology, McGill University, Montréal, Québec, Canada
| |
Collapse
|
14
|
Huynh LM, Shinagawa T, Ishii S. Two Histone Variants TH2A and TH2B Enhance Human Induced Pluripotent Stem Cell Generation. Stem Cells Dev 2016; 25:251-8. [DOI: 10.1089/scd.2015.0264] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Linh My Huynh
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, Tsukuba, Japan
- CREST Research Project of JST (Japan Science and Technology Agency), Tsukuba, Japan
- Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Toshie Shinagawa
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, Tsukuba, Japan
- CREST Research Project of JST (Japan Science and Technology Agency), Tsukuba, Japan
- Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shunsuke Ishii
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, Tsukuba, Japan
- CREST Research Project of JST (Japan Science and Technology Agency), Tsukuba, Japan
- Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| |
Collapse
|
15
|
Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T. Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming. Biochem Biophys Res Commun 2015; 464:929-35. [DOI: 10.1016/j.bbrc.2015.07.070] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/14/2015] [Indexed: 11/16/2022]
|
16
|
Abstract
Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism.
Collapse
Affiliation(s)
- Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
| |
Collapse
|
17
|
Saade E, Pirozhkova I, Aimbetov R, Lipinski M, Ogryzko V. Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis). Aging Cell 2015; 14:322-33. [PMID: 25720734 PMCID: PMC4406661 DOI: 10.1111/acel.12332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 12/22/2022] Open
Abstract
The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed.
Collapse
Affiliation(s)
- Evelyne Saade
- Faculty of Public Health Lebanese University LU Beirut Lebanon
| | - Iryna Pirozhkova
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Rakhan Aimbetov
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Marc Lipinski
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Vasily Ogryzko
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| |
Collapse
|
18
|
Shinagawa T, Huynh LM, Takagi T, Tsukamoto D, Tomaru C, Kwak HG, Dohmae N, Noguchi J, Ishii S. Disruption of Th2a and Th2b genes causes defects in spermatogenesis. Development 2015; 142:1287-92. [PMID: 25742800 DOI: 10.1242/dev.121830] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The variant histones TH2A and TH2B are abundant in the testis, but their roles in spermatogenesis remain elusive. Here, we show that male mutant mice lacking both Th2a and Th2b genes were sterile, with few sperm in the epididymis. In the mutant testis, the lack of TH2B was compensated for by overexpression of H2B, whereas overexpression of H2A was not observed, indicating a decrease in the total histone level. Mutant mice exhibited two defects: incomplete release of cohesin at interkinesis after meiosis I and histone replacement during spermiogenesis. In the mutant testis, secondary spermatocytes at interkinesis accumulated and cohesin was not released normally, suggesting that the retained cohesion of sister chromatids delayed the subsequent entry into meiosis II. In addition, impaired chromatin incorporation of TNP2 and degenerated spermatids were observed in the mutant testis. These results suggest that a loss of TH2A and TH2B function in chromatin dynamics or a decrease in the total histone levels causes defects in both cohesin release and histone replacement during spermatogenesis.
Collapse
Affiliation(s)
- Toshie Shinagawa
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Linh My Huynh
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Tsuyoshi Takagi
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Daisuke Tsukamoto
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Chinatsu Tomaru
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Ho-Geun Kwak
- Global Research Cluster, RIKEN, Graduate School of Science and Engineering, Saitama University, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Global Research Cluster, RIKEN, Graduate School of Science and Engineering, Saitama University, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Junko Noguchi
- Division of Animal Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Shunsuke Ishii
- Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan CREST Research Project of JST (Japan Science and Technology Agency), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| |
Collapse
|
19
|
Shinagawa T, Takagi T, Tsukamoto D, Tomaru C, Huynh LM, Sivaraman P, Kumarevel T, Inoue K, Nakato R, Katou Y, Sado T, Takahashi S, Ogura A, Shirahige K, Ishii S. Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells. Cell Stem Cell 2015; 14:217-27. [PMID: 24506885 DOI: 10.1016/j.stem.2013.12.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 10/01/2013] [Accepted: 12/22/2013] [Indexed: 10/25/2022]
Abstract
Expression of Oct3/4, Sox2, Klf4, and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). Somatic cell nuclear transfer (SCNT) can also be used for reprogramming, suggesting that factors present in oocytes could potentially augment OSKM-mediated induction of pluripotency. Here, we report that two histone variants, TH2A and TH2B, which are highly expressed in oocytes and contribute to activation of the paternal genome after fertilization, enhance OSKM-dependent generation of iPSCs and can induce reprogramming with Klf4 and Oct3/4 alone. TH2A and TH2B are enriched on the X chromosome during the reprogramming process, and their expression in somatic cells increases the DNase I sensitivity of chromatin. In addition, Xist deficiency, which was reported to enhance SCNT reprogramming efficiency, stimulates iPSC generation using TH2A/TH2B in conjunction with OSKM, but not OSKM alone. Thus, TH2A/TH2B may enhance reprogramming by introducing processes that normally operate in zygotes and during SCNT.
Collapse
Affiliation(s)
- Toshie Shinagawa
- Laboratory of Molecular Genetics, CREST Research Project of JST (Japan Science and Technology Agency), RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Department of Functional Genomics, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan.
| | - Tsuyoshi Takagi
- Laboratory of Molecular Genetics, CREST Research Project of JST (Japan Science and Technology Agency), RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Daisuke Tsukamoto
- Laboratory of Molecular Genetics, CREST Research Project of JST (Japan Science and Technology Agency), RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Chinatsu Tomaru
- Laboratory of Molecular Genetics, CREST Research Project of JST (Japan Science and Technology Agency), RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Department of Functional Genomics, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Linh My Huynh
- Laboratory of Molecular Genetics, CREST Research Project of JST (Japan Science and Technology Agency), RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Department of Functional Genomics, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Padavattan Sivaraman
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - Kimiko Inoue
- RIKEN BioResource Center, Tsukuba 305-0074, Japan
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; CREST, JST, K's Gobancho, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Yuki Katou
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; CREST, JST, K's Gobancho, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Takashi Sado
- Medical Institute of Bioregulation, Kyushu University, 812-8582 Fukuoka, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Atsuo Ogura
- RIKEN BioResource Center, Tsukuba 305-0074, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan; CREST, JST, K's Gobancho, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Shunsuke Ishii
- Laboratory of Molecular Genetics, CREST Research Project of JST (Japan Science and Technology Agency), RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; Department of Functional Genomics, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan.
| |
Collapse
|
20
|
Pentakota SK, Sandhya S, P Sikarwar A, Chandra N, Satyanarayana Rao MR. Mapping post-translational modifications of mammalian testicular specific histone variant TH2B in tetraploid and haploid germ cells and their implications on the dynamics of nucleosome structure. J Proteome Res 2014; 13:5603-17. [PMID: 25252820 DOI: 10.1021/pr500597a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Histones regulate a variety of chromatin templated events by their post-translational modifications (PTMs). Although there are extensive reports on the PTMs of canonical histones, the information on the histone variants remains very scanty. Here, we report the identification of different PTMs, such as acetylation, methylation, and phosphorylation of a major mammalian histone variant TH2B. Our mass spectrometric analysis has led to the identification of both conserved and unique modifications across tetraploid spermatocytes and haploid spermatids. We have also computationally derived the 3-dimensional model of a TH2B containing nucleosome in order to study the spatial orientation of the PTMs identified and their effect on nucleosome stability and DNA binding potential. From our nucleosome model, it is evident that substitution of specific amino acid residues in TH2B results in both differential histone-DNA and histone-histone contacts. Furthermore, we have also observed that acetylation on the N-terminal tail of TH2B weakens the interactions with the DNA. These results provide direct evidence that, similar to somatic H2B, the testis specific histone TH2B also undergoes multiple PTMs, suggesting the possibility of chromatin regulation by such covalent modifications in mammalian male germ cells.
Collapse
Affiliation(s)
- Satya Krishna Pentakota
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore, Karnataka 560064, India
| | | | | | | | | |
Collapse
|
21
|
Samson M, Jow MM, Wong CCL, Fitzpatrick C, Aslanian A, Saucedo I, Estrada R, Ito T, Park SKR, Yates JR, Chu DS. The specification and global reprogramming of histone epigenetic marks during gamete formation and early embryo development in C. elegans. PLoS Genet 2014; 10:e1004588. [PMID: 25299455 PMCID: PMC4191889 DOI: 10.1371/journal.pgen.1004588] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 07/09/2014] [Indexed: 11/18/2022] Open
Abstract
In addition to the DNA contributed by sperm and oocytes, embryos receive parent-specific epigenetic information that can include histone variants, histone post-translational modifications (PTMs), and DNA methylation. However, a global view of how such marks are erased or retained during gamete formation and reprogrammed after fertilization is lacking. To focus on features conveyed by histones, we conducted a large-scale proteomic identification of histone variants and PTMs in sperm and mixed-stage embryo chromatin from C. elegans, a species that lacks conserved DNA methylation pathways. The fate of these histone marks was then tracked using immunostaining. Proteomic analysis found that sperm harbor ∼2.4 fold lower levels of histone PTMs than embryos and revealed differences in classes of PTMs between sperm and embryos. Sperm chromatin repackaging involves the incorporation of the sperm-specific histone H2A variant HTAS-1, a widespread erasure of histone acetylation, and the retention of histone methylation at sites that mark the transcriptional history of chromatin domains during spermatogenesis. After fertilization, we show HTAS-1 and 6 histone PTM marks distinguish sperm and oocyte chromatin in the new embryo and characterize distinct paternal and maternal histone remodeling events during the oocyte-to-embryo transition. These include the exchange of histone H2A that is marked by ubiquitination, retention of HTAS-1, removal of the H2A variant HTZ-1, and differential reprogramming of histone PTMs. This work identifies novel and conserved features of paternal chromatin that are specified during spermatogenesis and processed in the embryo. Furthermore, our results show that different species, even those with diverged DNA packaging and imprinting strategies, use conserved histone modification and removal mechanisms to reprogram epigenetic information.
Collapse
Affiliation(s)
- Mark Samson
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Margaret M. Jow
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Catherine C. L. Wong
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
- Mass Spectrometry Division, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Colin Fitzpatrick
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Aaron Aslanian
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Israel Saucedo
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rodrigo Estrada
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Sung-kyu Robin Park
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Diana S. Chu
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| |
Collapse
|
22
|
Samans B, Yang Y, Krebs S, Sarode GV, Blum H, Reichenbach M, Wolf E, Steger K, Dansranjavin T, Schagdarsurengin U. Uniformity of nucleosome preservation pattern in Mammalian sperm and its connection to repetitive DNA elements. Dev Cell 2014; 30:23-35. [PMID: 24998597 DOI: 10.1016/j.devcel.2014.05.023] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 03/14/2014] [Accepted: 05/29/2014] [Indexed: 12/11/2022]
Abstract
Nucleosome-to-protamine exchange during mammalian spermiogenesis is essential for compaction and protection of paternal DNA. It is interesting that, depending on the species, 1% to 15% of nucleosomes are retained, but the generalizability and biological function of this retention are unknown. Here, we show concordantly in human and bovine that nucleosomes remained in sperm chromatin predominantly within distal intergenic regions and introns and associated with centromere repeats and retrotransposons (LINE1 and SINEs). In contrast, nucleosome depletion concerned particularly exons, 5'-UTR, 3'-UTR, TSS, and TTS and was associated with simple and low-complexity repeats. Overlap of human and bovine genes exhibiting nucleosome preservation in the promoter and gene body revealed a significant enrichment of signal transduction and RNA- and protein-processing factors. Our study demonstrates the genome-wide uniformity of the nucleosome preservation pattern in mammalian sperm and its connection to repetitive DNA elements and suggests a function in preimplantation processes for paternally derived nucleosomes.
Collapse
Affiliation(s)
- Birgit Samans
- Research Centre for Biosystems, Land Use and Nutrition, IFZ, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Yang Yang
- Clinic and Polyclinic of Urology, Pediatric Urology and Andrology, Department of Molecular Andrology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Gaurav Vilas Sarode
- Clinic and Polyclinic of Urology, Pediatric Urology and Andrology, Department of Molecular Andrology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Myriam Reichenbach
- Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Klaus Steger
- Clinic and Polyclinic of Urology, Pediatric Urology and Andrology, Department of Molecular Andrology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Temuujin Dansranjavin
- Clinic and Polyclinic of Urology, Pediatric Urology and Andrology, Department of Molecular Andrology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Undraga Schagdarsurengin
- Clinic and Polyclinic of Urology, Pediatric Urology and Andrology, Department of Molecular Andrology, Justus Liebig University Giessen, 35392 Giessen, Germany.
| |
Collapse
|
23
|
Urahama T, Horikoshi N, Osakabe A, Tachiwana H, Kurumizaka H. Structure of human nucleosome containing the testis-specific histone variant TSH2B. Acta Crystallogr F Struct Biol Commun 2014; 70:444-9. [PMID: 24699735 PMCID: PMC3976059 DOI: 10.1107/s2053230x14004695] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/28/2014] [Indexed: 11/10/2022] Open
Abstract
The human histone H2B variant TSH2B is highly expressed in testis and may function in the chromatin transition during spermatogenesis. In the present study, the crystal structure of the human testis-specific nucleosome containing TSH2B was determined at 2.8 Å resolution. A local structural difference between TSH2B and canonical H2B in nucleosomes was detected around the TSH2B-specific amino-acid residue Ser85. The TSH2B Ser85 residue does not interact with H4 in the nucleosome, but in the canonical nucleosome the H2B Asn84 residue (corresponding to the TSH2B Ser85 residue) forms water-mediated hydrogen bonds with the H4 Arg78 residue. In contrast, the other TSH2B-specific amino-acid residues did not induce any significant local structural changes in the TSH2B nucleosome. These findings may provide important information for understanding how testis-specific histone variants form nucleosomes during spermatogenesis.
Collapse
Affiliation(s)
- Takashi Urahama
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| |
Collapse
|
24
|
Every amino acid matters: essential contributions of histone variants to mammalian development and disease. Nat Rev Genet 2014; 15:259-71. [PMID: 24614311 DOI: 10.1038/nrg3673] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite a conserved role for histones as general DNA packaging agents, it is now clear that another key function of these proteins is to confer variations in chromatin structure to ensure dynamic patterns of transcriptional regulation in eukaryotes. The incorporation of histone variants is particularly important to this process. Recent knockdown and knockout studies in various cellular systems, as well as direct mutational evidence from human cancers, now suggest a crucial role for histone variant regulation in processes as diverse as differentiation and proliferation, meiosis and nuclear reprogramming. In this Review, we provide an overview of histone variants in the context of their unique functions during mammalian germ cell and embryonic development, and examine the consequences of aberrant histone variant regulation in human disease.
Collapse
|
25
|
Goudarzi A, Shiota H, Rousseaux S, Khochbin S. Genome-scale acetylation-dependent histone eviction during spermatogenesis. J Mol Biol 2014; 426:3342-9. [PMID: 24613302 DOI: 10.1016/j.jmb.2014.02.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/26/2014] [Accepted: 02/26/2014] [Indexed: 12/30/2022]
Abstract
A genome-wide histone hyperacetylation is known to occur in the absence of transcription in haploid male germ cells, spermatids, before and during the global histone eviction and their replacement by non-histone DNA-packaging proteins. Although the occurrence of this histone hyperacetylation has been correlated with histone removal for a long time, the underlying mechanisms have remained largely obscure. Important recent discoveries have not only shed light on how histone acetylation could drive a subsequent transformation in genome organization but also revealed that the associated nucleosome dismantlement is a multi-step process, requiring the contribution of histone variants, critical destabilizing histone modifications and chromatin readers, including Brdt, working together to achieve the full packaging of the male genome, indispensable for the propagation of life.
Collapse
Affiliation(s)
- Afsaneh Goudarzi
- Institut National de la Santé et de la Recherche Médicale U823 and Université Grenoble Alpes Institut Albert Bonniot, Grenoble F-38700, France
| | - Hitoshi Shiota
- Institut National de la Santé et de la Recherche Médicale U823 and Université Grenoble Alpes Institut Albert Bonniot, Grenoble F-38700, France
| | - Sophie Rousseaux
- Institut National de la Santé et de la Recherche Médicale U823 and Université Grenoble Alpes Institut Albert Bonniot, Grenoble F-38700, France
| | - Saadi Khochbin
- Institut National de la Santé et de la Recherche Médicale U823 and Université Grenoble Alpes Institut Albert Bonniot, Grenoble F-38700, France.
| |
Collapse
|
26
|
Abstract
The conversion of male germ cell chromatin to a nucleoprotamine structure is fundamental to the life cycle, yet the underlying molecular details remain obscure. Here we show that an essential step is the genome-wide incorporation of TH2B, a histone H2B variant of hitherto unknown function. Using mouse models in which TH2B is depleted or C-terminally modified, we show that TH2B directs the final transformation of dissociating nucleosomes into protamine-packed structures. Depletion of TH2B induces compensatory mechanisms that permit histone removal by up-regulating H2B and programming nucleosome instability through targeted histone modifications, including lysine crotonylation and arginine methylation. Furthermore, after fertilization, TH2B reassembles onto the male genome during protamine-to-histone exchange. Thus, TH2B is a unique histone variant that plays a key role in the histone-to-protamine packing of the male genome and guides genome-wide chromatin transitions that both precede and follow transmission of the male genome to the egg.
Collapse
|
27
|
Teperek M, Miyamoto K. Nuclear reprogramming of sperm and somatic nuclei in eggs and oocytes. Reprod Med Biol 2013; 12:133-149. [PMID: 24273450 PMCID: PMC3824936 DOI: 10.1007/s12522-013-0155-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/18/2013] [Indexed: 10/26/2022] Open
Abstract
Eggs and oocytes have a prominent ability to reprogram sperm nuclei for ensuring embryonic development. The reprogramming activity that eggs/oocytes intrinsically have towards sperm is utilised to reprogram somatic nuclei injected into eggs/oocytes in nuclear transfer (NT) embryos. NT embryos of various species can give rise to cloned animals, demonstrating that eggs/oocytes can confer totipotency even to somatic nuclei. However, many studies indicate that reprogramming of somatic nuclei is not as efficient as that of sperm nuclei. In this review, we explain how and why sperm and somatic nuclei are differentially reprogrammed in eggs/oocytes. Recent studies have shown that sperm chromatin is epigenetically modified to be adequate for early embryonic development, while somatic nuclei do not have such modifications. Moreover, epigenetic memories encoded in sperm chromatin are transgenerationally inherited, implying unique roles of sperm. We also discuss whether somatic nuclei can be artificially modified to acquire sperm-like chromatin states in order to increase the efficiency of nuclear reprogramming.
Collapse
Affiliation(s)
- Marta Teperek
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, CB2 1QN Cambridge, United Kingdom ; Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | | |
Collapse
|
28
|
|
29
|
Histone H2A (H2A.X and H2A.Z) variants in molluscs: molecular characterization and potential implications for chromatin dynamics. PLoS One 2012; 7:e30006. [PMID: 22253857 PMCID: PMC3256202 DOI: 10.1371/journal.pone.0030006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/11/2011] [Indexed: 11/28/2022] Open
Abstract
Histone variants are used by the cell to build specialized nucleosomes, replacing canonical histones and generating functionally specialized chromatin domains. Among many other processes, the specialization imparted by histone H2A (H2A.X and H2A.Z) variants to the nucleosome core particle constitutes the earliest response to DNA damage in the cell. Consequently, chromatin-based genotoxicity tests have been developed in those cases where enough information pertaining chromatin structure and dynamics is available (i.e., human and mouse). However, detailed chromatin knowledge is almost absent in most organisms, specially protostome animals. Molluscs (which represent sentinel organisms for the study of pollution) are not an exception to this lack of knowledge. In the present work we first identified the existence of functionally differentiated histone H2A.X and H2A.Z variants in the mussel Mytilus galloprovincialis (MgH2A.X and MgH2A.Z), a marine organism widely used in biomonitoring programs. Our results support the functional specialization of these variants based on: a) their active expression in different tissues, as revealed by the isolation of native MgH2A.X and MgH2A.Z proteins in gonad and hepatopancreas; b) the evolutionary conservation of different residues encompassing functional relevance; and c) their ability to confer specialization to nucleosomes, as revealed by nucleosome reconstitution experiments using recombinant MgH2A.X and MgH2A.Z histones. Given the seminal role of these variants in maintaining genomic integrity and regulating gene expression, their preliminary characterization opens up new potential applications for the future development of chromatin-based genotoxicity tests in pollution biomonitoring programs.
Collapse
|
30
|
Moosmann A, Campsteijn C, Jansen PW, Nasrallah C, Raasholm M, Stunnenberg HG, Thompson EM. Histone variant innovation in a rapidly evolving chordate lineage. BMC Evol Biol 2011; 11:208. [PMID: 21756361 PMCID: PMC3156773 DOI: 10.1186/1471-2148-11-208] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/15/2011] [Indexed: 01/04/2023] Open
Abstract
Background Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs on a background of genome architecture that shows global similarities from sponges to vertebrates, but the urochordate, Oikopleura dioica, a member of the sister group to vertebrates, exhibits profound modification of this ancestral architecture. Results We show that a histone complement of 47 gene loci encodes 31 histone variants, grouped in distinct sets of developmental expression profiles throughout the life cycle. A particularly diverse array of 15 male-specific histone variants was uncovered, including a testes-specific H4t, the first metazoan H4 sequence variant reported. Universal histone variants H3.3, CenH3, and H2A.Z are present but O. dioica lacks homologs of macroH2A and H2AX. The genome encodes many H2A and H2B variants and the repertoire of H2A.Z isoforms is expanded through alternative splicing, incrementally regulating the number of acetylatable lysine residues in the functionally important N-terminal "charge patch". Mass spectrometry identified 40 acetylation, methylation and ubiquitylation posttranslational modifications (PTMs) and showed that hallmark PTMs of "active" and "repressive" chromatin were present in O. dioica. No obvious reduction in silent heterochromatic marks was observed despite high gene density in this extraordinarily compacted chordate genome. Conclusions These results show that histone gene complements and their organization differ considerably even over modest phylogenetic distances. Substantial innovation among all core and linker histone variants has evolved in concert with adaptation of specific life history traits in this rapidly evolving chordate lineage.
Collapse
|
31
|
Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc Natl Acad Sci U S A 2010; 107:10454-9. [PMID: 20498094 DOI: 10.1073/pnas.1003064107] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A histone H3 variant, H3T, is highly expressed in the testis, suggesting that it may play an important role in the chromatin reorganization required for meiosis and/or spermatogenesis. In the present study, we found that the nucleosome containing human H3T is significantly unstable both in vitro and in vivo, as compared to the conventional nucleosome containing H3.1. The crystal structure of the H3T nucleosome revealed structural differences in the H3T regions on both ends of the central alpha2 helix, as compared to those of H3.1. The H3T-specific residues (Met71 and Val111) are the source of the structural differences observed between H3T and H3.1. A mutational analysis revealed that these residues are responsible for the reduced stability of the H3T-containing nucleosome. These physical and structural properties of the H3T-containing nucleosome may provide the basis of chromatin reorganization during spermatogenesis.
Collapse
|
32
|
Abstract
Histones wrap DNA to form nucleosome particles that compact eukaryotic genomes. Variant histones have evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, sperm packaging and other processes. 'Universal' histone variants emerged early in eukaryotic evolution and were later displaced for bulk packaging roles by the canonical histones (H2A, H2B, H3 and H4), the synthesis of which is coupled to DNA replication. Further specializations of histone variants have evolved in some lineages to perform additional tasks. Differences among histone variants in their stability, DNA wrapping, specialized domains that regulate access to DNA, and post-translational modifications, underlie the diverse functions that histones have acquired in evolution.
Collapse
|
33
|
González-Romero R, Rivera-Casas C, Ausió J, Méndez J, Eirín-López JM. Birth-and-death long-term evolution promotes histone H2B variant diversification in the male germinal cell line. Mol Biol Evol 2010; 27:1802-12. [PMID: 20194426 DOI: 10.1093/molbev/msq058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The rich diversity within each of the five histone families (H1, H2A, H2B, H3, and H4) can hardly be reconciled with the notion of homogenizing evolution. The prevalence of birth-and-death long-term evolution over concerted evolution has already been demonstrated in the linker histone H1 family as well as for the H2A, H3, and H4 core histone families. However, information about histone H2B is lacking. In the present work, we have analyzed the diversity of the members of this histone family across different eukaryotic genomes and have characterized the mechanisms involved in their long-term evolution. Our results reveal that, quite in contrast with other histones, H2B variants are subject to a very rapid process of diversification that primarily affects the male germinal cell lineage and involves their functional specialization probably as a consequence of neofunctionalization and subfunctionalization events after gene duplication. The overall parallelism observed between the molecular phylogenies and the relationships among the electrostatic potentials of the different variants suggests that the latter may have played a major structural selective constraint during H2B evolution. It thus seems that the reorganization of chromatin structure during spermiogenesis might have affected the evolutionary constraints driving histone H2B evolution, leading to an increase in diversity.
Collapse
Affiliation(s)
- Rodrigo González-Romero
- XENOMAR-CHROMEVOL Group, Departamento de Biología Celular y Molecular, Universidade da Coruña, Coruña, Spain
| | | | | | | | | |
Collapse
|
34
|
Gaucher J, Reynoird N, Montellier E, Boussouar F, Rousseaux S, Khochbin S. From meiosis to postmeiotic events: the secrets of histone disappearance. FEBS J 2009; 277:599-604. [PMID: 20015078 DOI: 10.1111/j.1742-4658.2009.07504.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
One of the most obscure phenomena in modern biology is the near genome-wide displacement of histones that occurs during the postmeiotic phases of spermatogenesis in many species. Here we review the literature to show that, during spermatogenic differentiation, three major molecular mechanisms come together to 'prepare' the nucleosomes for facilitated disassembly and histone removal.
Collapse
Affiliation(s)
- Jonathan Gaucher
- INSERM, U823, Université Joseph Fourier, Institut Albert Bonniot, Grenoble, France
| | | | | | | | | | | |
Collapse
|
35
|
MBD4-mediated glycosylase activity on a chromatin template is enhanced by acetylation. Mol Cell Biol 2008; 28:4734-44. [PMID: 18519584 DOI: 10.1128/mcb.00588-08] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of the MBD4 glycosylase to excise a mismatched base from DNA has been assessed in vitro using DNA substrates with different extents of cytosine methylation, in the presence or absence of reconstituted nucleosomes. Despite the enhanced ability of MBD4 to bind to methylated cytosines, the efficiency of its glycosylase activity on T/G mismatches was slightly dependent on the extent of methylation of the DNA substrate. The reduction in activity caused by competitor DNA was likewise unaffected by the methylation status of the substrate or the competitor. Our results also show that MBD4 efficiently processed T/G mismatches within the nucleosome. Furthermore, the glycolytic activity of the enzyme was not affected by the positioning of the mismatch within the nucleosome. However, histone hyperacetylation facilitated the efficiency with which the bases were excised from the nucleosome templates, irrespective of the position of the mismatch relative to the pseudodyad axis of symmetry of the nucleosome.
Collapse
|
36
|
sNASP, a histone H1-specific eukaryotic chaperone dimer that facilitates chromatin assembly. Biophys J 2008; 95:1314-25. [PMID: 18456819 DOI: 10.1529/biophysj.108.130021] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
NASP has been described as a histone H1 chaperone in mammals. However, the molecular mechanisms involved have not yet been characterized. Here, we show that this protein is not only present in mammals but is widely distributed throughout eukaryotes both in its somatic and testicular forms. The secondary structure of the human somatic version consists mainly of clusters of alpha-helices and exists as a homodimer in solution. The protein binds nonspecifically to core histone H2A-H2B dimers and H3-H4 tetramers but only forms specific complexes with histone H1. The formation of the NASP-H1 complexes is mediated by the N- and C-terminal domains of histone H1 and does not involve the winged helix domain that is characteristic of linker histones. In vitro chromatin reconstitution experiments show that this protein facilitates the incorporation of linker histones onto nucleosome arrays and hence is a bona fide linker histone chaperone.
Collapse
|
37
|
Eirín-López JM, Ishibashi T, Ausió J. H2A.Bbd: a quickly evolving hypervariable mammalian histone that destabilizes nucleosomes in an acetylation-independent way. FASEB J 2007; 22:316-26. [PMID: 17726088 DOI: 10.1096/fj.07-9255com] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Molecular evolutionary analyses revealed that histone H2A.Bbd is a highly variable quickly evolving mammalian replacement histone variant, in striking contrast to all other histones. At the nucleotide level, this variability appears to be the result of a larger amount of nonsynonymous variation, which affects to a lesser extent, the structural domain of the protein comprising the histone fold. The resulting amino acid sequence diversity can be predicted to affect the internucleosomal and intranucleosomal histone interactions. Our phylogenetic analysis has allowed us to identify several of the residues involved. The biophysical characterization of nucleosomes reconstituted with recombinant mouse H2A.Bbd and their comparison to similar data obtained with human H2A.Bbd clearly support this notion. Despite the high interspecific amino acid sequence variability, all of the H2A.Bbd variants exert similar structural effects at the nucleosome level, which result in an unfolded highly unstable nucleoprotein complex. Such structure resembles that previously described for the highly dynamically acetylated nucleosomes associated with transcriptionally active regions of the genome. Nevertheless, the structure of nucleosome core particles reconstituted from H2A.Bbd is not affected by the presence of a hyperacetylated histone complement. This suggests that replacement by H2A.Bbd provides an alternative mechanism to unfold chromatin structure, possibly in euchromatic regions, in a way that is not dependent on acetylation.
Collapse
Affiliation(s)
- José María Eirín-López
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building, 258a, Victoria, BC, Canada V8W 3P6
| | | | | |
Collapse
|
38
|
Govin J, Escoffier E, Rousseaux S, Kuhn L, Ferro M, Thévenon J, Catena R, Davidson I, Garin J, Khochbin S, Caron C. Pericentric heterochromatin reprogramming by new histone variants during mouse spermiogenesis. ACTA ACUST UNITED AC 2007; 176:283-94. [PMID: 17261847 PMCID: PMC2063955 DOI: 10.1083/jcb.200604141] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
During male germ cell postmeiotic maturation, dramatic chromatin reorganization occurs, which is driven by completely unknown mechanisms. For the first time, we describe a specific reprogramming of mouse pericentric heterochromatin. Initiated when histones undergo global acetylation in early elongating spermatids, this process leads to the establishment of new DNA packaging structures organizing the pericentric regions in condensing spermatids. Five new histone variants were discovered, which are expressed in late spermiogenic cells. Two of them, which we named H2AL1 and H2AL2, specifically mark the pericentric regions in condensing spermatids and participate in the formation of new nucleoprotein structures. Moreover, our investigations also suggest that TH2B, an already identified testis-specific H2B variant of unknown function, could provide a platform for the structural transitions accompanying the incorporation of these new histone variants.
Collapse
Affiliation(s)
- Jérôme Govin
- Institut National de la Santé et de la Recherche Médicale, U309, Institut Albert Bonniot, F-38700 Grenoble, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Singleton S, Zalensky A, Doncel GF, Morshedi M, Zalenskaya IA. Testis/sperm-specific histone 2B in the sperm of donors and subfertile patients: variability and relation to chromatin packaging. Hum Reprod 2006; 22:743-50. [PMID: 17110399 DOI: 10.1093/humrep/del439] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The compaction of human sperm chromatin is the result of replacement of approximately 85% of histones with protamines. Germ-line testis/sperm-specific histone 2B (TSH2B) has been detected in only approximately 30% of mature spermatozoa. Its level in the semen of subfertile patients varies; its function is unknown. We evaluated TSH2B in the sperm samples of 23 donors and 49 subfertile patients and assessed its association with chromatin compaction status. METHODS TSH2B level was measured using immunoblotting. Chromatin packaging quality was evaluated by staining with chromomycin A3 (CMA3) which marked spermatozoa with defective packaging. To assess both TSH2B and chromatin status in the same spermatozoon, CMA3 staining and TSH2B immunolocalization were performed sequentially. RESULTS A significant correlation (r = 0.55, P = 0.0027) was found between TSH2B level and percentage of CMA3-positive sperm in patient and donor semen samples. When individual spermatozoa were assessed for these parameters, 92% of TSH2B-containing cells were also CMA3 positive. Variation in the total sperm TSH2B level was less in donors than in patients. CONCLUSIONS CMA3 positive staining of TSH2B-containing individual spermatozoa and a significant correlation between the total TSH2B level and CMA3 percentage in semen samples suggest a structural role for TSH2B in sperm chromatin organization. Low variability of TSH2B level in donors implies a mechanism (however unknown) regulating this parameter.
Collapse
Affiliation(s)
- S Singleton
- The Jones Institute for Reproductive Medicine, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | | | | | | | | |
Collapse
|
40
|
Bernstein E, Hake SB. The nucleosome: a little variation goes a long wayThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2006; 84:505-17. [PMID: 16936823 DOI: 10.1139/o06-085] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Changes in the overall structure of chromatin are essential for the proper regulation of cellular processes, including gene activation and silencing, DNA repair, chromosome segregation during mitosis and meiosis, X chromosome inactivation in female mammals, and chromatin compaction during apoptosis. Such alterations of the chromatin template occur through at least 3 interrelated mechanisms: post-translational modifications of histones, ATP-dependent chromatin remodeling, and the incorporation (or replacement) of specialized histone variants into chromatin. Of these mechanisms, the exchange of variants into and out of chromatin is the least well understood. However, the exchange of conventional histones for variant histones has distinct and profound consequences within the cell. This review focuses on the growing number of mammalian histone variants, their particular biological functions and unique features, and how they may affect the structure of the nucleosome. We propose that a given nucleosome might not consist of heterotypic variants, but rather, that only specific histone variants come together to form a homotypic nucleosome, a hypothesis that we refer to as the nucleosome code. Such nucleosomes might in turn participate in marking specific chromatin domains that may contribute to epigenetic inheritance.
Collapse
Affiliation(s)
- Emily Bernstein
- Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, NY, NY 10021, USA
| | | |
Collapse
|
41
|
Thambirajah AA, Dryhurst D, Ishibashi T, Li A, Maffey AH, Ausió J. H2A.Z Stabilizes Chromatin in a Way That Is Dependent on Core Histone Acetylation. J Biol Chem 2006; 281:20036-44. [PMID: 16707487 DOI: 10.1074/jbc.m601975200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The functional and structural chromatin roles of H2A.Z are still controversial. This work represents a further attempt to resolve the current functional and structural dichotomy by characterizing chromatin structures containing native H2A.Z. We have analyzed the role of this variant in mediating the stability of the histone octamer in solution using gel-filtration chromatography at different pH. It was found that decreasing the pH from neutral to acidic conditions destabilized the histone complex. Furthermore, it was shown that the H2A.Z-H2B dimer had a reduced stability. Sedimentation velocity analysis of nucleosome core particles (NCPs) reconstituted from native H2A.Z-containing octamers indicated that these particles exhibit a very similar behavior to that of native NCPs consisting of canonical H2A. Sucrose gradient fractionation of native NCPs under different ionic strengths indicated that H2A.Z had a subtle tendency to fractionate with more stabilized populations. An extensive analysis of the salt-dependent dissociation of histones from hydroxyapatite-adsorbed chromatin revealed that, whereas H2A.Z co-elutes with H3-H4, hyperacetylation of histones (by treatment of chicken MSB cells with sodium butyrate) resulted in a significant fraction of this variant eluting with the canonical H2A. These studies also showed that the late elution of this variant (correlated to enhanced binding stability) was independent of the chromatin size and of the presence or absence of linker histones.
Collapse
Affiliation(s)
- Anita A Thambirajah
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | | | | | | | | | | |
Collapse
|
42
|
Boulard M, Gautier T, Mbele GO, Gerson V, Hamiche A, Angelov D, Bouvet P, Dimitrov S. The NH2 tail of the novel histone variant H2BFWT exhibits properties distinct from conventional H2B with respect to the assembly of mitotic chromosomes. Mol Cell Biol 2006; 26:1518-26. [PMID: 16449661 PMCID: PMC1367197 DOI: 10.1128/mcb.26.4.1518-1526.2006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have studied the functional and structural properties of nucleosomes reconstituted with H2BFWT, a recently identified putative histone variant of the H2B family with totally unknown function. We show that H2BFWT can replace the conventional histone H2B in the nucleosome. The presence of H2BFWT did not affect the overall structure of the nucleosome, and the H2BFWT nucleosomes exhibited the same stability as conventional nucleosomes. SWI/SNF was able to efficiently remodel and mobilize the H2BFWT nucleosomes. Importantly, H2BFWT, in contrast to conventional H2B, was unable to recruit chromosome condensation factors and to participate in the assembly of mitotic chromosomes. This was determined by the highly divergent (compared to conventional H2B) NH2 tail of H2BFWT. These data, in combination with the observations that H2BFWT was found by others in the sperm nuclei and appeared to be associated with the telomeric chromatin, suggest that H2BFWT could act as a specific epigenetic marker.
Collapse
Affiliation(s)
- Mathieu Boulard
- Institut Albert Bonniot, INSERM U309, 38706 La Tronche Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|