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Osipov YA, Posukh OV, Kalashnikova DA, Antoshina PA, Laktionov PP, Skrypnik PA, Belyakin SN, Singh PB. H3K9 and H4K20 methyltransferases are directly involved in the heterochromatinization of the paternal chromosomes in male Planococcus citri embryos. Chromosoma 2023; 132:317-328. [PMID: 37700063 DOI: 10.1007/s00412-023-00809-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/11/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Using a new method for bulk preparation of early stage embryos, we have investigated the role played by putative Planococcus citri H3K9 and H4K20 histone methyl transferases (HMTases) in regulating heterochromatinization of the imprinted paternal chromosomal set in male embryos. We found that H3K9 and H420 HMTases are required for heterochromatinization of the paternal chromosomes. We present evidence that both HMTases maintain the paternal "imprint" during the cleavage divisions when both parental chromosome sets are euchromatic. A testable model that accommodates our findings is proposed.
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Affiliation(s)
- Yakov A Osipov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Olga V Posukh
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Darya A Kalashnikova
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Polina A Antoshina
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Petr P Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Polina A Skrypnik
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Stepan N Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation.
| | - Prim B Singh
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation.
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, 010000, Nur-Sultan, Kazakhstan.
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Laktionov PP, Maksimov DA, Romanov SE, Antoshina PA, Posukh OV, White-Cooper H, Koryakov DE, Belyakin SN. Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis. Epigenetics Chromatin 2018; 11:14. [PMID: 29609617 PMCID: PMC5879934 DOI: 10.1186/s13072-018-0183-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/22/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND During Drosophila spermatogenesis, testis-specific meiotic arrest complex (tMAC) and testis-specific TBP-associated factors (tTAF) contribute to activation of hundreds of genes required for meiosis and spermiogenesis. Intriguingly, tMAC is paralogous to the broadly expressed complex Myb-MuvB (MMB)/dREAM and Mip40 protein is shared by both complexes. tMAC acts as a gene activator in spermatocytes, while MMB/dREAM was shown to repress gene activity in many cell types. RESULTS Our study addresses the intricate interplay between tMAC, tTAF, and MMB/dREAM during spermatogenesis. We used cell type-specific DamID to build the DNA-binding profiles of Cookie monster (tMAC), Cannonball (tTAF), and Mip40 (MMB/dREAM and tMAC) proteins in male germline cells. Incorporating the whole transcriptome analysis, we characterized the regulatory effects of these proteins and identified their gene targets. This analysis revealed that tTAFs complex is involved in activation of achi, vis, and topi meiosis arrest genes, implying that tTAFs may indirectly contribute to the regulation of Achi, Vis, and Topi targets. To understand the relationship between tMAC and MMB/dREAM, we performed Mip40 DamID in tTAF- and tMAC-deficient mutants demonstrating meiosis arrest phenotype. DamID profiles of Mip40 were highly dynamic across the stages of spermatogenesis and demonstrated a strong dependence on tMAC in spermatocytes. Integrative analysis of our data indicated that MMB/dREAM represses genes that are not expressed in spermatogenesis, whereas tMAC recruits Mip40 for subsequent gene activation in spermatocytes. CONCLUSIONS Discovered interdependencies allow to formulate a renewed model for tMAC and tTAFs action in Drosophila spermatogenesis demonstrating how tissue-specific genes are regulated.
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Affiliation(s)
- Petr P Laktionov
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | - Daniil A Maksimov
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | - Stanislav E Romanov
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | - Polina A Antoshina
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | - Olga V Posukh
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | | | - Dmitry E Koryakov
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090.,Novosibirsk State University, Novosibirsk, Russia, 630090
| | - Stepan N Belyakin
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090. .,Novosibirsk State University, Novosibirsk, Russia, 630090.
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Posukh OV, Maksimov DA, Laktionov PP, Koryakov DE, Belyakin SN. Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile. Epigenetics Chromatin 2017; 10:56. [PMID: 29191233 PMCID: PMC5709859 DOI: 10.1186/s13072-017-0163-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 11/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In eukaryotes, heterochromatin replicates late in S phase of the cell cycle and contains specific covalent modifications of histones. SuUR mutation found in Drosophila makes heterochromatin replicate earlier than in wild type and reduces the level of repressive histone modifications. SUUR protein was shown to be associated with moving replication forks, apparently through the interaction with PCNA. The biological process underlying the effects of SUUR on replication and composition of heterochromatin remains unknown. RESULTS Here we performed a functional dissection of SUUR protein effects on H3K27me3 level. Using hidden Markow model-based algorithm we revealed SuUR-sensitive chromosomal regions that demonstrated unusual characteristics: They do not contain Polycomb and require SUUR function to sustain H3K27me3 level. We tested the role of SUUR protein in the mechanisms that could affect H3K27me3 histone levels in these regions. We found that SUUR does not affect the initial H3K27me3 pattern formation in embryogenesis or Polycomb distribution in the chromosomes. We also ruled out the possible effect of SUUR on histone genes expression and its involvement in DSB repair. CONCLUSIONS Obtained results support the idea that SUUR protein contributes to the heterochromatin maintenance during the chromosome replication. A model that explains major SUUR-associated phenotypes is proposed.
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Affiliation(s)
- Olga V Posukh
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090
| | - Daniil A Maksimov
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090
| | - Petr P Laktionov
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090
| | - Dmitry E Koryakov
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090.,Novosibirsk State University, Pirogov str. 2, Novosibirsk, Russia
| | - Stepan N Belyakin
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090. .,Novosibirsk State University, Pirogov str. 2, Novosibirsk, Russia.
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Maksimov DA, Laktionov PP, Posukh OV, Belyakin SN, Koryakov DE. Genome-wide analysis of SU(VAR)3-9 distribution in chromosomes of Drosophila melanogaster. Chromosoma 2017; 127:85-102. [DOI: 10.1007/s00412-017-0647-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 02/07/2023]
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Andreyeva EN, Bernardo TJ, Kolesnikova TD, Lu X, Yarinich LA, Bartholdy BA, Guo X, Posukh OV, Healton S, Willcockson MA, Pindyurin AV, Zhimulev IF, Skoultchi AI, Fyodorov DV. Regulatory functions and chromatin loading dynamics of linker histone H1 during endoreplication in Drosophila. Genes Dev 2017; 31:603-616. [PMID: 28404631 PMCID: PMC5393055 DOI: 10.1101/gad.295717.116] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/03/2017] [Indexed: 12/22/2022]
Abstract
Here, Andreyeva et al. show that linker histone H1 is required for the underreplicated phenomenon in Drosophila salivary glands, in which tissues undergo endoreplication without cell division, and the latest replicating regions occasionally fail to complete endoreplication, resulting in underreplicated domains of polytene chromosomes. They demonstrate that H1 directly interacts with the suppressor of underreplication (SUUR) protein and is required for SUUR binding to chromatin in vivo and that the localization of H1 in chromatin changes profoundly during the endocycle. Eukaryotic DNA replicates asynchronously, with discrete genomic loci replicating during different stages of S phase. Drosophila larval tissues undergo endoreplication without cell division, and the latest replicating regions occasionally fail to complete endoreplication, resulting in underreplicated domains of polytene chromosomes. Here we show that linker histone H1 is required for the underreplication (UR) phenomenon in Drosophila salivary glands. H1 directly interacts with the Suppressor of UR (SUUR) protein and is required for SUUR binding to chromatin in vivo. These observations implicate H1 as a critical factor in the formation of underreplicated regions and an upstream effector of SUUR. We also demonstrate that the localization of H1 in chromatin changes profoundly during the endocycle. At the onset of endocycle S (endo-S) phase, H1 is heavily and specifically loaded into late replicating genomic regions and is then redistributed during the course of endoreplication. Our data suggest that cell cycle-dependent chromosome occupancy of H1 is governed by several independent processes. In addition to the ubiquitous replication-related disassembly and reassembly of chromatin, H1 is deposited into chromatin through a novel pathway that is replication-independent, rapid, and locus-specific. This cell cycle-directed dynamic localization of H1 in chromatin may play an important role in the regulation of DNA replication timing.
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Affiliation(s)
- Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Travis J Bernardo
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Tatyana D Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation.,Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Xingwu Lu
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Lyubov A Yarinich
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation.,Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Xiaohan Guo
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Olga V Posukh
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Sean Healton
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Michael A Willcockson
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation.,Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Posukh OV, Maksimov DA, Skvortsova KN, Koryakov DE, Belyakin SN. The effects of SUUR protein suggest its role in repressive chromatin renewal during replication in Drosophila. Nucleus 2016. [PMID: 26211696 DOI: 10.1080/19491034.2015.1074366] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Replication of chromosomes is central to heredity. To become available for replication machinery, DNA invariably needs to dissociate from chromatin proteins. Yet, chromatin landscape must be promptly re-established during or soon after replication. Although this process underlies the epigenetic inheritance, little is known about its molecular mechanisms. This mini-review is focused on Drosophila melanogaster SUppressor of UnderReplication (SUUR) protein, which is involved both in replication and chromatin maintenance in polytene tissues. Existing data suggest that it is involved in the regulation of chromatin renewal during replication. According to this model, SUUR protein moves along the chromosomes together with the replication complex. When the replication fork enters the repressed, H3K27me3- or H3K9me3-enriched, chromatin, SUUR-containing complex slows down the replisome until these histone modifications are properly placed on the newly-synthesized DNA strands. Suggested model provides an insight into the mechanism of epigenetic information inheritance. This hypothesis could be tested by further analysis of the interplay between local enrichment of repressive histone modifications and the replication fork progression rate.
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Affiliation(s)
- Olga V Posukh
- a Institute of Molecular and Cellular Biology SB RAS ; Novosibirsk , Russia
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Kolesnikova TD, Posukh OV, Andreyeva EN, Bebyakina DS, Ivankin AV, Zhimulev IF. Drosophila SUUR protein associates with PCNA and binds chromatin in a cell cycle-dependent manner. Chromosoma 2012; 122:55-66. [DOI: 10.1007/s00412-012-0390-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/25/2012] [Accepted: 10/22/2012] [Indexed: 01/06/2023]
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