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Djakovic L, Hennig T, Reinisch K, Milić A, Whisnant AW, Wolf K, Weiß E, Haas T, Grothey A, Jürges CS, Kluge M, Wolf E, Erhard F, Friedel CC, Dölken L. The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes. Nat Commun 2023; 14:4591. [PMID: 37524699 PMCID: PMC10390501 DOI: 10.1038/s41467-023-40217-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/19/2023] [Indexed: 08/02/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) infection and stress responses disrupt transcription termination by RNA Polymerase II (Pol II). In HSV-1 infection, but not upon salt or heat stress, this is accompanied by a dramatic increase in chromatin accessibility downstream of genes. Here, we show that the HSV-1 immediate-early protein ICP22 is both necessary and sufficient to induce downstream open chromatin regions (dOCRs) when transcription termination is disrupted by the viral ICP27 protein. This is accompanied by a marked ICP22-dependent loss of histones downstream of affected genes consistent with impaired histone repositioning in the wake of Pol II. Efficient knock-down of the ICP22-interacting histone chaperone FACT is not sufficient to induce dOCRs in ΔICP22 infection but increases dOCR induction in wild-type HSV-1 infection. Interestingly, this is accompanied by a marked increase in chromatin accessibility within gene bodies. We propose a model in which allosteric changes in Pol II composition downstream of genes and ICP22-mediated interference with FACT activity explain the differential impairment of histone repositioning downstream of genes in the wake of Pol II in HSV-1 infection.
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Affiliation(s)
- Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Katharina Reinisch
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Andrea Milić
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Adam W Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Katharina Wolf
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Elena Weiß
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Tobias Haas
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Arnhild Grothey
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Christopher S Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- Mildred Scheel Early Career Center, University of Würzburg, Beethovenstraße 1A, 97080, Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Amalienstr. 17, 80333, Munich, Germany.
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacher Straße 7, 97078, Würzburg, Germany.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), 97080, Würzburg, Germany.
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Piccinini G, Milani L. Germline-related molecular phenotype in Metazoa: conservation and innovation highlighted by comparative transcriptomics. EvoDevo 2023; 14:2. [PMID: 36717890 PMCID: PMC9885605 DOI: 10.1186/s13227-022-00207-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/27/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND In Metazoa, the germline represents the cell lineage devoted to the transmission of genetic heredity across generations. Its functions intuitively evoke the crucial roles that it plays in organism development and species evolution, and its establishment is tightly tied to animal multicellularity itself. The molecular toolkit expressed in germ cells has a high degree of conservation between species, and it also shares many components with the molecular phenotype of some animal totipotent cell lineages, like planarian neoblasts and sponge archaeocytes. The present study stems from these observations and represents a transcriptome-wide comparative analysis between germline-related samples of 9 animal species (7 phyla), comprehending also totipotent lineages classically considered somatic. RESULTS Differential expression analyses were performed for each species between germline-related and control somatic tissues. We then compared the different germline-related transcriptional profiles across the species without the need for an a priori set of genes. Through a phylostratigraphic analysis, we observed that the proportion of phylum- and Metazoa-specific genes among germline-related upregulated transcripts was lower than expected by chance for almost all species. Moreover, homologous genes related to proper DNA replication resulted the most common when comparing the considered species, while the regulation of transcription and post-transcriptional mechanisms appeared more variable, showing shared upregulated functions and domains, but very few homologous whole-length sequences. CONCLUSIONS Our wide-scale comparative analysis mostly confirmed previous molecular characterizations of specific germline-related lineages. Additionally, we observed a consistent signal throughout the whole data set, therefore comprehending both canonically defined germline samples (germ cells), and totipotent cell lineages classically considered somatic (neoblasts and archaeocytes). The phylostratigraphic analysis supported the less probable involvement of novel molecular factors in the germline-related transcriptional phenotype and highlighted the early origin of such cell programming and its conservation throughout evolution. Moreover, the fact that the mostly shared molecular factors were involved in DNA replication and repair suggests how fidelity in genetic material inheritance is a strong and conserved driver of germline-related molecular phenotype, while transcriptional and post-transcriptional regulations appear differently tuned among the lineages.
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Affiliation(s)
- Giovanni Piccinini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Liliana Milani
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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Jeong E, Martina JA, Contreras PS, Lee J, Puertollano R. The FACT complex facilitates expression of lysosomal and antioxidant genes through binding to TFEB and TFE3. Autophagy 2022; 18:2333-2349. [PMID: 35230915 PMCID: PMC9542721 DOI: 10.1080/15548627.2022.2029671] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TFEB (transcription factor EB) and TFE3 (transcription factor binding to IGHM enhancer 3) orchestrate the cellular response to a variety of stressors, including nutrient deprivation, oxidative stress and pathogens. Here we describe a novel interaction of TFEB and TFE3 with the FAcilitates Chromatin Transcription (FACT) complex, a heterodimeric histone chaperone consisting of SSRP1 and SUPT16H that mediates nucleosome disassembly and assembly, thus facilitating transcription. Extracellular stimuli, such as nutrient deprivation or oxidative stress, induce nuclear translocation and activation of TFEB and TFE3, which then associate with the FACT complex to regulate stress-induced gene transcription. Depletion of FACT does not affect TFEB activation, stability, or binding to the promoter of target genes. In contrast, reduction of FACT levels by siRNA or treatment with the FACT inhibitor curaxin, severely impairs induction of numerous antioxidant and lysosomal genes, revealing a crucial role of FACT as a regulator of cellular homeostasis. Furthermore, upregulation of antioxidant genes induced by TFEB over-expression is significantly reduced by curaxin, consistent with a role of FACT as a TFEB transcriptional activator. Together, our data show that chromatin remodeling at the promoter of stress-responsive genes by FACT is important for efficient expression of TFEB and TFE3 targets, thus providing a link between environmental changes, chromatin modifications and transcriptional regulation.Abbreviations: ADNP2, ADNP homeobox 2; ATP6V0D1, ATPase H+ transporting V0 subunit d1; ATP6V1A, ATPase H+ transporting V1 subunit A; ATP6V1C1, ATPase H+ transporting V1 subunit C1; CSNK2/CK2, casein kinase 2; CLCN7, chloride voltage-gated channel 7; CTSD, cathepsin D; CTSZ, cathepsin Z; EBSS, earle's balanced salt solution; FACT complex, facilitates chromatin transcription complex; FOXO3, forkhead box O3; HEXA, hexosaminidase subunit alpha; HIF1A, hypoxia inducible factor 1 subunit alpha; HMOX1, heme oxygenase 1; LAMP1, lysosomal associated membrane protein 1; MAFF, MAF bZIP transcription factor F; MAFG, MAF bZIP transcription factor G; MCOLN1, mucolipin TRP cation channel 1; MTORC1, mechanistic target of rapamycin kinase complex 1; NaAsO2, sodium arsenite; POLR2, RNA polymerase II; PPARGC1A, PPARG coactivator 1 alpha; PYROXD1, pyridine nucleotide-disulfide oxidoreductase domain 1; RRAGC, Ras related GTP binding C; SEC13, SEC13 homolog, nuclear pore and COPII coat complex component; SLC38A9, solute carrier family 38 member 9; SSRP1, structure specific recognition protein 1; SUPT16H, SPT16 homolog, facilitates chromatin remodeling subunit; TFEB, transcription factor EB; TFE3, transcription factor binding to IGHM enhancer 3; TXNRD1, thioredoxin reductase 1; UVRAG, UV radiation resistance associated; WDR59, WD repeat domain 59.
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Affiliation(s)
- Eutteum Jeong
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - José A. Martina
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Pablo S. Contreras
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Juhyung Lee
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rosa Puertollano
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA,CONTACT Rosa Puertollano Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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Mattola S, Salokas K, Aho V, Mäntylä E, Salminen S, Hakanen S, Niskanen EA, Svirskaite J, Ihalainen TO, Airenne KJ, Kaikkonen-Määttä M, Parrish CR, Varjosalo M, Vihinen-Ranta M. Parvovirus nonstructural protein 2 interacts with chromatin-regulating cellular proteins. PLoS Pathog 2022; 18:e1010353. [PMID: 35395063 PMCID: PMC9020740 DOI: 10.1371/journal.ppat.1010353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/20/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022] Open
Abstract
Autonomous parvoviruses encode at least two nonstructural proteins, NS1 and NS2. While NS1 is linked to important nuclear processes required for viral replication, much less is known about the role of NS2. Specifically, the function of canine parvovirus (CPV) NS2 has remained undefined. Here we have used proximity-dependent biotin identification (BioID) to screen for nuclear proteins that associate with CPV NS2. Many of these associations were seen both in noninfected and infected cells, however, the major type of interacting proteins shifted from nuclear envelope proteins to chromatin-associated proteins in infected cells. BioID interactions revealed a potential role for NS2 in DNA remodeling and damage response. Studies of mutant viral genomes with truncated forms of the NS2 protein suggested a change in host chromatin accessibility. Moreover, further studies with NS2 mutants indicated that NS2 performs functions that affect the quantity and distribution of proteins linked to DNA damage response. Notably, mutation in the splice donor site of the NS2 led to a preferred formation of small viral replication center foci instead of the large coalescent centers seen in wild-type infection. Collectively, our results provide insights into potential roles of CPV NS2 in controlling chromatin remodeling and DNA damage response during parvoviral replication. Parvoviruses are small, nonenveloped DNA viruses, that besides being noteworthy pathogens in many animal species, including humans, are also being developed as vectors for gene and cancer therapy. Canine parvovirus is an autonomously replicating parvovirus that encodes two nonstructural proteins, NS1 and NS2. NS1 is required for viral DNA replication and packaging, as well as gene expression. However, very little is known about the function of NS2. Our studies indicate that NS2 serves a previously undefined important function in chromatin modification and DNA damage responses. Therefore, it appears that although both NS1 and NS2 are needed for a productive infection they play very different roles in the process.
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Affiliation(s)
- Salla Mattola
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Kari Salokas
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Vesa Aho
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Salminen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Satu Hakanen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Einari A. Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Julija Svirskaite
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Teemu O. Ihalainen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kari J. Airenne
- Kuopio Center for Gene and Cell Therapy (KCT), Kuopio, Finland
| | | | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, University of Cornell, Ithaca, New York, United States of America
| | - Markku Varjosalo
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- * E-mail:
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Li X, Li H, Jing Q, Wang M, Hu T, Li L, Zhang Q, Liu M, Fu YV, Han J, Su D. Structural insights into multifunctionality of human FACT complex subunit hSSRP1. J Biol Chem 2021; 297:101360. [PMID: 34756889 PMCID: PMC8639466 DOI: 10.1016/j.jbc.2021.101360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023] Open
Abstract
Human structure-specific recognition protein 1 (hSSRP1) is an essential component of the facilitates chromatin transcription complex, which participates in nucleosome disassembly and reassembly during gene transcription and DNA replication and repair. Many functions, including nuclear localization, histone chaperone activity, DNA binding, and interaction with cellular proteins, are attributed to hSSRP1, which contains multiple well-defined domains, including four pleckstrin homology (PH) domains and a high-mobility group domain with two flanking disordered regions. However, little is known about the mechanisms by which these domains cooperate to carry out hSSRP1’s functions. Here, we report the biochemical characterization and structure of each functional domain of hSSRP1, including the N-terminal PH1, PH2, PH3/4 tandem PH, and DNA-binding high-mobility group domains. Furthermore, two casein kinase II binding sites in hSSRP1 were identified in the PH3/4 domain and in a disordered region (Gly617–Glu709) located in the C-terminus of hSSRP1. In addition, a histone H2A–H2B binding motif and a nuclear localization signal (Lys677‒Asp687) of hSSRP1 are reported for the first time. Taken together, these studies provide novel insights into the structural basis for hSSRP1 functionality.
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Affiliation(s)
- Xuehui Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Huiyan Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Qian Jing
- Research Laboratory of Tumor Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Mengxue Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tingting Hu
- College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan, China
| | - Li Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Qiuping Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Mengxin Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junhong Han
- Research Laboratory of Tumor Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
| | - Dan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China; Infectious Disease Drug Discovery Institute, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China.
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Ciardo D, Haccard O, Narassimprakash H, Cornu D, Guerrera IC, Goldar A, Marheineke K. Polo-like kinase 1 (Plk1) regulates DNA replication origin firing and interacts with Rif1 in Xenopus. Nucleic Acids Res 2021; 49:9851-9869. [PMID: 34469577 PMCID: PMC8464078 DOI: 10.1093/nar/gkab756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
The activation of eukaryotic DNA replication origins needs to be strictly controlled at multiple steps in order to faithfully duplicate the genome and to maintain its stability. How the checkpoint recovery and adaptation protein Polo-like kinase 1 (Plk1) regulates the firing of replication origins during non-challenged S phase remained an open question. Using DNA fiber analysis, we show that immunodepletion of Plk1 in the Xenopus in vitro system decreases replication fork density and initiation frequency. Numerical analyses suggest that Plk1 reduces the overall probability and synchrony of origin firing. We used quantitative chromatin proteomics and co-immunoprecipitations to demonstrate that Plk1 interacts with firing factors MTBP/Treslin/TopBP1 as well as with Rif1, a known regulator of replication timing. Phosphopeptide analysis by LC/MS/MS shows that the C-terminal domain of Rif1, which is necessary for its repressive action on origins through protein phosphatase 1 (PP1), can be phosphorylated in vitro by Plk1 on S2058 in its PP1 binding site. The phosphomimetic S2058D mutant interrupts the Rif1-PP1 interaction and modulates DNA replication. Collectively, our study provides molecular insights into how Plk1 regulates the spatio-temporal replication program and suggests that Plk1 controls origin activation at the level of large chromatin domains in vertebrates.
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Affiliation(s)
- Diletta Ciardo
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Olivier Haccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Hemalatha Narassimprakash
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - David Cornu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Ida Chiara Guerrera
- Proteomics platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris 75015, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kathrin Marheineke
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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Brossas C, Duriez B, Valton AL, Prioleau MN. Promoters are key organizers of the duplication of vertebrate genomes. Bioessays 2021; 43:e2100141. [PMID: 34319621 DOI: 10.1002/bies.202100141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 11/06/2022]
Abstract
In vertebrates, single cell analyses of replication timing patterns brought to light a very well controlled program suggesting a tight regulation on initiation sites. Mapping of replication origins with different methods has revealed discrete preferential sites, enriched in promoters and potential G-quadruplex motifs, which can aggregate into initiation zones spanning several tens of kilobases (kb). Another characteristic of replication origins is a nucleosome-free region (NFR). A modified yeast strain containing a humanized origin recognition complex (ORC) fires new origins at NFRs revealing their regulatory role. In cooperation with NFRs, the histone variant H2A.Z facilitates ORC loading through di-methylation of lysine 20 of histone H4. Recent studies using genome editing methods show that efficient initiation sites associated with transcriptional activity can synergize over several tens of kb by establishing physical contacts and lead to the formation of early domains of DNA replication demonstrating a co-regulation between replication initiation and transcription.
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Affiliation(s)
- Caroline Brossas
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Bénédicte Duriez
- IMRB, INSERM U955, Equipe GEIC2O, Faculté de Santé, Créteil, France
| | - Anne-Laure Valton
- Department of Biochemistry and Molecular Pharmacology, Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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You C, Zhang Y, Yang S, Wang X, Yao W, Jin W, Wang W, Hu X, Yang H. Proteomic Analysis of Generative and Vegetative Nuclei Reveals Molecular Characteristics of Pollen Cell Differentiation in Lily. FRONTIERS IN PLANT SCIENCE 2021; 12:641517. [PMID: 34163497 PMCID: PMC8215658 DOI: 10.3389/fpls.2021.641517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 06/13/2023]
Abstract
In plants, the cell fates of a vegetative cell (VC) and generative cell (GC) are determined after the asymmetric division of the haploid microspore. The VC exits the cell cycle and grows a pollen tube, while the GC undergoes further mitosis to produce two sperm cells for double fertilization. However, our understanding of the mechanisms underlying their fate differentiation remains limited. One major advantage of the nuclear proteome analysis is that it is the only method currently able to uncover the systemic differences between VC and GC due to GC being engulfed within the cytoplasm of VC, limiting the use of transcriptome. Here, we obtained pure preparations of the vegetative cell nuclei (VNs) and generative cell nuclei (GNs) from germinating lily pollens. Utilizing these high-purity VNs and GNs, we compared the differential nucleoproteins between them using state-of-the-art quantitative proteomic techniques. We identified 720 different amount proteins (DAPs) and grouped the results in 11 fate differentiation categories. Among them, we identified 29 transcription factors (TFs) and 10 cell fate determinants. Significant differences were found in the molecular activities of vegetative and reproductive nuclei. The TFs in VN mainly participate in pollen tube development. In comparison, the TFs in GN are mainly involved in cell differentiation and male gametogenesis. The identified novel TFs may play an important role in cell fate differentiation. Our data also indicate differences in nuclear pore complexes and epigenetic modifications: more nucleoporins synthesized in VN; more histone variants and chaperones; and structural maintenance of chromosome (SMC) proteins, chromatin remodelers, and DNA methylation-related proteins expressed in GN. The VC has active macromolecular metabolism and mRNA processing, while GC has active nucleic acid metabolism and translation. Moreover, the members of unfolded protein response (UPR) and programmed cell death accumulate in VN, and DNA damage repair is active in GN. Differences in the stress response of DAPs in VN vs. GN were also found. This study provides a further understanding of pollen cell differentiation mechanisms and also a sound basis for future studies of the molecular mechanisms behind cell fate differentiation.
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Affiliation(s)
- Chen You
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- College of Life Science, Henan Normal University, Xinxiang, China
| | - YuPing Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - ShaoYu Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xu Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - WeiHuan Jin
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - XiuLi Hu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hao Yang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Lyubitelev AV, Kirpichnikov MP, Studitsky VM. The Role of Linker Histones in Carcinogenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Falbo L, Costanzo V. Epigenetic regulation of replication origin assembly: A role for histone H1 and chromatin remodeling factors. Bioessays 2020; 43:e2000181. [PMID: 33165968 DOI: 10.1002/bies.202000181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/18/2022]
Abstract
During early embryonic development in several metazoans, accurate DNA replication is ensured by high number of replication origins. This guarantees rapid genome duplication coordinated with fast cell divisions. In Xenopus laevis embryos this program switches to one with a lower number of origins at a developmental stage known as mid-blastula transition (MBT) when cell cycle length increases and gene transcription starts. Consistent with this regulation, somatic nuclei replicate poorly when transferred to eggs, suggesting the existence of an epigenetic memory suppressing replication assembly origins at all available sites. Recently, it was shown that histone H1 imposes a non-permissive chromatin configuration preventing replication origin assembly on somatic nuclei. This somatic state can be erased by SSRP1, a subunit of the FACT complex. Here, we further develop the hypothesis that this novel form of epigenetic memory might impact on different areas of vertebrate biology going from nuclear reprogramming to cancer development.
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Affiliation(s)
- Lucia Falbo
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, Milan, 20139, Italy
| | - Vincenzo Costanzo
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, Milan, 20139, Italy.,Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
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Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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