1
|
Almalki NAR, Sabir JSM, Ibrahim A, Alhosin M, Asseri AH, Albiheyri RS, Zari AT, Bahieldin A, Javed A, Mély Y, Hamiche A, Mousli M, Bronner C. UHRF1 poly-auto-ubiquitination induced by the anti-cancer drug, thymoquinone, is involved in the DNA repair machinery recruitment. Int J Biochem Cell Biol 2024; 171:106582. [PMID: 38649007 DOI: 10.1016/j.biocel.2024.106582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
DNA methylation is one of the most important epigenetic mark involved in many physiologic cellular processes and pathologies. During mitosis, the transmission of DNA methylation patterns from a mother to the daughter cells is ensured through the action of the Ubiquitin-like, containing PHD and RING domains, 1/DNA methyltransferase 1 (UHRF1/DNMT1) tandem. UHRF1 is involved in the silencing of many tumor suppressor genes (TSGs) via mechanisms that remain largely to be deciphered. The present study investigated the role and the regulation of UHRF1 poly-ubiquitination induced by thymoquinone, a natural anti-cancer drug, known to enhance or re-activate the expression of TSGs. We found that the auto-ubiquitination of UHRF1, induced by TQ, is mediated by reactive oxygen species, and occurs following DNA damage. We demonstrated that the poly-ubiquitinated form of UHRF1 is K63-linked and can still silence the tumor suppressor gene p16INK4A/CDKN2A. We further showed that TQ-induced auto-ubiquitination is mediated via the activity of Tip60. Since this latter is known as a nuclear receptor co-factor, we investigated if the glucocorticoid receptor (GR) might be involved in the regulation of UHRF1 ubiquitination. Activation of the GR, with dexamethasone, did not influence auto-ubiquitination of UHRF1. However, we could observe that TQ induced a K48-linked poly-ubiquitination of GR, probably involved in the proteosomal degradation pathway. Mass-spectrometry analysis of FLAG-HA-tagged UHRF1 identified UHRF1 partners involved in DNA repair and showed that TQ increased their association with UHRF1, suggesting that poly-ubiquitination of UHRF1 is involved in the DNA repair process. We propose that poly-ubiquitination of UHRF1 serves as a scaffold to recruit the DNA repair machinery at DNA damage sites.
Collapse
Affiliation(s)
- Naif A R Almalki
- Department of Functional Genomics, Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR 7104, University of Strasbourg, "équipe labellisée" Ligue contre le Cancer, Illkirch-Graffenstaden 67404, France; Experimental Biochemistry unit, King Fahad medical research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jamal S M Sabir
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulkhaleg Ibrahim
- Department of Functional Genomics, Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR 7104, University of Strasbourg, "équipe labellisée" Ligue contre le Cancer, Illkirch-Graffenstaden 67404, France; National Research Centre for Tropical and Transboundary Diseases (NRCTTD), Alzentan 99316, Libya
| | - Mahmoud Alhosin
- Department of Biochemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Amer H Asseri
- Department of Biochemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Centre for Artificial Intelligence in Precision Medicines, King Abdul-Aziz University, Jeddah 21589, Saudi Arabia
| | - Raed S Albiheyri
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ali T Zari
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aqib Javed
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Faculty of Pharmacy, Illkirch-Graffenstaden 67401, France
| | - Yves Mély
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Faculty of Pharmacy, Illkirch-Graffenstaden 67401, France
| | - Ali Hamiche
- Department of Functional Genomics, Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR 7104, University of Strasbourg, "équipe labellisée" Ligue contre le Cancer, Illkirch-Graffenstaden 67404, France; Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marc Mousli
- Laboratory of Bioimaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Faculty of Pharmacy, Illkirch-Graffenstaden 67401, France
| | - Christian Bronner
- Department of Functional Genomics, Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR 7104, University of Strasbourg, "équipe labellisée" Ligue contre le Cancer, Illkirch-Graffenstaden 67404, France.
| |
Collapse
|
2
|
Belotti E, Lacoste N, Iftikhar A, Simonet T, Papin C, Osseni A, Streichenberger N, Mari PO, Girard E, Graies M, Giglia-Mari G, Dimitrov S, Hamiche A, Schaeffer L. H2A.Z is involved in premature aging and DSB repair initiation in muscle fibers. Nucleic Acids Res 2024; 52:3031-3049. [PMID: 38281187 PMCID: PMC11014257 DOI: 10.1093/nar/gkae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 01/19/2024] [Indexed: 01/30/2024] Open
Abstract
Histone variants are key epigenetic players, but their functional and physiological roles remain poorly understood. Here, we show that depletion of the histone variant H2A.Z in mouse skeletal muscle causes oxidative stress, oxidation of proteins, accumulation of DNA damages, and both neuromuscular junction and mitochondria lesions that consequently lead to premature muscle aging and reduced life span. Investigation of the molecular mechanisms involved shows that H2A.Z is required to initiate DNA double strand break repair by recruiting Ku80 at DNA lesions. This is achieved via specific interactions of Ku80 vWA domain with H2A.Z. Taken as a whole, our data reveal that H2A.Z containing nucleosomes act as a molecular platform to bring together the proteins required to initiate and process DNA double strand break repair.
Collapse
Affiliation(s)
- Edwige Belotti
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Nicolas Lacoste
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Arslan Iftikhar
- For Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, Parc d’innovation, 1 rue Laurent Fries, 67404 Ilkirch Cedex, France
| | - Thomas Simonet
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Christophe Papin
- For Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, Parc d’innovation, 1 rue Laurent Fries, 67404 Ilkirch Cedex, France
| | - Alexis Osseni
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Nathalie Streichenberger
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Pierre-Olivier Mari
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Emmanuelle Girard
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Mohamed Graies
- Institute for Advanced Biosciences (IAB), Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Giuseppina Giglia-Mari
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Stefan Dimitrov
- Institute for Advanced Biosciences (IAB), Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Ali Hamiche
- For Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, Parc d’innovation, 1 rue Laurent Fries, 67404 Ilkirch Cedex, France
| | - Laurent Schaeffer
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR 5261, 8 avenue Rockefeller, 69008 Lyon, France
- Centre de Biotechnologie Cellulaire, Hospices Civils de Lyon, Lyon, France
| |
Collapse
|
3
|
Papin C, Ibrahim A, Sabir JSM, Le Gras S, Stoll I, Albiheyri RS, Zari AT, Bahieldin A, Bellacosa A, Bronner C, Hamiche A. MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density. J Exp Clin Cancer Res 2023; 42:301. [PMID: 37957685 PMCID: PMC10644448 DOI: 10.1186/s13046-023-02882-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Inherited defects in the base-excision repair gene MBD4 predispose individuals to adenomatous polyposis and colorectal cancer, which is characterized by an accumulation of C > T transitions resulting from spontaneous deamination of 5'-methylcytosine. METHODS Here, we have investigated the potential role of MBD4 in regulating DNA methylation levels using genome-wide transcriptome and methylome analyses. Additionally, we have elucidated its function through a series of in vitro experiments. RESULTS Here we show that the protein MBD4 is required for DNA methylation maintenance and G/T mismatch repair. Transcriptome and methylome analyses reveal a genome-wide hypomethylation of promoters, gene bodies and repetitive elements in the absence of MBD4 in vivo. Methylation mark loss is accompanied by a broad transcriptional derepression phenotype affecting promoters and retroelements with low methylated CpG density. MBD4 in vivo forms a complex with the mismatch repair proteins (MMR), which exhibits high bi-functional glycosylase/AP-lyase endonuclease specific activity towards methylated DNA substrates containing a G/T mismatch. Experiments using recombinant proteins reveal that the association of MBD4 with the MMR protein MLH1 is required for this activity. CONCLUSIONS Our data identify MBD4 as an enzyme specifically designed to repair deaminated 5-methylcytosines and underscores its critical role in safeguarding against methylation damage. Furthermore, it illustrates how MBD4 functions in normal and pathological conditions.
Collapse
Affiliation(s)
- Christophe Papin
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Abdulkhaleg Ibrahim
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
- National Research Centre for Tropical and Transboundary Diseases (NRCTTD), Alzentan, 99316, Libya
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stéphanie Le Gras
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Isabelle Stoll
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France
| | - Raed S Albiheyri
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ali T Zari
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Centre of Excellence in Bionanoscience, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alfonso Bellacosa
- Cancer Biology Program, Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Christian Bronner
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France.
| | - Ali Hamiche
- Institut de Génétique Et Biologie Moléculaire Et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe Labélisée Ligue Contre Le Cancer, 1 Rue Laurent Fries, B.P. 10142, Illkirch, 67404, Cedex, France.
| |
Collapse
|
4
|
Valakos D, Klagkou E, Kokkalis A, Polyzos A, Kyrilis FL, Banos A, Vatsellas G, Pliatska M, Ford E, Stravopodis DJ, Thanos D. Combinatorial targeting of a specific EMT/MET network by macroH2A variants safeguards mesenchymal identity. PLoS One 2023; 18:e0288005. [PMID: 37432970 DOI: 10.1371/journal.pone.0288005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/16/2023] [Indexed: 07/13/2023] Open
Abstract
Generation of induced pluripotent stem cells from specialized cell types provides an excellent model to study how cells maintain their stability, and how they can change identity, especially in the context of disease. Previous studies have shown that chromatin safeguards cell identity by acting as a barrier to reprogramming. We investigated mechanisms by which the histone macroH2A variants inhibit reprogramming and discovered that they work as gate keepers of the mesenchymal cell state by blocking epithelial transition, a step required for reprogramming of mouse fibroblasts. More specifically, we found that individual macroH2A variants regulate the expression of defined sets of genes, whose overall function is to stabilize the mesenchymal gene expression program, thus resisting reprogramming. We identified a novel gene network (MSCN, mesenchymal network) composed of 63 macroH2A-regulated genes related to extracellular matrix, cell membrane, signaling and the transcriptional regulators Id2 and Snai2, all of which function as guardians of the mesenchymal phenotype. ChIP-seq and KD experiments revealed a macroH2A variant-specific combinatorial targeting of the genes reconstructing the MSCN, thus generating robustness in gene expression programs to resist cellular reprogramming.
Collapse
Affiliation(s)
- Dimitrios Valakos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Section of Biochemistry and Molecular Biology, Department of Biology, School of Science, National and Kapodistrian University of Athens (NKUA), Zografou, Athens, Greece
| | - Eleftheria Klagkou
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Section of Biochemistry and Molecular Biology, Department of Biology, School of Science, National and Kapodistrian University of Athens (NKUA), Zografou, Athens, Greece
| | - Antonis Kokkalis
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | | | - Fotis L Kyrilis
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Aggelos Banos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | | | - Maria Pliatska
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Ethan Ford
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Dimitrios J Stravopodis
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens (NKUA), Zografou, Athens, Greece
| | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| |
Collapse
|
5
|
Epigenetic Insights on PARP-1 Activity in Cancer Therapy. Cancers (Basel) 2022; 15:cancers15010006. [PMID: 36612003 PMCID: PMC9817704 DOI: 10.3390/cancers15010006] [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: 11/11/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
The regulation of chromatin state and histone protein eviction have been proven essential during transcription and DNA repair. Poly(ADP-ribose) (PAR) polymerase 1 (PARP-1) and poly(ADP-ribosyl)ation (PARylation) are crucial mediators of these processes by affecting DNA/histone epigenetic events. DNA methylation/hydroxymethylation patterns and histone modifications are established by mutual coordination between all epigenetic modifiers. This review will focus on histones and DNA/histone epigenetic machinery that are direct targets of PARP-1 activity by covalent and non-covalent PARylation. The effects of these modifications on the activity/recruitment of epigenetic enzymes at DNA damage sites or gene regulatory regions will be outlined. Furthermore, based on the achievements made to the present, we will discuss the potential application of epigenetic-based therapy as a novel strategy for boosting the success of PARP inhibitors, improving cell sensitivity or overcoming drug resistance.
Collapse
|
6
|
Wang F, Zhang Y, Li J, Xia H, Zhang D, Yao S. The pathogenesis and therapeutic strategies of heat stroke-induced liver injury. Crit Care 2022; 26:391. [PMID: 36528615 PMCID: PMC9758799 DOI: 10.1186/s13054-022-04273-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Heat stroke (HS) is a life-threatening systemic disease characterized by an elevated core body temperature of more than 40 ℃ and subsequent multiple organ dysfunction syndrome. With the growing frequency of global heatwaves, the incidence rate of HS has increased significantly, which has caused a huge burden on people's lives and health. Liver injury is a well-documented complication of HS and usually constitutes the direct cause of patient death. In recent years, a lot of research has been carried out on the pathogenesis and treatment strategies of HS-induced liver injury. In this review, we summarized the important pathogenesis of HS-induced liver injury that has been confirmed so far. In addition to the comprehensive effect of systemic factors such as heat cytotoxicity, coagulopathy, and systemic inflammatory response syndrome, excessive hepatocyte cell pyroptosis, dysfunction of Kupffer cells, abnormal expression of heat shock protein expression, and other factors are also involved in the pathogenesis of HS-induced liver injury. Furthermore, we have also established the current therapeutic strategies for HS-induced liver injury. Our study is of great significance in promoting the understanding of the pathogenesis and treatment of HS-induced liver injury.
Collapse
Affiliation(s)
- Fuquan Wang
- grid.33199.310000 0004 0368 7223Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Department of Anesthesiology, Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277, Jiefang Avenue, Wuhan, 430022 China
| | - Yan Zhang
- grid.33199.310000 0004 0368 7223Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Department of Anesthesiology, Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277, Jiefang Avenue, Wuhan, 430022 China
| | - Jianhua Li
- grid.190737.b0000 0001 0154 0904Chongqing university Jiangjin hospital, Chongqing, China
| | - Haifa Xia
- grid.33199.310000 0004 0368 7223Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Department of Anesthesiology, Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277, Jiefang Avenue, Wuhan, 430022 China
| | - Dingyu Zhang
- grid.33199.310000 0004 0368 7223Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Department of Anesthesiology, Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277, Jiefang Avenue, Wuhan, 430022 China ,grid.507952.c0000 0004 1764 577XWuhan Jinyintan Hospital, Wuhan, 430023 China
| | - Shanglong Yao
- grid.33199.310000 0004 0368 7223Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Department of Anesthesiology, Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277, Jiefang Avenue, Wuhan, 430022 China
| |
Collapse
|
7
|
Gómez-Marín E, Posavec-Marjanović M, Zarzuela L, Basurto-Cayuela L, Guerrero-Martínez JA, Arribas G, Yerbes R, Ceballos-Chávez M, Rodríguez-Paredes M, Tomé M, Durán RV, Buschbeck M, Reyes JC. The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFβ and Hippo pathways. Nucleic Acids Res 2022; 50:9838-9857. [PMID: 36124662 PMCID: PMC9508832 DOI: 10.1093/nar/gkac766] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/01/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022] Open
Abstract
High mobility group (HMG) proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. The protein HMG20A is predicted by the AlphaFold2 software to contain three distinct structural elements, which we have functionally characterized: i) an amino-terminal, intrinsically disordered domain with transactivation activity; ii) an HMG box with higher binding affinity for double-stranded, four-way-junction DNA than for linear DNA; and iii) a long coiled-coil domain. Our proteomic study followed by a deletion analysis and structural modeling demonstrates that HMG20A forms a complex with the histone reader PHF14, via the establishment of a two-stranded alpha-helical coiled-coil structure. siRNA-mediated knockdown of either PHF14 or HMG20A in MDA-MB-231 cells causes similar defects in cell migration, invasion and homotypic cell–cell adhesion ability, but neither affects proliferation. Transcriptomic analyses demonstrate that PHF14 and HMG20A share a large subset of targets. We show that the PHF14-HMG20A complex modulates the Hippo pathway through a direct interaction with the TEAD1 transcription factor. PHF14 or HMG20A deficiency increases epithelial markers, including E-cadherin and the epithelial master regulator TP63 and impaired normal TGFβ-trigged epithelial-to-mesenchymal transition. Taken together, these data indicate that PHF14 and HMG20A cooperate in regulating several pathways involved in epithelial–mesenchymal plasticity.
Collapse
Affiliation(s)
- Elena Gómez-Marín
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Melanija Posavec-Marjanović
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Laura Zarzuela
- Cell Dynamics and Signaling Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Laura Basurto-Cayuela
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - José A Guerrero-Martínez
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Gonzalo Arribas
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Rosario Yerbes
- Cell Dynamics and Signaling Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - María Ceballos-Chávez
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Manuel Rodríguez-Paredes
- Institute of Toxicology, University Medical Center Mainz, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Mercedes Tomé
- Cell Dynamics and Signaling Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Raúl V Durán
- Cell Dynamics and Signaling Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Marcus Buschbeck
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain.,Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain
| | - José C Reyes
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| |
Collapse
|
8
|
Longarini EJ, Matic I. The fast-growing business of Serine ADP-ribosylation. DNA Repair (Amst) 2022; 118:103382. [DOI: 10.1016/j.dnarep.2022.103382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022]
|
9
|
Naumenko KN, Sukhanova MV, Hamon L, Kurgina TA, Anarbaev RO, Mangerich A, Pastré D, Lavrik OI. The C-Terminal Domain of Y-Box Binding Protein 1 Exhibits Structure-Specific Binding to Poly(ADP-Ribose), Which Regulates PARP1 Activity. Front Cell Dev Biol 2022; 10:831741. [PMID: 35800891 PMCID: PMC9253770 DOI: 10.3389/fcell.2022.831741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Y-box-binding protein 1 (YB-1) is a multifunctional protein involved in the regulation of gene expression. Recent studies showed that in addition to its role in the RNA and DNA metabolism, YB-1 is involved in the regulation of PARP1 activity, which catalyzes poly(ADP-ribose) [PAR] synthesis under genotoxic stress through auto-poly(ADP-ribosyl)ation or protein trans-poly(ADP-ribosyl)ation. Nonetheless, the exact mechanism by which YB-1 regulates PAR synthesis remains to be determined. YB-1 contains a disordered Ala/Pro-rich N-terminal domain, a cold shock domain, and an intrinsically disordered C-terminal domain (CTD) carrying four clusters of positively charged amino acid residues. Here, we examined the functional role of the disordered CTD of YB-1 in PAR binding and in the regulation of PARP1-driven PAR synthesis in vitro. We demonstrated that the rate of PARP1-dependent synthesis of PAR is higher in the presence of YB-1 and is tightly controlled by the interaction between YB-1 CTD and PAR. Moreover, YB-1 acts as an effective cofactor in the PAR synthesis catalyzed by the PARP1 point mutants that generate various PAR polymeric structures, namely, short hypo- or hyperbranched polymers. We showed that either a decrease in chain length or an increase in branching frequency of PAR affect its binding affinity for YB-1 and YB-1–mediated stimulation of PARP1 enzymatic activity. These results provide important insight into the mechanism underlying the regulation of PARP1 activity by PAR-binding proteins containing disordered regions with clusters of positively charged amino acid residues, suggesting that YB-1 CTD-like domains may be considered PAR “readers” just as other known PAR-binding modules.
Collapse
Affiliation(s)
| | - Mariya V. Sukhanova
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Tatyana A. Kurgina
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Rashid O. Anarbaev
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Aswin Mangerich
- Department of Biology, Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Olga I. Lavrik
- LBCE, Institute Chemical Biology and Fundamental Medicine (ICBFM), Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- *Correspondence: Olga I. Lavrik,
| |
Collapse
|
10
|
Corujo D, Malinverni R, Carrillo-Reixach J, Meers O, Garcia-Jaraquemada A, Le Pannérer MM, Valero V, Pérez A, Del Río-Álvarez Á, Royo L, Pérez-González B, Raurell H, Acemel RD, Santos-Pereira JM, Garrido-Pontnou M, Gómez-Skarmeta JL, Pasquali L, Manyé J, Armengol C, Buschbeck M. MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines. Cell Rep 2022; 39:110988. [PMID: 35732123 DOI: 10.1016/j.celrep.2022.110988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/04/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022] Open
Abstract
MacroH2A histone variants have a function in gene regulation that is poorly understood at the molecular level. We report that macroH2A1.2 and macroH2A2 modulate the transcriptional ground state of cancer cells and how they respond to inflammatory cytokines. Removal of macroH2A1.2 and macroH2A2 in hepatoblastoma cells affects the contact frequency of promoters and distal enhancers coinciding with changes in enhancer activity or preceding them in response to the cytokine tumor necrosis factor alpha. Although macroH2As regulate genes in both directions, they globally facilitate the nuclear factor κB (NF-κB)-mediated response. In contrast, macroH2As suppress the response to the pro-inflammatory cytokine interferon gamma. MacroH2A2 has a stronger contribution to gene repression than macroH2A1.2. Taken together, our results suggest that macroH2As have a role in regulating the response of cancer cells to inflammatory signals on the level of chromatin structure. This is likely relevant for the interaction of cancer cells with immune cells of their microenvironment.
Collapse
Affiliation(s)
- David Corujo
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain; Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain
| | - Roberto Malinverni
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain
| | - Juan Carrillo-Reixach
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain; Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain; Doctoral Programme in Biomedicine, Universitat de Barcelona, Facultat de Farmàcia i Ciències de l'Alimentació, Barcelona 08028, Spain
| | - Arce Garcia-Jaraquemada
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Marguerite-Marie Le Pannérer
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain; PhD Programme in Biomedicine, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Vanesa Valero
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain
| | - Ainhoa Pérez
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain
| | - Álvaro Del Río-Álvarez
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain; Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Laura Royo
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain; Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain
| | - Beatriz Pérez-González
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Helena Raurell
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla 41013, Spain
| | - José M Santos-Pereira
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla 41013, Spain
| | | | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla 41013, Spain
| | - Lorenzo Pasquali
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Josep Manyé
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBEREHD), Madrid 28029, Spain
| | - Carolina Armengol
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain; Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona 08916, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBEREHD), Madrid 28029, Spain.
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, Badalona, Barcelona 08916, Spain; Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Barcelona 08916, Spain.
| |
Collapse
|
11
|
Ling X, Pan Z, Zhang H, Wu M, Gui Z, Yuan Q, Chen J, Peng J, Liu Z, Tan Q, Huang D, Xiu L, Liu L. PARP-1 modulates the expression of miR-223 through histone acetylation to involve in the hydroquinone-induced carcinogenesis of TK6 cells. J Biochem Mol Toxicol 2022; 36:e23142. [PMID: 35698848 DOI: 10.1002/jbt.23142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/31/2022] [Indexed: 11/12/2022]
Abstract
The upstream regulators of microRNAs were rarely reported. Hydroquinone (HQ) is the main metabolite of benzene, one of the important environmental factors contributing to leukemia and lymphoma. In HQ-induced malignant transformed TK6 (TK6-HT) cells, the expression of PARP-1 and miR-223 were upregulated. When in PARP-1 silencing TK6-HT cells, miR-223 was downregulated and the apoptotic cell number correspondingly increased. In TK6 cells treated with HQ for different terms, the expression of miR-223 and PARP-1 were dynamically observed and found to be decreased and increased, respectively. Trichostatin A could increase the expression of miR-223, then the expression of HDAC1-2 and nuclear factor kappa B were found to be increased, but that of mH2A was decreased. PARP-1 silencing inhibited the protein expression of H3Ac, mH2A, and H3K27ac. By co-immunoprecipitation experiment, PARP-1 and HDAC2 were found to form a regulatory complex. In conclusion, we demonstrated that the upregulation of PARP-1 mediated activation of acetylation to promote the transcription of miR-223 possibly via coregulating with HDAC2, an epigenetic regulation mechanism involved in cell malignant transformation resulting from long-term exposure to HQ, in which course, H3K27ac might be a specific marker for the activation of histone H3, which also gives hints for benzene exposure research.
Collapse
Affiliation(s)
- Xiaoxuan Ling
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Zhijie Pan
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Haiqiao Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Minhua Wu
- Department of Histology and Embryology, Guangdong Medical University, Zhanjiang, China
| | - Zhiming Gui
- Department of Urology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Qian Yuan
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Jialong Chen
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jianming Peng
- Huizhou Hospital for Occupational Disease Prevention and Treatment, Huizhou, China
| | - Zhidong Liu
- Huizhou Hospital for Occupational Disease Prevention and Treatment, Huizhou, China
| | - Qiang Tan
- Foshan Institute of Occupational Disease Prevention and Control, Foshan, China
| | - Dongsheng Huang
- Guangdong Medical University Affiliated Longhua District Central Hospital, Shenzhen, China
| | - Liangchang Xiu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Linhua Liu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| |
Collapse
|
12
|
Guberovic I, Farkas M, Corujo D, Buschbeck M. Evolution, structure and function of divergent macroH2A1 splice isoforms. Semin Cell Dev Biol 2022; 135:43-49. [PMID: 35422391 DOI: 10.1016/j.semcdb.2022.03.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
Abstract
The replacement of replication-coupled histones with non-canonical histone variants provides chromatin with additional properties and contributes to the plasticity of the epigenome. MacroH2A histone variants are counterparts of the replication-coupled histone H2A. They are characterized by a unique tripartite structure, consisting of a histone fold, an unstructured linker, and a globular macrodomain. MacroH2A1.1 and macroH2A1.2 are the result of alternative splicing of the MACROH2A1 gene and can have opposing biological functions. Here, we discuss the structural differences between the macrodomains of the two isoforms, resulting in differential ligand binding. We further discuss how this modulates gene regulation by the two isoforms, in cases resulting in opposing role of macroH2A1.1 and macroH2A1.2 in development and differentiation. Finally, we share recent insight in the evolution of macroH2As. Taken together, in this review, we aim to discuss in unprecedented detail distinct properties and functions of the fascinating macroH2A1 splice isoforms.
Collapse
Affiliation(s)
- Iva Guberovic
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
| | - Marina Farkas
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
| | - David Corujo
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain; Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain.
| |
Collapse
|
13
|
Recoules L, Heurteau A, Raynal F, Karasu N, Moutahir F, Bejjani F, Jariel-Encontre I, Cuvier O, Sexton T, Lavigne AC, Bystricky K. The histone variant macroH2A1.1 regulates RNA Polymerase II paused genes within defined chromatin interaction landscapes. J Cell Sci 2022; 135:275002. [PMID: 35362516 PMCID: PMC9016624 DOI: 10.1242/jcs.259456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
The histone variant macroH2A1.1 plays a role in cancer development and metastasis. To determine the underlying molecular mechanisms, we mapped the genome-wide localization of endogenous macroH2A1.1 in the human breast cancer cell line MDA-MB-231. We demonstrate that macroH2A1.1 specifically binds to active promoters and enhancers in addition to facultative heterochromatin. Selective knock down of macroH2A1.1 deregulates the expression of hundreds of highly active genes. Depending on the chromatin landscape, macroH2A1.1 acts through two distinct molecular mechanisms. The first mitigates excessive transcription by binding over domains including the promoter and the gene body. The second stimulates expression of RNA polymerase II (Pol II)-paused genes, including genes regulating mammary tumor cell migration. In contrast to the first mechanism, macroH2A1.1 specifically associates with the transcription start site of Pol II-paused genes. These processes occur in a predefined local 3D genome landscape, but do not require rewiring of enhancer-promoter contacts. We thus propose that macroH2A1.1 serves as a transcriptional modulator with a potential role in assisting the conversion of promoter-locked Pol II into a productive, elongating Pol II. Summary: Histone variant macroH2A1.1 binding to the TSS of genes dependent on Pol II pausing stimulates transcription by promoting Pol II release in a human triple-negative breast cancer cell model.
Collapse
Affiliation(s)
- Ludmila Recoules
- Molecular, Cellular and Developmental biology unit (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Alexandre Heurteau
- Molecular, Cellular and Developmental biology unit (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Flavien Raynal
- Molecular, Cellular and Developmental biology unit (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Nezih Karasu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC); CNRS, UMR7104; INSERM U1258; University of Strasbourg; Illkirch, France
| | - Fatima Moutahir
- Molecular, Cellular and Developmental biology unit (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Fabienne Bejjani
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS, UMR5535, F-34293 3# Equipe Labellisée Ligue Nationale contre le Cancer, France
| | - Isabelle Jariel-Encontre
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS, UMR5535, F-34293 3# Equipe Labellisée Ligue Nationale contre le Cancer, France
| | - Olivier Cuvier
- Molecular, Cellular and Developmental biology unit (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Thomas Sexton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC); CNRS, UMR7104; INSERM U1258; University of Strasbourg; Illkirch, France
| | - Anne-Claire Lavigne
- Molecular, Cellular and Developmental biology unit (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Kerstin Bystricky
- Molecular, Cellular and Developmental biology unit (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France.,Institut Universitaire de France (IUF), France
| |
Collapse
|
14
|
Unconventional metabolites in chromatin regulation. Biosci Rep 2022; 42:230604. [PMID: 34988581 PMCID: PMC8777195 DOI: 10.1042/bsr20211558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
Collapse
|
15
|
Wootton J, Soutoglou E. Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity. Front Genet 2022; 12:773426. [PMID: 34970302 PMCID: PMC8712883 DOI: 10.3389/fgene.2021.773426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.
Collapse
Affiliation(s)
- Jack Wootton
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Evi Soutoglou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| |
Collapse
|
16
|
Evolution of a histone variant involved in compartmental regulation of NAD metabolism. Nat Struct Mol Biol 2021; 28:1009-1019. [PMID: 34887560 DOI: 10.1038/s41594-021-00692-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]
Abstract
NAD metabolism is essential for all forms of life. Compartmental regulation of NAD+ consumption, especially between the nucleus and the mitochondria, is required for energy homeostasis. However, how compartmental regulation evolved remains unclear. In the present study, we investigated the evolution of the macrodomain-containing histone variant macroH2A1.1, an integral chromatin component that limits nuclear NAD+ consumption by inhibiting poly(ADP-ribose) polymerase 1 in vertebrate cells. We found that macroH2A originated in premetazoan protists. The crystal structure of the macroH2A macrodomain from the protist Capsaspora owczarzaki allowed us to identify highly conserved principles of ligand binding and pinpoint key residue substitutions, selected for during the evolution of the vertebrate stem lineage. Metabolic characterization of the Capsaspora lifecycle suggested that the metabolic function of macroH2A was associated with nonproliferative stages. Taken together, we provide insight into the evolution of a chromatin element involved in compartmental NAD regulation, relevant for understanding its metabolism and potential therapeutic applications.
Collapse
|
17
|
DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
Collapse
|
18
|
Abstract
Cancer is a complex disease characterized by loss of cellular homeostasis through genetic and epigenetic alterations. Emerging evidence highlights a role for histone variants and their dedicated chaperones in cancer initiation and progression. Histone variants are involved in processes as diverse as maintenance of genome integrity, nuclear architecture and cell identity. On a molecular level, histone variants add a layer of complexity to the dynamic regulation of transcription, DNA replication and repair, and mitotic chromosome segregation. Because these functions are critical to ensure normal proliferation and maintenance of cellular fate, cancer cells are defined by their capacity to subvert them. Hijacking histone variants and their chaperones is emerging as a common means to disrupt homeostasis across a wide range of cancers, particularly solid tumours. Here we discuss histone variants and histone chaperones as tumour-promoting or tumour-suppressive players in the pathogenesis of cancer.
Collapse
Affiliation(s)
| | - Dan Filipescu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | |
Collapse
|
19
|
Lone IN, Sengez B, Hamiche A, Dimitrov S, Alotaibi H. The Role of Histone Variants in the Epithelial-To-Mesenchymal Transition. Cells 2020; 9:cells9112499. [PMID: 33213091 PMCID: PMC7698467 DOI: 10.3390/cells9112499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 11/16/2022] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) is a physiological process activated during early embryogenesis, which continues to shape tissues and organs later on. It is also hijacked by tumor cells during metastasis. The regulation of EMT has been the focus of many research groups culminating in the last few years and resulting in an elaborate transcriptional network buildup. However, the implication of epigenetic factors in the control of EMT is still in its infancy. Recent discoveries pointed out that histone variants, which are key epigenetic players, appear to be involved in EMT control. This review summarizes the available data on histone variants' function in EMT that would contribute to a better understanding of EMT itself and EMT-related diseases.
Collapse
Affiliation(s)
- Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
| | - Burcu Sengez
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67400 Illkirch, France;
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé-Allée des Alpes, 38700 La Tronche, France
| | - Hani Alotaibi
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey; (I.N.L.); (B.S.); (S.D.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
- Correspondence: ; Tel.: +90-232-299-4100 (ext. 5071)
| |
Collapse
|
20
|
LSH mediates gene repression through macroH2A deposition. Nat Commun 2020; 11:5647. [PMID: 33159050 PMCID: PMC7648012 DOI: 10.1038/s41467-020-19159-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The human Immunodeficiency Centromeric Instability Facial Anomalies (ICF) 4 syndrome is a severe disease with increased mortality caused by mutation in the LSH gene. Although LSH belongs to a family of chromatin remodeling proteins, it remains unknown how LSH mediates its function on chromatin in vivo. Here, we use chemical-induced proximity to rapidly recruit LSH to an engineered locus and find that LSH specifically induces macroH2A1.2 and macroH2A2 deposition in an ATP-dependent manner. Tethering of LSH induces transcriptional repression and silencing is dependent on macroH2A deposition. Loss of LSH decreases macroH2A enrichment at repeat sequences and results in transcriptional reactivation. Likewise, reduction of macroH2A by siRNA interference mimicks transcriptional reactivation. ChIP-seq analysis confirmed that LSH is a major regulator of genome-wide macroH2A distribution. Tethering of ICF4 mutations fails to induce macroH2A deposition and ICF4 patient cells display reduced macroH2A deposition and transcriptional reactivation supporting a pathogenic role for altered marcoH2A deposition. We propose that LSH is a major chromatin modulator of the histone variant macroH2A and that its ability to insert marcoH2A into chromatin and transcriptionally silence is disturbed in the ICF4 syndrome. The human ICF 4 syndrome is caused by mutation of the chromatin remodeller LSH. Here, the authors show that LSH depletion disrupts the ability of histone variant macroH2A to insert into chromatin and silence transcription.
Collapse
|
21
|
Broggi G, Filetti V, Ieni A, Rapisarda V, Ledda C, Vitale E, Varricchio S, Russo D, Lombardo C, Tuccari G, Caltabiano R, Loreto C. MacroH2A1 Immunoexpression in Breast Cancer. Front Oncol 2020; 10:1519. [PMID: 32974186 PMCID: PMC7471871 DOI: 10.3389/fonc.2020.01519] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022] Open
Abstract
MacroH2A1 has two splice isoforms, macroH2A1.1 and macroH2A1.2, that have been studied in several form of cancer. In the literature there are not many scientific papers dealing with the role of macroH2A1 in breast cancer. Breast cancer is the most frequent form of malignancy in females. It tend to metastasize to the bone in ~70% of patients. Despite treatment, new bone metastases will still occur in 30–50% of cases with advanced disease. Overall 5-year survival after the diagnosis of bone metastasis is ~20%. Osteoclasts and osteoblasts of the bone microenvironment are engaged by soluble factors released by neoplastic cells, resulting in bone matrix breakdown. This malfunction enhances the proliferation of the cancer cells, creating a vicious cycle. We investigated immunohistochemical expression of macroH2A1 in primitive breast cancer, focusing on the comparison of metastatic and non-metastatic cases. Furthermore, the immunohistochemical expression of macroH2A1 has been evaluated both in all cases of nodal metastases and in distant metastases. Our data demonstrated that macroH2A1 expression was higher expressed in metastatic breast cancer (77%) vs. non-metastatic breast cancer (32%). Also in analyzed metastases cases, a high macroH2A1 expression was detected: 85 and 80% in nodal and distant metastases cases, respectively. These results supported the fact that macroH2A1 is more highly expressed in breast cancer with worst prognosis.
Collapse
Affiliation(s)
- Giuseppe Broggi
- Section of Anatomic Pathology, Department Gian Filippo Ingrassia, University of Catania, Catania, Italy
| | - Veronica Filetti
- Human Anatomy and Histology, Department of Biomedical and Biotechnology Sciences, University of Catania, Catania, Italy
| | - Antonio Ieni
- Department of Human Pathology in Adult and Developmental Age "Gaetano Barresi", Section of Pathology, University of Messina, Messina, Italy
| | - Venerando Rapisarda
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Caterina Ledda
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Ermanno Vitale
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Silvia Varricchio
- Department of Advanced Biomedical Sciences, Pathology Unit, University of Naples Federico II, Naples, Italy
| | - Daniela Russo
- Department of Advanced Biomedical Sciences, Pathology Unit, University of Naples Federico II, Naples, Italy
| | - Claudia Lombardo
- Human Anatomy and Histology, Department of Biomedical and Biotechnology Sciences, University of Catania, Catania, Italy
| | - Giovanni Tuccari
- Department of Human Pathology in Adult and Developmental Age "Gaetano Barresi", Section of Pathology, University of Messina, Messina, Italy
| | - Rosario Caltabiano
- Section of Anatomic Pathology, Department Gian Filippo Ingrassia, University of Catania, Catania, Italy
| | - Carla Loreto
- Human Anatomy and Histology, Department of Biomedical and Biotechnology Sciences, University of Catania, Catania, Italy
| |
Collapse
|
22
|
Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
Collapse
Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| |
Collapse
|
23
|
Sebastian R, Hosogane EK, Sun EG, Tran AD, Reinhold WC, Burkett S, Sturgill DM, Gudla PR, Pommier Y, Aladjem MI, Oberdoerffer P. Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability. Mol Cell 2020; 79:836-845.e7. [PMID: 32649884 DOI: 10.1016/j.molcel.2020.06.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 04/24/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
The inactive X chromosome (Xi) is inherently susceptible to genomic aberrations. Replication stress (RS) has been proposed as an underlying cause, but the mechanisms that protect from Xi instability remain unknown. Here, we show that macroH2A1.2, an RS-protective histone variant enriched on the Xi, is required for Xi integrity and female survival. Mechanistically, macroH2A1.2 counteracts its structurally distinct and equally Xi-enriched alternative splice variant, macroH2A1.1. Comparative proteomics identified a role for macroH2A1.1 in alternative end joining (alt-EJ), which accounts for Xi anaphase defects in the absence of macroH2A1.2. Genomic instability was rescued by simultaneous depletion of macroH2A1.1 or alt-EJ factors, and mice deficient for both macroH2A1 variants harbor no overt female defects. Notably, macroH2A1 splice variant imbalance affected alt-EJ capacity also in tumor cells. Together, these findings identify macroH2A1 splicing as a modulator of genome maintenance that ensures Xi integrity and may, more broadly, predict DNA repair outcome in malignant cells.
Collapse
Affiliation(s)
- Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Eri K Hosogane
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Eric G Sun
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, Frederick, MD 21702, USA
| | - David M Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Prabhakar R Gudla
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
24
|
Simonet NG, Thackray JK, Vazquez BN, Ianni A, Espinosa-Alcantud M, Morales-Sanfrutos J, Hurtado-Bagès S, Sabidó E, Buschbeck M, Tischfield J, De La Torre C, Esteller M, Braun T, Olivella M, Serrano L, Vaquero A. SirT7 auto-ADP-ribosylation regulates glucose starvation response through mH2A1. SCIENCE ADVANCES 2020; 6:eaaz2590. [PMID: 32832656 PMCID: PMC7439345 DOI: 10.1126/sciadv.aaz2590] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Sirtuins are key players of metabolic stress response. Originally described as deacetylases, some sirtuins also exhibit poorly understood mono-adenosine 5'-diphosphate (ADP)-ribosyltransferase (mADPRT) activity. We report that the deacetylase SirT7 is a dual sirtuin, as it also features auto-mADPRT activity. SirT7 mADPRT occurs at a previously undefined active site, and its abrogation alters SirT7 chromatin distribution. We identify an epigenetic pathway by which ADP-ribosyl-SirT7 is recognized by the ADP-ribose reader mH2A1.1 under glucose starvation, inducing SirT7 relocalization to intergenic regions. SirT7 promotes mH2A1 enrichment in a subset of nearby genes, many of them involved in second messenger signaling, resulting in their specific up- or down-regulation. The expression profile of these genes under calorie restriction is consistently abrogated in SirT7-deficient mice, resulting in impaired activation of autophagy. Our work provides a novel perspective on sirtuin duality and suggests a role for SirT7/mH2A1.1 axis in glucose homeostasis and aging.
Collapse
Affiliation(s)
- Nicolás G. Simonet
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Catalonia, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Joshua K. Thackray
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Berta N. Vazquez
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Catalonia, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Alessandro Ianni
- Max Planck Institute for Heart and Lung Research, Department of Cardiac Development and Remodelling, Bad Nauheim, Germany
| | - Maria Espinosa-Alcantud
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Catalonia, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Julia Morales-Sanfrutos
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Sarah Hurtado-Bagès
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, 08916 Badalona, Barcelona, Catalonia, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Marcus Buschbeck
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, 08916 Badalona, Barcelona, Catalonia, Spain
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Jay Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
| | - Carolina De La Torre
- Proteomics Unit, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Catalonia, Spain
- Proteomics Unit, Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Department of Cardiac Development and Remodelling, Bad Nauheim, Germany
| | - Mireia Olivella
- Bioinformatics Area, School of International Studies, ESCI-UPF, Barcelona, Catalonia, Spain
- Bioinformatics and Medical Statistics Group, UST, Universitat de Vic–Universitat Central de Catalunya (UVIC-UCC), Barcelona, Catalonia, Spain
| | - Lourdes Serrano
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, 145 Bevier Road, Piscataway, NJ 08854, USA
- Department of Science, BMCC, The City University of New York (CUNY), 199 Chambers Street N699P, New York, NY 10007, USA
| | - Alejandro Vaquero
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Catalonia, Spain
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de l’Hospitalet, 199-203, 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| |
Collapse
|
25
|
Gerazova-Efremova K, Kjovkarovska SD, Domazetovska S, Miova B. Nicotinamide and heat preconditioning - Effects on hepatic HSP70, carbohydrate and oxidative disturbances in STZ-induced diabetic rats. J Therm Biol 2020; 91:102645. [PMID: 32716886 DOI: 10.1016/j.jtherbio.2020.102645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/25/2020] [Accepted: 06/11/2020] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Nicotinamide (NA) is known to have antioxidant potential and partially to protect insulin-secreting cells against diabetogenic agent STZ (streptozotocin). In a combination to heat stress (HS), NA is also known to induce heat-shock proteins (HSPs) production. Heat preconditioning (HP) and HSPs have cytoprotective effects against development of cellular injury caused by application of subsequent stressor. We aimed to determine if pretreatment with NA and HP (as HSP70 -inducers) can affect STZ-induced diabetic disturbances in rats. METHODS NA-pretreatment (250 mg/kg b.w., 7 days) and heat preconditioning (41 ± 1 °C, 45 min) of diabetic rats was performed. The changes in hepatic carbohydrate- and antioxidative-related enzymes and substrates were investigated. RESULTS NA-pretreatment, alone or in combination with HS, resulted in significant increase of HSP70 concentration in the liver of control and diabetic rats. Compared to diabetic controls, pretreatment with NA, in combination with HP, resulted in decrease of blood and liver glucose, increase of glycogen and glucose-6-phosphate level, increase of glycogenolytic/glycolytic enzymes, decrease of gluconeogenic enzymes, as well as an increase of glutathione content and glutathione peroxidase, decrease of glutathione reductase and catalase activities. CONCLUSIONS NA is a potent HSP70 coinducer, alone or in a combination with HS in the liver of both control and diabetic rats. Pretreatment with NA, accompanied by HP, has a pronounced corrective effect on STZ-induced diabetes disturbances in the key hepatic carbohydrate- and antioxidative-related parameters. It seems that this corrective effect is based on the increased production of hepatic HSP70.
Collapse
Affiliation(s)
| | - Suzana Dinevska- Kjovkarovska
- Department of Experimental Physiology and Biochemistry, Institute of Biology Faculty of Natural Sciences and Mathematics, University "St Cyril and Methodius", Skopje, R. North Macedonia.
| | - Saska Domazetovska
- PHI University Clinic of Clinical Biochemistry, Clinical Center Mother Theresa Skopje, R. North Macedonia.
| | - Biljana Miova
- Department of Experimental Physiology and Biochemistry, Institute of Biology Faculty of Natural Sciences and Mathematics, University "St Cyril and Methodius", Skopje, R. North Macedonia.
| |
Collapse
|
26
|
The Histone Variant MacroH2A1 Regulates Key Genes for Myogenic Cell Fusion in a Splice-Isoform Dependent Manner. Cells 2020; 9:cells9051109. [PMID: 32365743 PMCID: PMC7290658 DOI: 10.3390/cells9051109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
MacroH2A histone variants have functions in differentiation, somatic cell reprogramming and cancer. However, at present, it is not clear how macroH2As affect gene regulation to exert these functions. We have parted from the initial observation that loss of total macroH2A1 led to a change in the morphology of murine myotubes differentiated ex vivo. The fusion of myoblasts to myotubes is a key process in embryonic myogenesis and highly relevant for muscle regeneration after acute or chronic injury. We have focused on this physiological process, to investigate the functions of the two splice isoforms of macroH2A1. Individual perturbation of the two isoforms in myotubes forming in vitro from myogenic C2C12 cells showed an opposing phenotype, with macroH2A1.1 enhancing, and macroH2A1.2 reducing, fusion. Differential regulation of a subset of fusion-related genes encoding components of the extracellular matrix and cell surface receptors for adhesion correlated with these phenotypes. We describe, for the first time, splice isoform-specific phenotypes for the histone variant macroH2A1 in a physiologic process and provide evidence for a novel underlying molecular mechanism of gene regulation.
Collapse
|
27
|
Hurtado-Bagès S, Knobloch G, Ladurner AG, Buschbeck M. The taming of PARP1 and its impact on NAD + metabolism. Mol Metab 2020; 38:100950. [PMID: 32199820 PMCID: PMC7300387 DOI: 10.1016/j.molmet.2020.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/10/2020] [Accepted: 01/24/2020] [Indexed: 12/21/2022] Open
Abstract
Background Poly-ADP-ribose polymerases (PARPs) are key mediators of cellular stress response. They are intimately linked to cellular metabolism through the consumption of NAD+. PARP1/ARTD1 in the nucleus is the major NAD+ consuming activity and plays a key role in maintaining genomic integrity. Scope of review In this review, we discuss how different organelles are linked through NAD+ metabolism and how PARP1 activation in the nucleus can impact the function of distant organelles. We discuss how differentiated cells tame PARP1 function by upregulating an endogenous inhibitor, the histone variant macroH2A1.1. Major conclusions The presence of macroH2A1.1, particularly in differentiated cells, raises the threshold for the activation of PARP1 with consequences for DNA repair, gene transcription, and NAD+ homeostasis. Beyond DNA repair, PARP1 is essential for metabolic homeostasis. Epigenetic mechanisms prevent metabolic disorders through PARP1 taming. Beyond cancer, the development of PARP1 inhibitors offers diverse clinical potential.
Collapse
Affiliation(s)
- Sarah Hurtado-Bagès
- Josep Carreras Leukemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916, Badalona, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gunnar Knobloch
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Andreas G Ladurner
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany; Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, 81377, Munich, Germany.
| | - Marcus Buschbeck
- Josep Carreras Leukemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916, Badalona, Spain; Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), 08916, Badalona, Spain.
| |
Collapse
|
28
|
MacroH2A1 Regulation of Poly(ADP-Ribose) Synthesis and Stability Prevents Necrosis and Promotes DNA Repair. Mol Cell Biol 2019; 40:MCB.00230-19. [PMID: 31636161 PMCID: PMC6908255 DOI: 10.1128/mcb.00230-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
Through its ability to bind the ends of poly(ADP-ribose) (PAR) chains, the function of the histone variant macroH2A1.1, including its ability to regulate transcription, is coupled to PAR polymerases (PARPs). PARP1 also has a major role in DNA damage response (DDR) signaling, and our results show that macroH2A1 alters the kinetics of PAR accumulation following acute DNA damage by both suppressing PARP activity and simultaneously protecting PAR chains from degradation. Through its ability to bind the ends of poly(ADP-ribose) (PAR) chains, the function of the histone variant macroH2A1.1, including its ability to regulate transcription, is coupled to PAR polymerases (PARPs). PARP1 also has a major role in DNA damage response (DDR) signaling, and our results show that macroH2A1 alters the kinetics of PAR accumulation following acute DNA damage by both suppressing PARP activity and simultaneously protecting PAR chains from degradation. In this way, we demonstrate that macroH2A1 prevents cellular NAD+ depletion, subsequently preventing necrotic cell death that would otherwise occur due to PARP overactivation. We also show that macroH2A1-dependent PAR stabilization promotes efficient repair of oxidative DNA damage. While the role of PAR in recruiting and regulating macrodomain-containing proteins has been established, our results demonstrate that, conversely, macrodomain-containing proteins, and specifically those containing macroH2A1, can regulate PARP1 function through a novel mechanism that promotes both survival and efficient repair during DNA damage response.
Collapse
|
29
|
Alemasova EE, Lavrik OI. Poly(ADP-ribosyl)ation by PARP1: reaction mechanism and regulatory proteins. Nucleic Acids Res 2019; 47:3811-3827. [PMID: 30799503 PMCID: PMC6486540 DOI: 10.1093/nar/gkz120] [Citation(s) in RCA: 258] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is posttranslational modification of proteins by linear or branched chains of ADP-ribose units, originating from NAD+. The central enzyme for PAR production in cells and the main target of poly(ADP-ribosyl)ation during DNA damage is poly(ADP-ribose) polymerase 1 (PARP1). PARP1 ability to function as a catalytic and acceptor protein simultaneously made a considerable contribution to accumulation of contradictory data. This topic is directly related to other questions, such as the stoichiometry of PARP1 molecules in auto-modification reaction, direction of the chain growth during PAR elongation and functional coupling of PARP1 with PARylation targets. Besides DNA damage necessary for the folding of catalytically active PARP1, other mechanisms appear to be required for the relevant intensity and specificity of PARylation reaction. Indeed, in recent years, PARP research has been enriched by the discovery of novel PARP1 interaction partners modulating its enzymatic activity. Understanding the details of PARP1 catalytic mechanism and its regulation is especially important in light of PARP-targeted therapy and may significantly aid to PARP inhibitors drug design. In this review we summarize old and up-to-date literature to clarify several points concerning PARylation mechanism and discuss different ways for regulation of PAR synthesis by accessory proteins reported thus far.
Collapse
Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| |
Collapse
|
30
|
Bereshchenko O, Lo Re O, Nikulenkov F, Flamini S, Kotaskova J, Mazza T, Le Pannérer MM, Buschbeck M, Giallongo C, Palumbo G, Li Volti G, Pazienza V, Cervinek L, Riccardi C, Krejci L, Pospisilova S, Stewart AF, Vinciguerra M. Deficiency and haploinsufficiency of histone macroH2A1.1 in mice recapitulate hematopoietic defects of human myelodysplastic syndrome. Clin Epigenetics 2019; 11:121. [PMID: 31439048 PMCID: PMC6704528 DOI: 10.1186/s13148-019-0724-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022] Open
Abstract
Background Epigenetic regulation is important in hematopoiesis, but the involvement of histone variants is poorly understood. Myelodysplastic syndromes (MDS) are heterogeneous clonal hematopoietic stem cell (HSC) disorders characterized by ineffective hematopoiesis. MacroH2A1.1 is a histone H2A variant that negatively correlates with the self-renewal capacity of embryonic, adult, and cancer stem cells. MacroH2A1.1 is a target of the frequent U2AF1 S34F mutation in MDS. The role of macroH2A1.1 in hematopoiesis is unclear. Results MacroH2A1.1 mRNA levels are significantly decreased in patients with low-risk MDS presenting with chromosomal 5q deletion and myeloid cytopenias and tend to be decreased in MDS patients carrying the U2AF1 S34F mutation. Using an innovative mouse allele lacking the macroH2A1.1 alternatively spliced exon, we investigated whether macroH2A1.1 regulates HSC homeostasis and differentiation. The lack of macroH2A1.1 decreased while macroH2A1.1 haploinsufficiency increased HSC frequency upon irradiation. Moreover, bone marrow transplantation experiments showed that both deficiency and haploinsufficiency of macroH2A1.1 resulted in enhanced HSC differentiation along the myeloid lineage. Finally, RNA-sequencing analysis implicated macroH2A1.1-mediated regulation of ribosomal gene expression in HSC homeostasis. Conclusions Together, our findings suggest a new epigenetic process contributing to hematopoiesis regulation. By combining clinical data with a discrete mutant mouse model and in vitro studies of human and mouse cells, we identify macroH2A1.1 as a key player in the cellular and molecular features of MDS. These data justify the exploration of macroH2A1.1 and associated proteins as therapeutic targets in hematological malignancies. Electronic supplementary material The online version of this article (10.1186/s13148-019-0724-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Oxana Bereshchenko
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy.
| | - Oriana Lo Re
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Fedor Nikulenkov
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sara Flamini
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy
| | - Jana Kotaskova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics unit, San Giovanni Rotondo, Italy
| | - Marguerite-Marie Le Pannérer
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Campus ICO-Germans Trias I Pujol, Badalona, Spain.,Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Marcus Buschbeck
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Campus ICO-Germans Trias I Pujol, Badalona, Spain.,Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Cesarina Giallongo
- Division of Hematology, A.O.U. Policlinico-OVE, University of Catania, Catania, Italy
| | - Giuseppe Palumbo
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, Catania, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Valerio Pazienza
- Gastroenterology unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Libor Cervinek
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Carlo Riccardi
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy
| | - Lumir Krejci
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Manlio Vinciguerra
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.
| |
Collapse
|
31
|
Cholewa-Waclaw J, Shah R, Webb S, Chhatbar K, Ramsahoye B, Pusch O, Yu M, Greulich P, Waclaw B, Bird AP. Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic. Proc Natl Acad Sci U S A 2019; 116:14995-15000. [PMID: 31289233 PMCID: PMC6660794 DOI: 10.1073/pnas.1903549116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here, we integrate quantitative, multidimensional experimental analysis and mathematical modeling to indicate that MeCP2 is a global transcriptional regulator whose binding to DNA creates "slow sites" in gene bodies. We hypothesize that waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shockwaves in nonequilibrium physics transport models. This mechanism differs from conventional gene-regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings point to a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene-expression patterns are choreographed.
Collapse
Affiliation(s)
- Justyna Cholewa-Waclaw
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, United Kingdom
| | - Ruth Shah
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, United Kingdom
| | - Shaun Webb
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, United Kingdom
| | - Kashyap Chhatbar
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, United Kingdom
| | - Bernard Ramsahoye
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Campus, EH4 2XU Edinburgh, United Kingdom
| | - Oliver Pusch
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Miao Yu
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093
| | - Philip Greulich
- Mathematical Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, SO17 1BJ Southampton, United Kingdom
| | - Bartlomiej Waclaw
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, United Kingdom
| | - Adrian P Bird
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, United Kingdom;
| |
Collapse
|
32
|
Abstract
Proteotoxic stress, that is, stress caused by protein misfolding and aggregation, triggers the rapid and global reprogramming of transcription at genes and enhancers. Genome-wide assays that track transcriptionally engaged RNA polymerase II (Pol II) at nucleotide resolution have provided key insights into the underlying molecular mechanisms that regulate transcriptional responses to stress. In addition, recent kinetic analyses of transcriptional control under heat stress have shown how cells 'prewire' and rapidly execute genome-wide changes in transcription while concurrently becoming poised for recovery. The regulation of Pol II at genes and enhancers in response to heat stress is coupled to chromatin modification and compartmentalization, as well as to co-transcriptional RNA processing. These mechanistic features seem to apply broadly to other coordinated genome-regulatory responses.
Collapse
|
33
|
Histone variant macroH2A: from chromatin deposition to molecular function. Essays Biochem 2019; 63:59-74. [DOI: 10.1042/ebc20180062] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/01/2023]
Abstract
Abstract
The eukaryotic genome is regulated in the context of chromatin. Specialized histones, known as histone variants, incorporate into chromatin to replace their canonical counterparts and represent an important layer of regulation to diversify the structural characteristics and functional outputs of chromatin. MacroH2A is an unusual histone variant with a bulky C-terminal non-histone domain that distinguishes it from all other histones. It is a critical player in stabilizing differentiated cell identity by posing as a barrier to somatic cell reprogramming toward pluripotency and acts as a tumor suppressor in a wide range of cancers. MacroH2A histones are generally regarded as repressive variants that are enriched at the inactive X chromosome (Xi) and broad domains across autosomal chromatin. Recent studies have shed light on to how macroH2A influences transcriptional outputs within distinct genomic contexts and revealed new intriguing molecular functions of macroH2A variants beyond transcriptional regulation. Furthermore, the mechanisms of its mysterious chromatin deposition are beginning to be unraveled, facilitating our understanding of its complex regulation of genome function.
Collapse
|
34
|
Gerazova-Efremova K, Dinevska-Kjovkarovska S, Miova B. Heat-Shock Protein 70-Mediated Heat Preconditioning Attenuates Hepatic Carbohydrate and Oxidative Disturbances in Rats With Type 1 Diabetes. Can J Diabetes 2019; 43:345-353. [PMID: 30853267 DOI: 10.1016/j.jcjd.2019.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/26/2018] [Accepted: 01/04/2019] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Heat preconditioning and heat-shock protein (HSP) synthesis have significant cytoprotective effects against the development of cellular injury caused by the application of a subsequent stressor, which were found to depend on the time period between the stressors. We aimed to determine the most efficient recovery time (6 h or 24 h) following heat-stress exposure and prior application of diabetic streptozotocin (STZ) on the moderation of carbohydrate and oxidative metabolic disturbances caused by diabetes. METHODS Experiment animals (Wistar rats) were exposed to acute heat stress at 41±1°C for 45 min, followed by 6-h or 24-h recovery times at room temperature before sacrifice or STZ administration. RESULTS Our findings indicate that acute heat stress with 6-h or 24-h recovery periods results in a significant rise in the hepatic heat-shock protein 70 (HSP70) levels (even more so after 24 h), glycogen breakdown and stable glycemia, followed by reduced glycolytic and gluconeogenic activity (after 24 h) (glucose-6-phosphatase, fructose-1,6-bisphosphatase); stimulates antioxidative activity (glutathione peroxidase, glutathione reductase) (after 6 h); and decreases glutathione and catalase activity (after 24 h). Heat preconditioning (with 6-h and 24-h recovery periods) prior to STZ-induced diabetes increases HSP70 levels and causes lower serum glucose levels, higher glycogen and glucose-6-phosphate levels, lower glucose-6-phosphatase levels and glycogen phosphorylase and hexokinase levels but also elevates glutathione reductase and glutathione peroxidase activity compared to untreated STZ animals. CONCLUSIONS Based on our findings, heat preconditioning and HSP70 induction in rats with type 1 diabetes attenuates STZ-induced metabolic alterations in hepatic carbohydrate metabolism and oxidative states. These changes are more evident at 24 h recovery post-acute heat stress, based on the most evident accumulation of HSP70 in this time frame.
Collapse
Affiliation(s)
- Katerina Gerazova-Efremova
- Department of Experimental Physiology and Biochemistry, Institute of Biology, Faculty of Natural Sciences and Mathematics, University of Saints Cyril and Methodius, Skopje, Republic of Macedonia
| | - Suzana Dinevska-Kjovkarovska
- Department of Experimental Physiology and Biochemistry, Institute of Biology, Faculty of Natural Sciences and Mathematics, University of Saints Cyril and Methodius, Skopje, Republic of Macedonia
| | - Biljana Miova
- Department of Experimental Physiology and Biochemistry, Institute of Biology, Faculty of Natural Sciences and Mathematics, University of Saints Cyril and Methodius, Skopje, Republic of Macedonia.
| |
Collapse
|
35
|
MacroH2A1 chromatin specification requires its docking domain and acetylation of H2B lysine 20. Nat Commun 2018; 9:5143. [PMID: 30510186 PMCID: PMC6277393 DOI: 10.1038/s41467-018-07189-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 10/13/2018] [Indexed: 12/23/2022] Open
Abstract
The histone variant macroH2A1 localizes to two functionally distinct chromatin subtypes marked by either H3K27me3 or H2B acetylations, where it is thought to directly regulate transcription. The recent finding, that macroH2A1 regulates mitochondrial respiration by globally dampening PARP activity, requires the field to re-evaluate which functions of macroH2A1 are due to global effects on cellular metabolism and which are direct effects determined by macroH2A1 chromatin localization. Here, we demonstrate macroH2A1 incorporation into H2B-acetylated chromatin requires a feature in its histone-fold domain, distinguishing this process from incorporation into H3K27me3-containing chromatin in which multiple features of macroH2A1 are sufficient for targeting. In addition, we identify H2BK20 acetylation as a critical modification required to target macroH2A1 to H2B-acetylated chromatin. Our findings have allowed us to definitively establish that macroH2A1's regulation of an important transcriptional program, the senescence-associated secretory phenotype (SASP), requires its accurate genomic localization.
Collapse
|
36
|
Hurtado-Bagès S, Guberovic I, Buschbeck M. The MacroH2A1.1 - PARP1 Axis at the Intersection Between Stress Response and Metabolism. Front Genet 2018; 9:417. [PMID: 30356649 PMCID: PMC6189284 DOI: 10.3389/fgene.2018.00417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/06/2018] [Indexed: 12/12/2022] Open
Abstract
The exchange of replication-coupled canonical histones by histone variants endows chromatin with specific features. The replacement of the canonical H2A histone for the histone variant macroH2A is one of the most remarkable epigenetic modifications. The three vertebrate macroH2A proteins have a unique tripartite structure consisting of H2A-like domain, unstructured linker, and macrodomain. Macrodomains are ancient globular folds that are able to bind nicotinamide adenine dinucleotide (NAD+) derived metabolites. Here, we will briefly describe the physiological relevance of the metabolite binding in the context of chromatin. In particular, we will focus on the macroH2A1.1 isoform that binds ADP-ribose and poly-ADP-ribose polymerase 1 (PARP1) enzyme, a cellular stress sensor. We will discuss the impact of this interaction in the context of cancer, senescence, cell stress and energy metabolism.
Collapse
Affiliation(s)
- Sarah Hurtado-Bagès
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Ph.D. Program in Biomedicine, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Iva Guberovic
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Ph.D. Program in Biomedicine, Faculty of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
| | - Marcus Buschbeck
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| |
Collapse
|
37
|
Transcription-associated histone pruning demarcates macroH2A chromatin domains. Nat Struct Mol Biol 2018; 25:958-970. [PMID: 30291361 PMCID: PMC6178985 DOI: 10.1038/s41594-018-0134-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 08/17/2018] [Indexed: 02/01/2023]
Abstract
The histone variant macroH2A occupies large repressive domains throughout the genome, however mechanisms underlying its precise deposition remain poorly understood. Here, we characterized de novo chromatin deposition of macroH2A2 using temporal genomic profiling in murine-derived fibroblasts devoid of all macroH2A isoforms. We find that macroH2A2 is first pervasively deposited genome-wide at both steady state domains and adjacent transcribed regions, the latter of which are subsequently pruned, establishing mature macroH2A2 domains. Pruning of macroH2A2 can be counteracted by chemical inhibition of transcription. Further, CRISPR/Cas9-based locus-specific transcriptional manipulation reveals that gene activation depletes pre-existing macroH2A2, while silencing triggers ectopic macroH2A2 accumulation. We demonstrate that the FACT (facilitates chromatin transcription) complex is required for macroH2A2 pruning within transcribed chromatin. Taken together, we have identified active chromatin as a boundary for macroH2A domains through a transcription-associated ‘pruning’ mechanism that establishes and maintains the faithful genomic localization of macroH2A variants.
Collapse
|
38
|
Kozlowski M, Corujo D, Hothorn M, Guberovic I, Mandemaker IK, Blessing C, Sporn J, Gutierrez-Triana A, Smith R, Portmann T, Treier M, Scheffzek K, Huet S, Timinszky G, Buschbeck M, Ladurner AG. MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms. EMBO Rep 2018; 19:embr.201744445. [PMID: 30177554 DOI: 10.15252/embr.201744445] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 01/22/2023] Open
Abstract
MacroH2A histone variants suppress tumor progression and act as epigenetic barriers to induced pluripotency. How they impart their influence on chromatin plasticity is not well understood. Here, we analyze how the different domains of macroH2A proteins contribute to chromatin structure and dynamics. By solving the crystal structure of the macrodomain of human macroH2A2 at 1.7 Å, we find that its putative binding pocket exhibits marked structural differences compared with the macroH2A1.1 isoform, rendering macroH2A2 unable to bind ADP-ribose. Quantitative binding assays show that this specificity is conserved among vertebrate macroH2A isoforms. We further find that macroH2A histones reduce the transient, PARP1-dependent chromatin relaxation that occurs in living cells upon DNA damage through two distinct mechanisms. First, macroH2A1.1 mediates an isoform-specific effect through its ability to suppress PARP1 activity. Second, the unstructured linker region exerts an additional repressive effect that is common to all macroH2A proteins. In the absence of DNA damage, the macroH2A linker is also sufficient for rescuing heterochromatin architecture in cells deficient for macroH2A.
Collapse
Affiliation(s)
- Marek Kozlowski
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - David Corujo
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,PhD Programme of Genetics, Universitat de Barcelona, Barcelona, Spain
| | | | - Iva Guberovic
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Imke K Mandemaker
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Charlotte Blessing
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Judith Sporn
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Rebecca Smith
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Mathias Treier
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Sebastien Huet
- Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, Rennes, France
| | - Gyula Timinszky
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Marcus Buschbeck
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain .,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Andreas G Ladurner
- Biomedical Center, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany .,Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, Munich, Germany
| |
Collapse
|
39
|
Ibrahim A, Alhosin M, Papin C, Ouararhni K, Omran Z, Zamzami MA, Al-Malki AL, Choudhry H, Mély Y, Hamiche A, Mousli M, Bronner C. Thymoquinone challenges UHRF1 to commit auto-ubiquitination: a key event for apoptosis induction in cancer cells. Oncotarget 2018; 9:28599-28611. [PMID: 29983883 PMCID: PMC6033341 DOI: 10.18632/oncotarget.25583] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/19/2018] [Indexed: 01/26/2023] Open
Abstract
Down-regulation of UHRF1 (Ubiquitin-like containing PHD and Ring Finger 1) in Jurkat cells, induced by natural anticancer compounds such as thymoquinone, allows re-expression of tumor suppressor genes such as p73 and p16INK4A . In order to decipher the mechanisms of UHRF1 down-regulation, we investigated the kinetic of expression of HAUSP (herpes virus-associated ubiquitin-specific protease), UHRF1, cleaved caspase-3 and p73 in Jurkat cells treated with thymoquinone. We found that thymoquinone induced degradation of UHRF1, correlated with a sharp decrease in HAUSP and an increase in cleaved caspase-3 and p73. UHRF1 concomitantly underwent a rapid ubiquitination in response to thymoquinone and this effect was not observed in the cells expressing mutant UHRF1 RING domain, suggesting that UHRF1 commits an auto-ubiquitination through its RING domain in response to thymoquinone treatment. Exposure of cells to Z-DEVD, an inhibitor of caspase-3 markedly reduced the thymoquinone-induced down-regulation of UHRF1, while proteosomal inhibitor MG132 had no such effect. The present findings indicate that thymoquinone induces in cancer cells a fast UHRF1 auto-ubiquitination through its RING domain associated with HAUSP down-regulation. They further suggest that thymoquinone-induced UHRF1 auto-ubiquitination followed by its degradation is a key event in inducing apoptosis through a proteasome-independent mechanism.
Collapse
Affiliation(s)
- Abdulkhaleg Ibrahim
- Institut De Génétique Et De Biologie Moléculaire Et Cellulaire (IGBMC), INSERM U1258 CNRS UMR 7104, Université de Strasbourg, Illkirch, France.,BioTechnology Research Center (BTRC), Tripoli, Lybia
| | - Mahmoud Alhosin
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Christophe Papin
- Institut De Génétique Et De Biologie Moléculaire Et Cellulaire (IGBMC), INSERM U1258 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Institut De Génétique Et De Biologie Moléculaire Et Cellulaire (IGBMC), INSERM U1258 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Ziad Omran
- College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulrahman Labeed Al-Malki
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yves Mély
- CNRS UMR 7021 Laboratoire de Bioimagerie et Pathologies, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Ali Hamiche
- Institut De Génétique Et De Biologie Moléculaire Et Cellulaire (IGBMC), INSERM U1258 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - Marc Mousli
- CNRS UMR 7021 Laboratoire de Bioimagerie et Pathologies, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Christian Bronner
- Institut De Génétique Et De Biologie Moléculaire Et Cellulaire (IGBMC), INSERM U1258 CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| |
Collapse
|
40
|
Poly(ADP-Ribose) Polymerase 1 Promotes the Human Heat Shock Response by Facilitating Heat Shock Transcription Factor 1 Binding to DNA. Mol Cell Biol 2018; 38:MCB.00051-18. [PMID: 29661921 DOI: 10.1128/mcb.00051-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/11/2018] [Indexed: 01/09/2023] Open
Abstract
The heat shock response (HSR) is characterized by the rapid and robust induction of heat shock proteins (HSPs), including HSP70, in response to heat shock and is regulated by heat shock transcription factor 1 (HSF1) in mammalian cells. Poly(ADP-ribose) polymerase 1 (PARP1), which can form a complex with HSF1 through the scaffold protein PARP13, has been suggested to be involved in the HSR. However, its effects on and the regulatory mechanisms of the HSR are not well understood. Here we show that prior to heat shock, the HSF1-PARP13-PARP1 complex binds to the HSP70 promoter. In response to heat shock, activated and auto-PARylated PARP1 dissociates from HSF1-PARP13 and is redistributed throughout the HSP70 locus. Remarkably, chromatin in the HSP70 promoter is initially PARylated at high levels and decondensed, whereas chromatin in the gene body is moderately PARylated afterwards. Activated HSF1 then binds to the promoter efficiently and promotes the HSR. Chromatin PARylation and HSF1 binding to the promoter are also facilitated by the phosphorylation-dependent dissociation of PARP13. Furthermore, the HSR and proteostasis capacity are reduced by pretreatment with genotoxic stresses, which disrupt the ternary complex. These results illuminate one of the priming mechanisms of the HSR that facilitates the binding of HSF1 to DNA during heat shock.
Collapse
|
41
|
Post-Translational Modifications of H2A Histone Variants and Their Role in Cancer. Cancers (Basel) 2018; 10:cancers10030059. [PMID: 29495465 PMCID: PMC5876634 DOI: 10.3390/cancers10030059] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/19/2018] [Accepted: 02/25/2018] [Indexed: 12/12/2022] Open
Abstract
Histone variants are chromatin components that replace replication-coupled histones in a fraction of nucleosomes and confer particular characteristics to chromatin. H2A variants represent the most numerous and diverse group among histone protein families. In the nucleosomal structure, H2A-H2B dimers can be removed and exchanged more easily than the stable H3-H4 core. The unstructured N-terminal histone tails of all histones, but also the C-terminal tails of H2A histones protrude out of the compact structure of the nucleosome core. These accessible tails are the preferential target sites for a large number of post-translational modifications (PTMs). While some PTMs are shared between replication-coupled H2A and H2A variants, many modifications are limited to a specific histone variant. The present review focuses on the H2A variants H2A.Z, H2A.X, and macroH2A, and summarizes their functions in chromatin and how these are linked to cancer development and progression. H2A.Z primarily acts as an oncogene and macroH2A and H2A.X as tumour suppressors. We further focus on the regulation by PTMs, which helps to understand a degree of context dependency.
Collapse
|
42
|
Quénet D. Histone Variants and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:1-39. [DOI: 10.1016/bs.ircmb.2017.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
43
|
QKI5-mediated alternative splicing of the histone variant macroH2A1 regulates gastric carcinogenesis. Oncotarget 2017; 7:32821-34. [PMID: 27092877 PMCID: PMC5078054 DOI: 10.18632/oncotarget.8739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/28/2016] [Indexed: 12/18/2022] Open
Abstract
Alternative pre-mRNA splicing is a key mechanism for increasing proteomic diversity and modulating gene expression. Emerging evidence indicated that the splicing program is frequently dysregulated during tumorigenesis. Cancer cells produce protein isoforms that can promote growth and survival. The RNA-binding protein QKI5 is a critical regulator of alternative splicing in expanding lists of primary human tumors and tumor cell lines. However, its biological role and regulatory mechanism are poorly defined in gastric cancer (GC) development and progression. In this study, we demonstrated that the downregulation of QKI5 was associated with pTNM stage and pM state of GC patients. Re-introduction of QKI5 could inhibit GC cell proliferation, migration, and invasion in vitro and in vivo, which might be due to the altered splicing pattern of macroH2A1 pre-mRNA, leading to the accumulation of macroH2A1.1 isoform. Furthermore, QKI5 could inhibit cyclin L1 expression via promoting macroH2A1.1 production. Thus, this study identified a novel regulatory axis involved in gastric tumorigenesis and provided a new strategy for GC therapy.
Collapse
|
44
|
Lo Re O, Vinciguerra M. Histone MacroH2A1: A Chromatin Point of Intersection between Fasting, Senescence and Cellular Regeneration. Genes (Basel) 2017; 8:genes8120367. [PMID: 29206173 PMCID: PMC5748685 DOI: 10.3390/genes8120367] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022] Open
Abstract
Histone variants confer chromatin unique properties. They have specific genomic distribution, regulated by specific deposition and removal machineries. Histone variants, mostly of canonical histones H2A, H2B and H3, have important roles in early embryonic development, in lineage commitment of stem cells, in the converse process of somatic cell reprogramming to pluripotency and, in some cases, in the modulation of animal aging and life span. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1.1 and macroH2A1.2, regulating cell plasticity and proliferation, during pluripotency and tumorigenesis. Furthermore, macroH2A1 participates in the formation of senescence-associated heterochromatic foci (SAHF) in senescent cells, and multiple lines of evidence in genetically modified mice suggest that macroH2A1 integrates nutritional cues from the extracellular environment to transcriptional programs. Here, we review current molecular evidence based on next generation sequencing data, cell assays and in vivo models supporting different mechanisms that could mediate the function of macroH2A1 in health span and life span. We will further discuss context-dependent and isoform-specific functions. The aim of this review is to provide guidance to assess histone variant macroH2A1 potential as a therapeutic intervention point.
Collapse
Affiliation(s)
- Oriana Lo Re
- Center for Translational Medicine, International Clinical Research Center, St'Anne University Hospital, Brno 656 91, Czech Republic.
- Faculty of Medicine, Masaryk University, Brno 656 91, Czech Republic.
| | - Manlio Vinciguerra
- Center for Translational Medicine, International Clinical Research Center, St'Anne University Hospital, Brno 656 91, Czech Republic.
- Faculty of Medicine, Masaryk University, Brno 656 91, Czech Republic.
- Division of Medicine, Institute for Liver and Digestive Health, University College London (UCL), London WC1E 6BT, UK.
| |
Collapse
|
45
|
The HSF1-PARP13-PARP1 complex facilitates DNA repair and promotes mammary tumorigenesis. Nat Commun 2017; 8:1638. [PMID: 29158484 PMCID: PMC5696371 DOI: 10.1038/s41467-017-01807-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/13/2017] [Indexed: 01/23/2023] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is involved in DNA repair, chromatin structure, and transcription. However, the mechanisms that regulate PARP1 distribution on DNA are poorly understood. Here, we show that heat shock transcription factor 1 (HSF1) recruits PARP1 through the scaffold protein PARP13. In response to DNA damage, activated and auto-poly-ADP-ribosylated PARP1 dissociates from HSF1–PARP13, and redistributes to DNA lesions and DNA damage-inducible gene loci. Histone deacetylase 1 maintains PARP1 in the ternary complex by inactivating PARP1 through deacetylation. Blocking ternary complex formation impairs redistribution of PARP1 during DNA damage, which reduces gene expression and DNA repair. Furthermore, ternary complex formation and PARP1 redistribution protect cells from DNA damage by promoting DNA repair, and support growth of BRCA1-null mammary tumors, which are sensitive to PARP inhibitors. Our findings identify HSF1 as a regulator of genome integrity and define this function as a guarding mechanism for a specific type of mammary tumorigenesis. PARP1 recruitment to DNA lesions is critical for DNA damage repair but how DNA damage induces PARP1 redistribution is largely unknown. Here, the authors provide evidence that PARP1 redistribution and DNA repair in tumor cells depend on the formation of a HSF1–PARP13–PARP1 complex.
Collapse
|
46
|
Posavec Marjanović M, Hurtado-Bagès S, Lassi M, Valero V, Malinverni R, Delage H, Navarro M, Corujo D, Guberovic I, Douet J, Gama-Perez P, Garcia-Roves PM, Ahel I, Ladurner AG, Yanes O, Bouvet P, Suelves M, Teperino R, Pospisilik JA, Buschbeck M. MacroH2A1.1 regulates mitochondrial respiration by limiting nuclear NAD + consumption. Nat Struct Mol Biol 2017; 24:902-910. [PMID: 28991266 PMCID: PMC5791885 DOI: 10.1038/nsmb.3481] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023]
Abstract
Histone variants are structural components of eukaryotic chromatin that can replace replication-coupled histones in the nucleosome. The histone variant macroH2A1.1 contains a macrodomain capable of binding NAD+-derived metabolites. Here we report that macroH2A1.1 is rapidly induced during myogenic differentiation through a switch in alternative splicing, and that myotubes that lack macroH2A1.1 have a defect in mitochondrial respiratory capacity. We found that the metabolite-binding macrodomain was essential for sustained optimal mitochondrial function but dispensable for gene regulation. Through direct binding, macroH2A1.1 inhibits basal poly-ADP ribose polymerase 1 (PARP-1) activity and thus reduces nuclear NAD+ consumption. The resultant accumulation of the NAD+ precursor NMN allows for maintenance of mitochondrial NAD+ pools that are critical for respiration. Our data indicate that macroH2A1.1-containing chromatin regulates mitochondrial respiration by limiting nuclear NAD+ consumption and establishing a buffer of NAD+ precursors in differentiated cells.
Collapse
Affiliation(s)
- Melanija Posavec Marjanović
- Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
- PhD Program in Biomedicine, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sarah Hurtado-Bagès
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- PhD Program in Biomedicine, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maximilian Lassi
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Vanesa Valero
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Roberto Malinverni
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Hélène Delage
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Miriam Navarro
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain
- Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - David Corujo
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Iva Guberovic
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Julien Douet
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Pau Gama-Perez
- Department of Physiological Sciences II, Faculty of Medicine - University of Barcelona, Spain
| | - Pablo M. Garcia-Roves
- Department of Physiological Sciences II, Faculty of Medicine - University of Barcelona, Spain
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Andreas G. Ladurner
- Biomedical Center Munich (BMC) - Physiological Chemistry, Center for Integrated Protein Science Munich, Munich Cluster for Systems Neurology, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Oscar Yanes
- Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain
- Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Philippe Bouvet
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Mònica Suelves
- Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Raffaele Teperino
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Marcus Buschbeck
- Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| |
Collapse
|
47
|
Cedeno RJ, Nakauka-Ddamba A, Yousefi M, Sterling S, Leu NA, Li N, Pehrson JR, Lengner CJ. The histone variant macroH2A confers functional robustness to the intestinal stem cell compartment. PLoS One 2017; 12:e0185196. [PMID: 28934364 PMCID: PMC5608326 DOI: 10.1371/journal.pone.0185196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/07/2017] [Indexed: 12/20/2022] Open
Abstract
A stem cell's epigenome directs cell fate during development, homeostasis, and regeneration. Epigenetic dysregulation can lead to inappropriate cell fate decisions, aberrant cell function, and even cancer. The histone variant macroH2A has been shown to influence gene expression, guide cell fate, and safeguard against genotoxic stress. Interestingly, mice lacking functional macroH2A histones (hereafter referred to as macroH2A DKO) are viable and fertile; yet suffer from increased perinatal death and reduced weight and size compared to wildtype (WT). Here, we ask whether the ostensible reduced vigor of macroH2A DKO mice extends to intestinal stem cell (ISC) function during homeostasis, regeneration, and oncogenesis. Lgr5-eGFP-IRES-CreERT2 or Hopx-CreERT2::Rosa26-LSL-tdTomato ISC reporter mice or the C57BL/6J-Apcmin/J murine intestinal adenoma model were bred into a macroH2A DKO or strain-matched WT background and assessed for ISC functionality, regeneration and tumorigenesis. High-dose (12Gy) whole-body γ-irradiation was used as an injury model. We show that macroH2A is dispensable for intestinal homeostasis and macroH2A DKO mice have similar numbers of active crypt-base columnar ISCs (CBCs). MacroH2A DKO intestine exhibits impaired regeneration following injury, despite having significantly more putative reserve ISCs. DKO reserve ISCs disproportionately undergo apoptosis compared to WT after DNA damage infliction. Interestingly, a macroH2A DKO background does not significantly increase tumorigenesis in the Apcmin model of intestinal adenoma. We conclude that macroH2A influences reserve ISC number and function during homeostasis and regeneration. These data suggest macroH2A enhances reserve ISC survival after DNA damage and thus confers functional robustness to the intestinal epithelium.
Collapse
Affiliation(s)
- Ryan James Cedeno
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Cell and Molecular Biology Graduate Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States of America
| | - Angela Nakauka-Ddamba
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Maryam Yousefi
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Cell and Molecular Biology Graduate Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States of America
| | - Stephanie Sterling
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Center for Animal Transgenesis, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Nicolae Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Center for Animal Transgenesis, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Ning Li
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - John R Pehrson
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Christopher Joachim Lengner
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Center for Animal Transgenesis, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.,Center for Molecular Studies in Digestive and Liver Disease, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
48
|
Gupte R, Liu Z, Kraus WL. PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev 2017; 31:101-126. [PMID: 28202539 PMCID: PMC5322727 DOI: 10.1101/gad.291518.116] [Citation(s) in RCA: 457] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this review, Gupte et al. discuss new findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair as well as recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates. Supporting these advances is a host of methodological approaches from chemical biology, proteomics, genomics, cell biology, and genetics that have propelled new discoveries in the field. New findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair have been complemented by recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. These studies have begun to reveal the promising ways in which PARPs may be targeted therapeutically for the treatment of disease. In this review, we discuss these topics and relate them to the future directions of the field.
Collapse
Affiliation(s)
- Rebecca Gupte
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ziying Liu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| |
Collapse
|
49
|
The Drosophila DAXX-Like Protein (DLP) Cooperates with ASF1 for H3.3 Deposition and Heterochromatin Formation. Mol Cell Biol 2017; 37:MCB.00597-16. [PMID: 28320872 DOI: 10.1128/mcb.00597-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/09/2017] [Indexed: 01/22/2023] Open
Abstract
Histone variants are nonallelic isoforms of canonical histones, and they are deposited, in contrast to canonical histones, in a replication-independent (RI) manner. RI deposition of H3.3, a histone variant from the H3.3 family, is mediated in mammals by distinct pathways involving either the histone regulator A (HIRA) complex or the death-associated protein (DAXX)/α-thalassemia X-linked mental retardation protein (ATRX) complex. Here, we investigated the function of the Drosophila DAXX-like protein (DLP) by using both fly genetic approaches and protein biochemistry. DLP specifically interacts with H3.3 and shows a prominent localization on the base of the X chromosome, where it appears to act in concert with XNP, the Drosophila homolog of ATRX, in heterochromatin assembly and maintenance. The functional association between DLP and XNP is further supported by a series of experiments that illustrate genetic interactions and the DLP-XNP-dependent localization of specific chromosomal proteins. In addition, DLP both participates in the RI deposition of H3.3 and associates with anti-silencing factor 1 (ASF1). We suggest, in agreement with a recently proposed model, that DLP and ASF1 are part of a predeposition complex, which is recruited by XNP and is necessary to prevent DNA exposure in the nucleus.
Collapse
|
50
|
Ciccarone F, Zampieri M, Caiafa P. PARP1 orchestrates epigenetic events setting up chromatin domains. Semin Cell Dev Biol 2016; 63:123-134. [PMID: 27908606 DOI: 10.1016/j.semcdb.2016.11.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/05/2016] [Accepted: 11/24/2016] [Indexed: 01/18/2023]
Abstract
Epigenetic events include reversible modifications of DNA and histone tails driving chromatin organization and thus transcription. The epigenetic regulation is a highly integrated process underlying the plasticity of the genomic information both in the context of complex physiological and pathological processes. The global regulatory aspects of epigenetic events are largely unknown. PARylation and PARP1 are recently emerging as multi-level regulatory effectors that modulate the topology of chromatin by orchestrating very different processes. This review focuses in particular on the role of PARP1 in epigenetics, trying to build a comprehensive perspective of its involvement in the regulation of epigenetic modifications of histones and DNA, contextualizing it in the global organization of chromatin domains in the nucleus.
Collapse
Affiliation(s)
- Fabio Ciccarone
- Department of Biology, Faculty of Mathematics, Physics and Natural Sciences, University of Rome 'Tor Vergata', Rome, Italy
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Haematology, Faculty of Pharmacy and Medicine, 'Sapienza' University of Rome, Rome, Italy; Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Haematology, Faculty of Pharmacy and Medicine, 'Sapienza' University of Rome, Rome, Italy; Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy.
| |
Collapse
|