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Lorzadeh A, Ye G, Sharma S, Jadhav U. DNA methylation-dependent and -independent binding of CDX2 directs activation of distinct developmental and homeostatic genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579850. [PMID: 38405700 PMCID: PMC10888781 DOI: 10.1101/2024.02.11.579850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of TFs. However, how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci is still not well understood. Here we show that Cdx2 - a pioneer TF that binds distinct targets in developing versus adult intestinal epithelial cells - has a preferential affinity for a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at embryonic and fetal Cdx2 target loci and the specifically methylated state of the CpG during development allows selective Cdx2 binding and activation of developmental enhancers and linked genes. Conversely, demethylation at these enhancers prohibits ectopic Cdx2 binding in adult cells, where Cdx2 binds its canonical motif without a CpG. This differential Cdx2 binding allows for corecruitment of Ctcf and Hnf4, facilitating the establishment of intestinal superenhancers during development and enhancers mediating adult homeostatic functions, respectively. Induced gain of DNA methylation in the adult mouse epithelium or cultured cells causes ectopic recruitment of Cdx2 to the developmental target loci and facilitates cobinding of the partner TFs. Together, our results demonstrate that the differential CpG motif requirements for Cdx2 binding to developmental versus adult target sites allow it to navigate different DNA methylation profiles and activate cell type-specific genes at appropriate times.
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Affiliation(s)
- Alireza Lorzadeh
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - George Ye
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - Sweta Sharma
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - Unmesh Jadhav
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
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Sobotka AA, Tempera I. PARP1 as an Epigenetic Modulator: Implications for the Regulation of Host-Viral Dynamics. Pathogens 2024; 13:131. [PMID: 38392869 PMCID: PMC10891851 DOI: 10.3390/pathogens13020131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The principal understanding of the Poly(ADP-ribose) polymerase (PARP) regulation of genomes has been focused on its role in DNA repair; however, in the past few years, an additional role for PARPs and PARylation has emerged in regulating viral-host interactions. In particular, in the context of DNA virus infection, PARP1-mediated mechanisms of gene regulations, such as the involvement with cellular protein complexes responsible for the folding of the genome into the nucleus, the formation of chromatin loops connecting distant regulatory genomic regions, and other methods of transcriptional regulation, provide additional ways through which PARPs can modulate the function of both the host and the viral genomes during viral infection. In addition, potential viral amplification of the activity of PARPs on the host genome can contribute to the pathogenic effect of viral infection, such as viral-driven oncogenesis, opening the possibility that PARP inhibition may represent a potential therapeutic approach to target viral infection. This review will focus on the role of PARPs, particularly PARP1, in regulating the infection of DNA viruses.
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Affiliation(s)
- Asher A. Sobotka
- Wistar Institute, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Dobrica MO, Varghese CS, Harris JM, Ferguson J, Magri A, Arnold R, Várnai C, Parish JL, McKeating JA. CTCF regulates hepatitis B virus cccDNA chromatin topology. J Gen Virol 2024; 105. [PMID: 38175123 DOI: 10.1099/jgv.0.001939] [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] [Indexed: 01/05/2024] Open
Abstract
Hepatitis B Virus (HBV) is a small DNA virus that replicates via an episomal covalently closed circular DNA (cccDNA) that serves as the transcriptional template for viral mRNAs. The host protein, CCCTC-binding factor (CTCF), is a key regulator of cellular transcription by maintaining epigenetic boundaries, nucleosome phasing, stabilisation of long-range chromatin loops and directing alternative exon splicing. We previously reported that CTCF binds two conserved motifs within Enhancer I of the HBV genome and represses viral transcription, however, the underlying mechanisms were not identified. We show that CTCF depletion in cells harbouring cccDNA-like HBV molecules and in de novo infected cells resulted in an increase in spliced transcripts, which was most notable in the abundant SP1 spliced transcript. In contrast, depletion of CTCF in cell lines with integrated HBV DNA had no effect on the abundance of viral transcripts and in line with this observation there was limited evidence for CTCF binding to viral integrants, suggesting that CTCF-regulation of HBV transcription is specific to episomal cccDNA. Analysis of HBV chromatin topology by Assay for Transposase Accessible Chromatin Sequencing (ATAC-Seq) revealed an accessible region spanning Enhancers I and II and the basal core promoter (BCP). Mutating the CTCF binding sites within Enhancer I resulted in a dramatic rearrangement of chromatin accessibility where the open chromatin region was no longer detected, indicating loss of the phased nucleosome up- and down-stream of the HBV enhancer/BCP. These data demonstrate that CTCF functions to regulate HBV chromatin conformation and nucleosomal positioning in episomal maintained cccDNA, which has important consequences for HBV transcription regulation.
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Affiliation(s)
- Mihaela Olivia Dobrica
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Present address: Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Christy Susan Varghese
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - Jack Ferguson
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Present address: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Andrea Magri
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Csilla Várnai
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- National Institute for Health and Care Research (NIHR) Birmingham Biomedical Research Centre, Oxford, UK
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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Dhahri H, Fondufe-Mittendorf YN. Exploring the interplay between PARP1 and circRNA biogenesis and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1823. [PMID: 37957925 PMCID: PMC11089078 DOI: 10.1002/wrna.1823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/15/2023]
Abstract
PARP1 (poly-ADP-ribose polymerase 1) is a multidomain protein with a flexible and self-folding structure that allows it to interact with a wide range of biomolecules, including nucleic acids and target proteins. PARP1 interacts with its target molecules either covalently via PARylation or non-covalently through its PAR moieties induced by auto-PARylation. These diverse interactions allow PARP1 to participate in complex regulatory circuits and cellular functions. Although the most studied PARP1-mediated functions are associated with DNA repair and cellular stress response, subsequent discoveries have revealed additional biological functions. Based on these findings, PARP1 is now recognized as a major modulator of gene expression. Several discoveries show that this multifunctional protein has been intimately connected to several steps of mRNA biogenesis, from transcription initiation to mRNA splicing, polyadenylation, export, and translation of mRNA to proteins. Nevertheless, our understanding of PARP1's involvement in the biogenesis of both coding and noncoding RNA, notably circular RNA (circRNA), remains restricted. In this review, we outline the possible roles of PARP1 in circRNA biogenesis. A full examination of the regulatory roles of PARP1 in nuclear processes with an emphasis on circRNA may reveal new avenues to control dysregulation implicated in the pathogenesis of several diseases such as neurodegenerative disorders and cancers. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Hejer Dhahri
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
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O’Sullivan J, Kothari C, Caron MC, Gagné JP, Jin Z, Nonfoux L, Beneyton A, Coulombe Y, Thomas M, Atalay N, Meng X, Milano L, Jean D, Boisvert FM, Kaufmann S, Hendzel M, Masson JY, Poirier G. ZNF432 stimulates PARylation and inhibits DNA resection to balance PARPi sensitivity and resistance. Nucleic Acids Res 2023; 51:11056-11079. [PMID: 37823600 PMCID: PMC10639050 DOI: 10.1093/nar/gkad791] [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: 12/13/2022] [Revised: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Zinc finger (ZNF) motifs are some of the most frequently occurring domains in the human genome. It was only recently that ZNF proteins emerged as key regulators of genome integrity in mammalian cells. In this study, we report a new role for the Krüppel-type ZNF-containing protein ZNF432 as a novel poly(ADP-ribose) (PAR) reader that regulates the DNA damage response. We show that ZNF432 is recruited to DNA lesions via DNA- and PAR-dependent mechanisms. Remarkably, ZNF432 stimulates PARP-1 activity in vitro and in cellulo. Knockdown of ZNF432 inhibits phospho-DNA-PKcs and increases RAD51 foci formation following irradiation. Moreover, purified ZNF432 preferentially binds single-stranded DNA and impairs EXO1-mediated DNA resection. Consequently, the loss of ZNF432 in a cellular system leads to resistance to PARP inhibitors while its overexpression results in sensitivity. Taken together, our results support the emerging concept that ZNF-containing proteins can modulate PARylation, which can be embodied by the pivotal role of ZNF432 to finely balance the outcome of PARPi response by regulating homologous recombination.
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Affiliation(s)
- Julia O’Sullivan
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Marie-Christine Caron
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Zhigang Jin
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Yan Coulombe
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Mélissa Thomas
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - X Wei Meng
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Larissa Milano
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Dominique Jean
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
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6
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Beneyton A, Nonfoux L, Gagné JP, Rodrigue A, Kothari C, Atalay N, Hendzel M, Poirier G, Masson JY. The dynamic process of covalent and non-covalent PARylation in the maintenance of genome integrity: a focus on PARP inhibitors. NAR Cancer 2023; 5:zcad043. [PMID: 37609662 PMCID: PMC10440794 DOI: 10.1093/narcan/zcad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023] Open
Abstract
Poly(ADP-ribosylation) (PARylation) by poly(ADP-ribose) polymerases (PARPs) is a highly regulated process that consists of the covalent addition of polymers of ADP-ribose (PAR) through post-translational modifications of substrate proteins or non-covalent interactions with PAR via PAR binding domains and motifs, thereby reprogramming their functions. This modification is particularly known for its central role in the maintenance of genomic stability. However, how genomic integrity is controlled by an intricate interplay of covalent PARylation and non-covalent PAR binding remains largely unknown. Of importance, PARylation has caught recent attention for providing a mechanistic basis of synthetic lethality involving PARP inhibitors (PARPi), most notably in homologous recombination (HR)-deficient breast and ovarian tumors. The molecular mechanisms responsible for the anti-cancer effect of PARPi are thought to implicate both catalytic inhibition and trapping of PARP enzymes on DNA. However, the relative contribution of each on tumor-specific cytotoxicity is still unclear. It is paramount to understand these PAR-dependent mechanisms, given that resistance to PARPi is a challenge in the clinic. Deciphering the complex interplay between covalent PARylation and non-covalent PAR binding and defining how PARP trapping and non-trapping events contribute to PARPi anti-tumour activity is essential for developing improved therapeutic strategies. With this perspective, we review the current understanding of PARylation biology in the context of the DNA damage response (DDR) and the mechanisms underlying PARPi activity and resistance.
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Affiliation(s)
- Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Amélie Rodrigue
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AlbertaT6G 1Z2, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
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7
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Bassal MA. The Interplay between Dysregulated Metabolism and Epigenetics in Cancer. Biomolecules 2023; 13:944. [PMID: 37371524 DOI: 10.3390/biom13060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Cellular metabolism (or energetics) and epigenetics are tightly coupled cellular processes. It is arguable that of all the described cancer hallmarks, dysregulated cellular energetics and epigenetics are the most tightly coregulated. Cellular metabolic states regulate and drive epigenetic changes while also being capable of influencing, if not driving, epigenetic reprogramming. Conversely, epigenetic changes can drive altered and compensatory metabolic states. Cancer cells meticulously modify and control each of these two linked cellular processes in order to maintain their tumorigenic potential and capacity. This review aims to explore the interplay between these two processes and discuss how each affects the other, driving and enhancing tumorigenic states in certain contexts.
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Affiliation(s)
- Mahmoud Adel Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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Barker R, Biernacka K, Kingshott G, Sewell A, Gwiti P, Martin RM, Lane JA, McGeagh L, Koupparis A, Rowe E, Oxley J, Perks CM, Holly JMP. Associations of CTCF and FOXA1 with androgen and IGF pathways in men with localized prostate cancer. Growth Horm IGF Res 2023; 69-70:101533. [PMID: 37086646 DOI: 10.1016/j.ghir.2023.101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/24/2023]
Abstract
AIMS To examine associations between the transcription factors CCCTC-binding factor (CTCF) and forkhead box protein A1 (FOXA1) and the androgen receptor (AR) and their association with components of the insulin-like growth factor (IGF)-pathway in a cohort of men with localized prostate cancer. METHODS Using prostate tissue samples collected during the Prostate cancer: Evidence of Exercise and Nutrition Trial (PrEvENT) trial (N = 70 to 92, depending on section availability), we assessed the abundance of CTCF, FOXA1, AR, IGFIR, p-mTOR, PTEN and IGFBP-2 proteins using a modified version of the Allred scoring system. Validation studies were performed using large, publicly available datasets (TCGA) (N = 489). RESULTS We identified a strong correlation between CTCF and AR staining with benign prostate tissue. CTCF also strongly associated with the IGFIR, with PTEN and with phospho-mTOR. FOXA1 was also correlated with staining for the IGF-IR, with IGFBP-2 and with staining for activated phosphor-mTOR. The staining for the IGF-IR was strongly correlated with the AR. CONCLUSION Our findings emphasise the close and complex links between the endocrine controls, well known to play an important role in prostate cancer, and the transcription factors implicated by the recent genetic evidence.
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Affiliation(s)
- Rachel Barker
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Kalina Biernacka
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Georgina Kingshott
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - Alex Sewell
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK
| | - Paida Gwiti
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK; Department of Pathology, North West Anglia NHS Foundation Trust, Peterborough PE3 9GZ, UK
| | - Richard M Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK; National Institute for Health Research, Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Biomedical Research Unit Offices, University Hospitals Bristol Education Centre, Dental Hospital, Lower Maudlin Street, Bristol BS1 2LY, UK
| | - J Athene Lane
- Bristol Trials Centre, Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK
| | - Lucy McGeagh
- Supportive Cancer Care Research Group, Faculty of Health and Life Sciences, Oxford Institute of Nursing, Midwifery and Allied Health Research, Oxford Brookes University, Jack Straws Lane, Marston, Oxford OX3 0FL, UK
| | - Anthony Koupparis
- Department of Urology, Bristol Urological Institute, Southmead Hospital, Bristol BS10 5NB, UK
| | - Edward Rowe
- Department of Urology, Bristol Urological Institute, Southmead Hospital, Bristol BS10 5NB, UK
| | - Jon Oxley
- Department of Cellular Pathology, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK
| | - Claire M Perks
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK.
| | - Jeff M P Holly
- IGF & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK
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9
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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10
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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.
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Bound NT, Vandenberg CJ, Kartikasari AER, Plebanski M, Scott CL. Improving PARP inhibitor efficacy in high-grade serous ovarian carcinoma: A focus on the immune system. Front Genet 2022; 13:886170. [PMID: 36159999 PMCID: PMC9505691 DOI: 10.3389/fgene.2022.886170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is a genomically unstable malignancy responsible for over 70% of all deaths due to ovarian cancer. With roughly 50% of all HGSOC harboring defects in the homologous recombination (HR) DNA repair pathway (e.g., BRCA1/2 mutations), the introduction of poly ADP-ribose polymerase inhibitors (PARPi) has dramatically improved outcomes for women with HR defective HGSOC. By blocking the repair of single-stranded DNA damage in cancer cells already lacking high-fidelity HR pathways, PARPi causes the accumulation of double-stranded DNA breaks, leading to cell death. Thus, this synthetic lethality results in PARPi selectively targeting cancer cells, resulting in impressive efficacy. Despite this, resistance to PARPi commonly develops through diverse mechanisms, such as the acquisition of secondary BRCA1/2 mutations. Perhaps less well documented is that PARPi can impact both the tumour microenvironment and the immune response, through upregulation of the stimulator of interferon genes (STING) pathway, upregulation of immune checkpoints such as PD-L1, and by stimulating the production of pro-inflammatory cytokines. Whilst targeted immunotherapies have not yet found their place in the clinic for HGSOC, the evidence above, as well as ongoing studies exploring the synergistic effects of PARPi with immune agents, including immune checkpoint inhibitors, suggests potential for targeting the immune response in HGSOC. Additionally, combining PARPi with epigenetic-modulating drugs may improve PARPi efficacy, by inducing a BRCA-defective phenotype to sensitise resistant cancer cells to PARPi. Finally, invigorating an immune response during PARPi therapy may engage anti-cancer immune responses that potentiate efficacy and mitigate the development of PARPi resistance. Here, we will review the emerging PARPi literature with a focus on PARPi effects on the immune response in HGSOC, as well as the potential of epigenetic combination therapies. We highlight the potential of transforming HGSOC from a lethal to a chronic disease and increasing the likelihood of cure.
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Affiliation(s)
- Nirashaa T. Bound
- Cancer Biology and Stem Cells, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Cancer Ageing and Vaccines (CAVA), Translational Immunology & Nanotechnology Research Program, School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Cassandra J. Vandenberg
- Cancer Biology and Stem Cells, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Apriliana E. R. Kartikasari
- Cancer Ageing and Vaccines (CAVA), Translational Immunology & Nanotechnology Research Program, School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Magdalena Plebanski
- Cancer Ageing and Vaccines (CAVA), Translational Immunology & Nanotechnology Research Program, School of Health & Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Clare L. Scott
- Cancer Biology and Stem Cells, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
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12
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Zong W, Gong Y, Sun W, Li T, Wang ZQ. PARP1: Liaison of Chromatin Remodeling and Transcription. Cancers (Basel) 2022; 14:cancers14174162. [PMID: 36077699 PMCID: PMC9454564 DOI: 10.3390/cancers14174162] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a covalent post-translational modification and plays a key role in the immediate response of cells to stress signals. Poly(ADP-ribose) polymerase 1 (PARP1), the founding member of the PARP superfamily, synthesizes long and branched polymers of ADP-ribose (PAR) onto acceptor proteins, thereby modulating their function and their local surrounding. PARP1 is the most prominent of the PARPs and is responsible for the production of about 90% of PAR in the cell. Therefore, PARP1 and PARylation play a pleotropic role in a wide range of cellular processes, such as DNA repair and genomic stability, cell death, chromatin remodeling, inflammatory response and gene transcription. PARP1 has DNA-binding and catalytic activities that are important for DNA repair, yet also modulate chromatin conformation and gene transcription, which can be independent of DNA damage response. PARP1 and PARylation homeostasis have also been implicated in multiple diseases, including inflammation, stroke, diabetes and cancer. Studies of the molecular action and biological function of PARP1 and PARylation provide a basis for the development of pharmaceutic strategies for clinical applications. This review focuses primarily on the role of PARP1 in the regulation of chromatin remodeling and transcriptional activation.
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Affiliation(s)
- Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Correspondence: (W.Z.); or (Z.-Q.W.)
| | - Yamin Gong
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- College of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, 07743 Jena, Germany
- Correspondence: (W.Z.); or (Z.-Q.W.)
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13
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Varghese CS, Parish JL, Ferguson J. Lying low-chromatin insulation in persistent DNA virus infection. Curr Opin Virol 2022; 55:101257. [PMID: 35998396 DOI: 10.1016/j.coviro.2022.101257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/08/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022]
Abstract
Persistent virus infections are achieved when the intricate balance of virus replication, host-cell division and successful immune evasion is met. The genomes of persistent DNA viruses are either maintained as extrachromosomal episomes or can integrate into the host genome. Common to both these strategies of persistence is the chromatinisation of viral DNA by cellular histones which, like host DNA, are subject to epigenetic modification. Epigenetic repression of viral genes required for lytic replication occurs, while genes required for latent or persistent infection are maintained in an active chromatin state. Viruses utilise host-cell chromatin insulators, which function to maintain epigenetic boundaries and enforce this strict transcriptional programme. Here, we review insulator protein function in virus transcription control, focussing on CCCTC-binding factor (CTCF) and cofactors. We describe CTCF-dependent activities in virus transcription regulation through epigenetic and promoter-enhancer insulation, three-dimensional chromatin looping and manipulation of transcript splicing.
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Affiliation(s)
- Christy S Varghese
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, UK
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, UK.
| | - Jack Ferguson
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2TT, UK
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14
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Human PARP1 Facilitates Transcription through a Nucleosome and Histone Displacement by Pol II In Vitro. Int J Mol Sci 2022; 23:ijms23137107. [PMID: 35806109 PMCID: PMC9266421 DOI: 10.3390/ijms23137107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Human poly(ADP)-ribose polymerase-1 (PARP1) is a global regulator of various cellular processes, from DNA repair to gene expression. The underlying mechanism of PARP1 action during transcription remains unclear. Herein, we have studied the role of human PARP1 during transcription through nucleosomes by RNA polymerase II (Pol II) in vitro. PARP1 strongly facilitates transcription through mononucleosomes by Pol II and displacement of core histones in the presence of NAD+ during transcription, and its NAD+-dependent catalytic activity is essential for this process. Kinetic analysis suggests that PARP1 facilitates formation of “open” complexes containing nucleosomal DNA partially uncoiled from the octamer and allowing Pol II progression along nucleosomal DNA. Anti-cancer drug and PARP1 catalytic inhibitor olaparib strongly represses PARP1-dependent transcription. The data suggest that the negative charge on protein(s) poly(ADP)-ribosylated by PARP1 interact with positively charged DNA-binding surfaces of histones transiently exposed during transcription, facilitating transcription through chromatin and transcription-dependent histone displacement/exchange.
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15
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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.
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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
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16
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A Long-Lasting PARP1-Activation Mediates Signal-Induced Gene Expression. Cells 2022; 11:cells11091576. [PMID: 35563882 PMCID: PMC9101275 DOI: 10.3390/cells11091576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
This overview presents recent evidence for a long-lasting PARP1 activation by a variety of signal transduction mechanisms, mediating signal-induced gene expression and chromatin remodeling. This mode of PARP1 activation has been reported in a variety of cell types, under physiological conditions. In this mechanism, PARP1 is not transiently activated by binding to DNA breaks. Moreover, damaged DNA interfered with this long-lasting PARP1 activation.
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17
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Yuan Z, Ge L, Zhang W, Lv X, Wang S, Cao X, Sun W. Preliminary Results about Lamb Meat Tenderness Based on the Study of Novel Isoforms and Alternative Splicing Regulation Pathways Using Iso-seq, RNA-seq and CTCF ChIP-seq Data. Foods 2022; 11:foods11081068. [PMID: 35454655 PMCID: PMC9025809 DOI: 10.3390/foods11081068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 01/27/2023] Open
Abstract
Tenderness is an important indicator of meat quality. Novel isoforms associated with meat tenderness and the role of the CCCTC-binding factor (CTCF) in regulating alternative splicing to produce isoforms in sheep are largely unknown. The current project studied six sheep from two crossbred populations (Dorper × Hu × Hu, DHH and Dorper × Dorper × Hu, DDH) with divergent meat tenderness. Pooled Iso-seq data were used to annotate the sheep genomes. Then, the updated genome annotation and six RNA-seq data were combined to identify differentially expressed isoforms (DEIs) in muscles between DHH and DDH. These data were also combined with peaks detected from CTCF ChIP-seq data to investigate the regulatory role of CTCF for the alternative splicing. As a result, a total of 624 DEIs were identified between DDH and DHH. For example, isoform 7.524.18 transcribed from CAPN3 may be associated with meat tenderness. In addition, a total of 86 genes were overlapped between genes with transcribed DEIs and genes in differential peaks identified by CTCF ChIP-seq. Among these overlapped genes, ANKRD23 produces different isoforms which may be regulated by CTCF via methylation. As preliminary research, our results identified novel isoforms associated with meat tenderness and revealed the possible regulating mechanisms of alternative splicing to produce isoforms.
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Affiliation(s)
- Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Weibo Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
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18
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Huang D, Kraus WL. The expanding universe of PARP1-mediated molecular and therapeutic mechanisms. Mol Cell 2022; 82:2315-2334. [PMID: 35271815 DOI: 10.1016/j.molcel.2022.02.021] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022]
Abstract
ADP-ribosylation (ADPRylation) is a post-translational modification of proteins catalyzed by ADP-ribosyl transferase (ART) enzymes, including nuclear PARPs (e.g., PARP1 and PARP2). Historically, studies of ADPRylation and PARPs have focused on DNA damage responses in cancers, but more recent studies elucidate diverse roles in a broader array of biological processes. Here, we summarize the expanding array of molecular mechanisms underlying the biological functions of nuclear PARPs with a focus on PARP1, the founding member of the family. This includes roles in DNA repair, chromatin regulation, gene expression, ribosome biogenesis, and RNA biology. We also present new concepts in PARP1-dependent regulation, including PAR-dependent post-translational modifications, "ADPR spray," and PAR-mediated biomolecular condensate formation. Moreover, we review advances in the therapeutic mechanisms of PARP inhibitors (PARPi) as well as the progress on the mechanisms of PARPi resistance. Collectively, the recent progress in the field has yielded new insights into the expanding universe of PARP1-mediated molecular and therapeutic mechanisms in a variety of biological processes.
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Affiliation(s)
- Dan Huang
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China.
| | - 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, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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19
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Dugar G, Hofmann A, Heermann DW, Hamoen LW. A chromosomal loop anchor mediates bacterial genome organization. Nat Genet 2022; 54:194-201. [PMID: 35075232 DOI: 10.1038/s41588-021-00988-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/19/2021] [Indexed: 12/22/2022]
Abstract
Nucleoprotein complexes play an integral role in genome organization of both eukaryotes and prokaryotes. Apart from their role in locally structuring and compacting DNA, several complexes are known to influence global organization by mediating long-range anchored chromosomal loop formation leading to spatial segregation of large sections of DNA. Such megabase-range interactions are ubiquitous in eukaryotes, but have not been demonstrated in prokaryotes. Here, using a genome-wide sedimentation-based approach, we found that a transcription factor, Rok, forms large nucleoprotein complexes in the bacterium Bacillus subtilis. Using chromosome conformation capture and live-imaging of DNA loci, we show that these complexes robustly interact with each other over large distances. Importantly, these Rok-dependent long-range interactions lead to anchored chromosomal loop formation, thereby spatially isolating large sections of DNA, as previously observed for insulator proteins in eukaryotes.
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Affiliation(s)
- Gaurav Dugar
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| | - Andreas Hofmann
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Dieter W Heermann
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Leendert W Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
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20
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Alharbi AB, Schmitz U, Bailey CG, Rasko JEJ. CTCF as a regulator of alternative splicing: new tricks for an old player. Nucleic Acids Res 2021; 49:7825-7838. [PMID: 34181707 PMCID: PMC8373115 DOI: 10.1093/nar/gkab520] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Three decades of research have established the CCCTC-binding factor (CTCF) as a ubiquitously expressed chromatin organizing factor and master regulator of gene expression. A new role for CTCF as a regulator of alternative splicing (AS) has now emerged. CTCF has been directly and indirectly linked to the modulation of AS at the individual transcript and at the transcriptome-wide level. The emerging role of CTCF-mediated regulation of AS involves diverse mechanisms; including transcriptional elongation, DNA methylation, chromatin architecture, histone modifications, and regulation of splicing factor expression and assembly. CTCF thereby appears to not only co-ordinate gene expression regulation but contributes to the modulation of transcriptomic complexity. In this review, we highlight previous discoveries regarding the role of CTCF in AS. In addition, we summarize detailed mechanisms by which CTCF mediates AS regulation. We propose opportunities for further research designed to examine the possible fate of CTCF-mediated alternatively spliced genes and associated biological consequences. CTCF has been widely acknowledged as the 'master weaver of the genome'. Given its multiple connections, further characterization of CTCF's emerging role in splicing regulation might extend its functional repertoire towards a 'conductor of the splicing orchestra'.
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Affiliation(s)
- Adel B Alharbi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
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21
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Cheng X, Joseph A, Castro V, Chen-Liaw A, Skidmore Z, Ueno T, Fujisawa JI, Rauch DA, Challen GA, Martinez MP, Green P, Griffith M, Payton JE, Edwards JR, Ratner L. Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF. PLoS Pathog 2021; 17:e1009577. [PMID: 34019588 PMCID: PMC8174705 DOI: 10.1371/journal.ppat.1009577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 06/03/2021] [Accepted: 04/22/2021] [Indexed: 11/30/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus that causes an aggressive T-cell malignancy and a variety of inflammatory conditions. The integrated provirus includes a single binding site for the epigenomic insulator, CCCTC-binding protein (CTCF), but its function remains unclear. In the current study, a mutant virus was examined that eliminates the CTCF-binding site. The mutation did not disrupt the kinetics and levels of virus gene expression, or establishment of or reactivation from latency. However, the mutation disrupted the epigenetic barrier function, resulting in enhanced DNA CpG methylation downstream of the CTCF binding site on both strands of the integrated provirus and H3K4Me3, H3K36Me3, and H3K27Me3 chromatin modifications both up- and downstream of the site. A majority of clonal cell lines infected with wild type HTLV-1 exhibited increased plus strand gene expression with CTCF knockdown, while expression in mutant HTLV-1 clonal lines was unaffected. These findings indicate that CTCF binding regulates HTLV-1 gene expression, DNA and histone methylation in an integration site dependent fashion. Human T-cell leukemia virus type 1 (HTLV-1) is a cause of leukemia and lymphoma as well as several inflammatory medical disorders. The virus integrates in the host cell DNA, and it has a single binding site for a protein designated CTCF. This protein is important in the regulation of many DNA viruses, as well as many properties of normal and malignant cells. In order to define the role of CTCF binding to HTLV, we analyzed a mutant virus lacking the binding site. We found that this mutation variably affected gene expression, DNA and histone modification, suggesting a key role in regulation of virus replication in infected cells.
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Affiliation(s)
- Xiaogang Cheng
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ancy Joseph
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Victor Castro
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Alice Chen-Liaw
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Zachary Skidmore
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Takaharu Ueno
- Department of Microbiology, Kansai Medical University, Osaka, Japan
| | | | - Daniel A. Rauch
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Grant A. Challen
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Michael P. Martinez
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Patrick Green
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jacqueline E. Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - John R. Edwards
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Phamacogenomics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Lee Ratner
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
- * E-mail:
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22
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Zampieri M, Bacalini MG, Barchetta I, Scalea S, Cimini FA, Bertoccini L, Tagliatesta S, De Matteis G, Zardo G, Cavallo MG, Reale A. Increased PARylation impacts the DNA methylation process in type 2 diabetes mellitus. Clin Epigenetics 2021; 13:114. [PMID: 34001206 PMCID: PMC8130175 DOI: 10.1186/s13148-021-01099-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
Background Epigenetic modifications, such as DNA methylation, can influence the genetic susceptibility to type 2 diabetes mellitus (T2DM) and the progression of the disease. Our previous studies demonstrated that the regulation of the DNA methylation pattern involves the poly(ADP-ribosyl)ation (PARylation) process, a post-translational modification of proteins catalysed by the poly(ADP-ribose) polymerase (PARP) enzymes. Experimental data showed that the hyperactivation of PARylation is associated with impaired glucose metabolism and the development of T2DM. Aims of this case–control study were to investigate the association between PARylation and global and site-specific DNA methylation in T2DM and to evaluate metabolic correlates. Results Data were collected from 61 subjects affected by T2DM and 48 healthy individuals, recruited as controls. Global levels of poly(ADP-ribose) (PAR, a surrogate of PARP activity), cytosine methylation (5-methylcytosine, 5mC) and de-methylation intermediates 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) were determined in peripheral blood cells by ELISA-based methodologies. Site-specific DNA methylation profiling of SOCS3, SREBF1 and TXNIP candidate genes was performed by mass spectrometry-based bisulfite sequencing, methyl-sensitive endonucleases digestion and by DNA immuno-precipitation. T2DM subjects presented higher PAR levels than controls. In T2DM individuals, increased PAR levels were significantly associated with higher HbA1c levels and the accumulation of the de-methylation intermediates 5hmC and 5fC in the genome. In addition, T2DM patients with higher PAR levels showed reduced methylation with increased 5hmC and 5fC levels in specific SOCS3 sites, up-regulated SOCS3 expression compared to both T2DM subjects with low PAR levels and controls. Conclusions This study demonstrates the activation of PARylation processes in patients with T2DM, particularly in those with poor glycaemic control. PARylation is linked to dysregulation of DNA methylation pattern via activation of the DNA de-methylation cascade and may be at the basis of the differential gene expression observed in presence of diabetes. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01099-1.
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Affiliation(s)
- Michele Zampieri
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | | | - Ilaria Barchetta
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Stefania Scalea
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Flavia Agata Cimini
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Laura Bertoccini
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Stefano Tagliatesta
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Giovanna De Matteis
- Research Centre for Animal Production and Aquaculture, Consiglio Per La Ricerca in Agricoltura E L'Analisi Dell'Economia Agraria (CREA), 00015, Monterotondo, Italy
| | - Giuseppe Zardo
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy
| | - Maria Gisella Cavallo
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy.
| | - Anna Reale
- Department of Experimental Medicine, Faculty of Medicine and Dentistry, Sapienza University of Rome, 00161, Rome, Italy.
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23
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Ummarino S, Hausman C, Di Ruscio A. The PARP Way to Epigenetic Changes. Genes (Basel) 2021; 12:446. [PMID: 33804735 PMCID: PMC8003872 DOI: 10.3390/genes12030446] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022] Open
Abstract
ADP-ribosylation, is a reversible post-translational modification implicated in major biological functions. Poly ADP-ribose polymerases (PARP) are specialized enzymes that catalyze the addition of ADP ribose units from "nicotinamide adenine dinucleotide-donor molecules" to their target substrates. This reaction known as PARylation modulates essential cellular processes including DNA damage response, chromatin remodeling, DNA methylation and gene expression. Herein, we discuss emerging roles of PARP1 in chromatin remodeling and epigenetic regulation, focusing on its therapeutic implications for cancer treatment and beyond.
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Affiliation(s)
- Simone Ummarino
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
| | - Clinton Hausman
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
| | - Annalisa Di Ruscio
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA;
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
- Beth Israel Deaconess Medical Center, Cancer Research Institute, Boston, MA 02215, USA
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24
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Eleazer R, Fondufe‐Mittendorf YN. The multifaceted role of PARP1 in RNA biogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1617. [PMID: 32656996 PMCID: PMC7856298 DOI: 10.1002/wrna.1617] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/11/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022]
Abstract
Poly(ADP-ribose) polymerases (PARPs) are abundant nuclear proteins that synthesize ADP ribose polymers (pADPr) and catalyze the addition of (p)ADPr to target biomolecules. PARP1, the most abundant and well-studied PARP, is a multifunctional enzyme that participates in numerous critical cellular processes. A considerable amount of PARP research has focused on PARP1's role in DNA damage. However, an increasing body of evidence outlines more routine roles for PARP and PARylation in nearly every step of RNA biogenesis and metabolism. PARP1's involvement in these RNA processes is pleiotropic and has been ascribed to PARP1's unique flexible domain structures. PARP1 domains are modular self-arranged enabling it to recognize structurally diverse substrates and to act simultaneously through multiple discrete mechanisms. These mechanisms include direct PARP1-protein binding, PARP1-nucleic acid binding, covalent PARylation of target molecules, covalent autoPARylation, and induction of noncovalent interactions with PAR molecules. A combination of these mechanisms has been implicated in PARP1's context-specific regulation of RNA biogenesis and metabolism. We examine the mechanisms of PARP1 regulation in transcription initiation, elongation and termination, co-transcriptional splicing, RNA export, and post-transcriptional RNA processing. Finally, we consider promising new investigative avenues for PARP1 involvement in these processes with an emphasis on PARP1 regulation of subcellular condensates. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Rebekah Eleazer
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Yvonne N. Fondufe‐Mittendorf
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
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25
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Luo X, Zhang T, Zhai Y, Wang F, Zhang S, Wang G. Effects of DNA Methylation on TFs in Human Embryonic Stem Cells. Front Genet 2021; 12:639461. [PMID: 33708244 PMCID: PMC7940757 DOI: 10.3389/fgene.2021.639461] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/14/2021] [Indexed: 12/24/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism for gene regulation. The conventional view of DNA methylation is that DNA methylation could disrupt protein-DNA interactions and repress gene expression. Several recent studies reported that DNA methylation could alter transcription factors (TFs) binding sequence specificity in vitro. Here, we took advantage of the large sets of ChIP-seq data for TFs and whole-genome bisulfite sequencing data in many cell types to perform a systematic analysis of the protein-DNA methylation in vivo. We observed that many TFs could bind methylated DNA regions, especially in H1-hESC cells. By locating binding sites, we confirmed that some TFs could bind to methylated CpGs directly. The different proportion of CpGs at TF binding specificity motifs in different methylation statuses shows that some TFs are sensitive to methylation and some could bind to the methylated DNA with different motifs, such as CEBPB and CTCF. At the same time, TF binding could interactively alter local DNA methylation. The TF hypermethylation binding sites extensively overlap with enhancers. And we also found that some DNase I hypersensitive sites were specifically hypermethylated in H1-hESC cells. At last, compared with TFs' binding regions in multiple cell types, we observed that CTCF binding to high methylated regions in H1-hESC were not conservative. These pieces of evidence indicate that TFs that bind to hypermethylation DNA in H1-hESC cells may associate with enhancers to regulate special biological functions.
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Affiliation(s)
- Ximei Luo
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Tianjiao Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yixiao Zhai
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China
| | - Fang Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Shumei Zhang
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China
| | - Guohua Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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26
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Köritzer J, Blenn C, Bürkle A, Beneke S. Mitochondria are devoid of poly(ADP-ribose)polymerase-1, but harbor its product oligo(ADP-ribose). J Cell Biochem 2021; 122:507-523. [PMID: 33417272 DOI: 10.1002/jcb.29887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022]
Abstract
There are conflicting data about localization of poly(ADP-ribose)polymerase-1 and its product poly(ADP-ribose) in mitochondria. To finally clarify the discussion, we investigated with biochemical and cell biological methods the potential presence of poly(ADP-ribose) polymerase-1 in these organelles. Our data show that endogenous and overexpressed poly(ADP-ribose)polymerase 1 is only localized to the nucleus with a clear exclusion of cytosolic compartments. In addition, highly purified mitochondria devoid of nuclear contaminations do not contain poly(ADP-ribose)polymerase-1. Although no poly(ADP-ribose)polymerase-1 enzyme is detectable in mitochondria, a shorter variant of its product poly(ADP-ribose) is present, associated specifically with a small subset of mitochondrial proteins as revealed by immunoprecipitation and protein fingerprint analysis. These proteins are located at key-points of the Krebs-cycle, are chaperones involved in mitochondrial functionality and quality-control, and are RNA-binding proteins important for transcript stability, respectively. Of note, despite the fact that especially poly(ADP-ribose)polymerase-1 is its own major target for modification, we could not detect this enzyme by mass spectrometry in these organelles. These data suggests a new way of targeted nuclear-mitochondrial signaling, mediated by nuclear poly(ADP-ribosyl)ation dependent on poly(ADP-ribose)polymerase-1.
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Affiliation(s)
- Julia Köritzer
- Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Christian Blenn
- Institute of Pharmacology and Toxicology, University of Zurich/Vetsuisse, Zurich, Switzerland
| | - Alexander Bürkle
- Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Sascha Beneke
- Molecular Toxicology Group, University of Konstanz, Konstanz, Germany.,Human and Environmental Toxicology Group, University of Konstanz, Konstanz, Germany
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27
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Xie N, Zhang L, Gao W, Huang C, Huber PE, Zhou X, Li C, Shen G, Zou B. NAD + metabolism: pathophysiologic mechanisms and therapeutic potential. Signal Transduct Target Ther 2020; 5:227. [PMID: 33028824 PMCID: PMC7539288 DOI: 10.1038/s41392-020-00311-7] [Citation(s) in RCA: 372] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) and its metabolites function as critical regulators to maintain physiologic processes, enabling the plastic cells to adapt to environmental changes including nutrient perturbation, genotoxic factors, circadian disorder, infection, inflammation and xenobiotics. These effects are mainly achieved by the driving effect of NAD+ on metabolic pathways as enzyme cofactors transferring hydrogen in oxidation-reduction reactions. Besides, multiple NAD+-dependent enzymes are involved in physiology either by post-synthesis chemical modification of DNA, RNA and proteins, or releasing second messenger cyclic ADP-ribose (cADPR) and NAADP+. Prolonged disequilibrium of NAD+ metabolism disturbs the physiological functions, resulting in diseases including metabolic diseases, cancer, aging and neurodegeneration disorder. In this review, we summarize recent advances in our understanding of the molecular mechanisms of NAD+-regulated physiological responses to stresses, the contribution of NAD+ deficiency to various diseases via manipulating cellular communication networks and the potential new avenues for therapeutic intervention.
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Affiliation(s)
- Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Lu Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Wei Gao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Peter Ernst Huber
- CCU Molecular and Radiation Oncology, German Cancer Research Center; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Xiaobo Zhou
- First Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Changlong Li
- West China School of Basic Medical Sciences & Forensic Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guobo Shen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
| | - Bingwen Zou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
- CCU Molecular and Radiation Oncology, German Cancer Research Center; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.
- Department of Thoracic Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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28
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Hu G, Dong X, Gong S, Song Y, Hutchins AP, Yao H. Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions. Nucleic Acids Res 2020; 48:9606-9620. [PMID: 32885250 PMCID: PMC7515718 DOI: 10.1093/nar/gkaa705] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 07/27/2020] [Accepted: 08/14/2020] [Indexed: 11/14/2022] Open
Abstract
CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators by co-localization analysis with CTCF. We screened all factors that had ChIP-seq data in humans by co-localization analysis with human super conserved CTCF (hscCTCF) binding sites, and identified many new factors that overlapped with hscCTCF binding sites. Combined with CTCF loop information, we observed that clustered factors could promote CTCF loops. After in-depth mining of each factor, we found that many factors might have the potential to promote CTCF loops. Our data further demonstrated that BHLHE40 affected CTCF loops by regulating CTCF binding. Together, this study revealed that many factors have the potential to participate in or regulate CTCF loops, and discovered a new role for BHLHE40 in modulating CTCF loop formation.
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Affiliation(s)
- Gongcheng Hu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaotao Dong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shixin Gong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yawei Song
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Damaschke NA, Gawdzik J, Avilla M, Yang B, Svaren J, Roopra A, Luo JH, Yu YP, Keles S, Jarrard DF. CTCF loss mediates unique DNA hypermethylation landscapes in human cancers. Clin Epigenetics 2020; 12:80. [PMID: 32503656 PMCID: PMC7275597 DOI: 10.1186/s13148-020-00869-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
Background The chromatin insulator CCCTC-binding factor (CTCF) displays tissue-specific DNA binding sites that regulate transcription and chromatin organization. Despite evidence linking CTCF to the protection of epigenetic states through barrier insulation, the impact of CTCF loss on genome-wide DNA methylation sites in human cancer remains undefined. Results Here, we demonstrate that prostate and breast cancers within The Cancer Genome Atlas (TCGA) exhibit frequent copy number loss of CTCF and that this loss is associated with increased DNA methylation events that occur preferentially at CTCF binding sites. CTCF sites differ among tumor types and result in tissue-specific methylation patterns with little overlap between breast and prostate cancers. DNA methylation and transcriptome profiling in vitro establish that forced downregulation of CTCF leads to spatially distinct DNA hypermethylation surrounding CTCF binding sites, loss of CTCF binding, and decreased gene expression that is also seen in human tumors. DNA methylation inhibition reverses loss of expression at these CTCF-regulated genes. Conclusion These findings establish CTCF loss as a major mediator in directing localized DNA hypermethylation events in a tissue-specific fashion and further support its role as a driver of the cancer phenotype.
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Affiliation(s)
- Nathan A Damaschke
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Joseph Gawdzik
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Mele Avilla
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Bing Yang
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - John Svaren
- Waisman Center and Department of Comparative Biosciences, University of Wisconsin, Madison, WI, USA
| | - Avtar Roopra
- Department of Neuroscience, University of Wisconsin, Madison, WI, USA
| | - Jian-Hua Luo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yan P Yu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sunduz Keles
- Department of Biostatistic and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - David F Jarrard
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA. .,University of Wisconsin Carbone Comprehensive Cancer Center, Madison, WI, USA. .,Environmental and Molecular Toxicology, University of Wisconsin, Madison, WI, USA. .,7037 Wisconsin Institute for Medical Research, 1111 Highland Avenue, Madison, WI, 53705, USA.
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30
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Habieb MSED, Younis FE, Safan M, Allam HK. PARP1-DNMT1-CTCF complex and the apoptotic-induced factor mRNA expressions in workers occupationally exposed to benzene. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:22648-22657. [PMID: 32319058 DOI: 10.1007/s11356-020-08614-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Exposure to benzene is a common occupational hazard as well as a hematopoietic system intoxicant, but the entire picture of its molecular pathogenesis is still hazy. Its leukemogenic effect could be attributed to DNA damage, decreased repair capacity, altered methylation patterns, and defective apoptosis. Poly ADP-ribose polymerase1, DNA methyltransferase1, and CCCTC-binding factor (PARP1-DNMT1-CTCF) complex play an essential role in methylation maintenance and DNA damage repair response. This study aimed to assess the expression of PARP1, PAR glycohydrolases (PARG), DNMT1, CTCF, and apoptosis-inducing factor (AIF) in subjects occupationally exposed to benzene. A total of 200 subjects were enrolled in this study: 100 workers occupationally exposed to benzene (painters and decorators) and 100 unexposed office workers. Occupational exposure data were obtained. The biochemical and hematological evaluations were done. Quantitative reverse transcription polymerase chain reaction (RT-PCR) was used to assess mRNA expression of PARP1, PARG, DNMT1, CTCF, and AIF. Both biochemical and hematological parameters were within normal limits; workplace benzene air concentration was significantly higher in exposed workers than the levels among controls (P < 0.001). Significant decrease in mRNA levels of PARP1, DNMT1, CTCF, and AIF was noticed among the exposed group (P = 0.01, P < 0.001, P = 0.004, P < 0.001, respectively) in comparison with the control group, while PARG showed non-significant difference (P = 0.16). There was a significant negative correlation between workplace benzene air concentration and expression levels of PARP1, DNMT1, and AIF. The reduced expression of PARP1, DNMT1, CTCF, and AIF observed in exposed workers may represent one of the first benzene-induced changes that might threaten erythropoiesis.
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Affiliation(s)
- Mona Salah El-Din Habieb
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin Al-Kom, Menoufia, Egypt
| | - Faten Ezzelarab Younis
- Department of Public Health and Community Medicine, Faculty of Medicine, Menoufia University, Shebin Al-Kom, Menoufia, Egypt
| | - Manal Safan
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin Al-Kom, Menoufia, Egypt
| | - Heba Khodary Allam
- Department of Public Health and Community Medicine, Faculty of Medicine, Menoufia University, Shebin Al-Kom, Menoufia, Egypt.
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31
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Sutcu HH, Matta E, Ishchenko AA. Role of PARP-catalyzed ADP-ribosylation in the Crosstalk Between DNA Strand Breaks and Epigenetic Regulation. J Mol Biol 2019:S0022-2836(19)30719-3. [PMID: 31866292 DOI: 10.1016/j.jmb.2019.12.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022]
Abstract
Covalent linkage of ADP-ribose units to proteins catalyzed by poly(ADP-ribose) polymerases (PARPs) plays important signaling functions in a plethora of cellular processes including DNA damage response, chromatin organization, and gene transcription. Poly- and mono-ADP-ribosylation of target macromolecules are often responsible both for the initiation and for coordination of these processes in mammalian cells. Currently, the number of cellular targets for ADP-ribosylation is rapidly expanding, and the molecular mechanisms underlying the broad substrate specificity of PARPs present enormous interest. In this review, the roles of PARP-mediated modifications of protein and nucleic acids, the readers of ADP-ribosylated structures, and the origin and function of programmed DNA strand breaks in PARP activation, transcription regulation, and DNA demethylation are discussed.
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Affiliation(s)
- Haser H Sutcu
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Elie Matta
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France.
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32
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Höflmayer D, Steinhoff A, Hube-Magg C, Kluth M, Simon R, Burandt E, Tsourlakis MC, Minner S, Sauter G, Büscheck F, Wilczak W, Steurer S, Huland H, Graefen M, Haese A, Heinzer H, Schlomm T, Jacobsen F, Hinsch A, Poos AM, Oswald M, Rippe K, König R, Schroeder C. Expression of CCCTC-binding factor (CTCF) is linked to poor prognosis in prostate cancer. Mol Oncol 2019; 14:129-138. [PMID: 31736271 DOI: 10.1002/1878-0261.12597] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 01/06/2023] Open
Abstract
The chromatin-organizing factor CCCTC-binding factor (CTCF) is involved in transcriptional regulation, DNA-loop formation, and telomere maintenance. To evaluate the clinical impact of CTCF in prostate cancer, we analyzed CTCF expression by immunohistochemistry on a tissue microarray containing 17 747 prostate cancers. Normal prostate tissue showed negative to low CTCF expression, while in prostate cancers, CTCF expression was seen in 7726 of our 12 555 (61.5%) tumors and was considered low in 44.6% and high in 17% of cancers. Particularly, high CTCF expression was significantly associated with the presence of the transmembrane protease, serine 2:ETS-related gene fusion: Only 10% of ERG-negative cancers, but 30% of ERG-positive cancers had high-level CTCF expression (P < 0.0001). CTCF expression was significantly associated with advanced pathological tumor stage, high Gleason grade (P < 0.0001 each), nodal metastasis (P = 0.0122), and early biochemical recurrence (P < 0.0001). Multivariable modeling revealed that the prognostic impact of CTCF was independent from established presurgical parameters such as clinical stage and Gleason grade of the biopsy. Comparison with key molecular alterations showed strong associations with the expression of the Ki-67 proliferation marker and presence of phosphatase and tensin homolog deletions (P < 0.0001 each). The results of our study identify CTCF expression as a candidate biomarker for prognosis assessment in prostate cancer.
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Affiliation(s)
- Doris Höflmayer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Amélie Steinhoff
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | | | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Franziska Büscheck
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Alexander Haese
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Hans Heinzer
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Germany
| | - Thorsten Schlomm
- Department of Urology, Charité - Universitätsmedizin Berlin, Germany
| | - Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Andrea Hinsch
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Germany
| | - Alexandra M Poos
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biosciences, Heidelberg University, Germany.,Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Cornelia Schroeder
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, Germany
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33
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Evidence for Decreased Nucleolar PARP-1 as an Early Marker of Cognitive Impairment. Neural Plast 2019; 2019:4383258. [PMID: 31827497 PMCID: PMC6885846 DOI: 10.1155/2019/4383258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 09/11/2019] [Accepted: 10/01/2019] [Indexed: 11/21/2022] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a nuclear protein that regulates gene expression through poly(ADP)-ribosylation, resulting in the loosening of chromatin structure. PARP-1 enzymatic activity has been shown to be necessary for the expression of several genes required for memory formation and consolidation. Previously, we showed that nucleolar PARP-1 is significantly decreased in hippocampal pyramidal cells in Alzheimer's disease (AD). We proposed that the displacement of PARP-1 from the nucleolus results in downregulation of new rRNA expression and ribosome biogenesis, leading to cognitive impairment. To further investigate the relationship between nucleolar PARP-1 and memory impairment, we examined PARP-1 expression in the hippocampi of individuals with mild cognitive impairment (MCI) compared to control and AD cases. We used immunohistochemical techniques to examine the nucleolar distribution of PARP-1 in the Cornu Ammonis (CA region) of the hippocampus. PARP-1 positive cells were then scored for the presence or absence of PARP-1 in the nucleolus. We found a significant decrease of PARP-1 staining in the nucleolar compartment of hippocampal pyramidal cells in MCI compared with Control and AD. When the four CA (CA1-4) regions were considered separately, only the CA1 region showed significant differences in nucleolar PARP-1 with Control > AD > MCI cases. Categorization of nucleolar PARP-1 into “distinct” and “diffuse” groups suggest that most of the changes occur within the distinct group. In addition, measurements of the nucleolar diameter of nucleolar PARP-1 positive cells in CA2 and CA4 showed Control > MCI. Thus, MCI cases had a lower percentage of PARP-1 nucleolar positive cells in CA1 and smaller nucleolar diameters in CA2 and CA4, compared to Control. Our data suggest that disruption of nucleolar form and function is an early and important step in the progression of cognitive impairment.
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Nanan KK, Sturgill DM, Prigge MF, Thenoz M, Dillman AA, Mandler MD, Oberdoerffer S. TET-Catalyzed 5-Carboxylcytosine Promotes CTCF Binding to Suboptimal Sequences Genome-wide. iScience 2019; 19:326-339. [PMID: 31404833 PMCID: PMC6699469 DOI: 10.1016/j.isci.2019.07.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/23/2019] [Accepted: 07/25/2019] [Indexed: 01/01/2023] Open
Abstract
The mechanisms supporting dynamic regulation of CTCF-binding sites remain poorly understood. Here we describe the TET-catalyzed 5-methylcytosine derivative, 5-carboxylcytosine (5caC), as a factor driving new CTCF binding within genomic DNA. Through a combination of in vivo and in vitro approaches, we reveal that 5caC generally strengthens CTCF association with DNA and facilitates binding to suboptimal sequences. Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ~13,000 new CTCF sites. The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength. As CTCF has multiple roles in gene expression, these findings have wide-reaching implications and point to induced 5caC as a potential mechanism to achieve differential CTCF binding in cells.
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Affiliation(s)
- Kyster K Nanan
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David M Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria F Prigge
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Morgan Thenoz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allissa A Dillman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Zimmerman D, Patel K, Hall M, Elmer J. Enhancement of transgene expression by nuclear transcription factor Y and CCCTC-binding factor. Biotechnol Prog 2018; 34:1581-1588. [PMID: 30294957 DOI: 10.1002/btpr.2712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/03/2018] [Accepted: 08/17/2018] [Indexed: 12/23/2022]
Abstract
If a transgene is effectively delivered to a cell, its expression may still be limited by epigenetic mechanisms that silence the transgene. Indeed, once the transgene reaches the nucleus, it may be bound by histone proteins and condensed into heterochromatin or associated with repressor proteins that block transcription. In this study, we sought to enhance transgene expression by adding binding motifs for several different epigenetic enzymes either upstream or downstream of two promoters (CMV and EF1α). Screening these plasmids revealed that luciferase expression was enhanced 10-fold (10.4 ± 5.8) by the addition of a CCAAT box just upstream of the EF1α promoter to recruit nuclear transcription factor Y (NF-Y), while inserting a CCCTC-binding factor (CTCF) motif downstream of the EF1α promoter enhanced expression at least 14-fold (14.03 ± 6.54). ChIP assays confirmed that NF-Y and CTCF bound to the motifs that were added to each plasmid, but the presence of NF-Y and CTCF did not significantly affect the levels of histone acetylation (H3K9ac) or methylation (H3K9me3). Overall, these results show that transgene expression from the EF1α promoter can be significantly increased with motifs that recruit NF-Y or CTCF. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1581-1588, 2018.
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Affiliation(s)
- Devon Zimmerman
- Dept. of Chemical Engineering, Villanova University, Villanova, PA, 19085
| | - Krupa Patel
- Dept. of Chemical Engineering, Villanova University, Villanova, PA, 19085
| | - Matthew Hall
- Dept. of Chemical Engineering, Villanova University, Villanova, PA, 19085
| | - Jacob Elmer
- Dept. of Chemical Engineering, Villanova University, Villanova, PA, 19085
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36
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DNA methylation dynamics in aging: how far are we from understanding the mechanisms? Mech Ageing Dev 2018; 174:3-17. [DOI: 10.1016/j.mad.2017.12.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
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37
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PARP1 Stabilizes CTCF Binding and Chromatin Structure To Maintain Epstein-Barr Virus Latency Type. J Virol 2018; 92:JVI.00755-18. [PMID: 29976663 PMCID: PMC6146685 DOI: 10.1128/jvi.00755-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/26/2018] [Indexed: 12/14/2022] Open
Abstract
EBV is a human gammaherpesvirus that infects more than 95% of individuals worldwide. Upon infection, EBV circularizes as an episome and establishes a chronic, latent infection in B cells. In doing so, the virus utilizes host cell machinery to regulate and maintain the viral genome. In otherwise healthy individuals, EBV infection is typically nonpathological; however, latent infection is potentially oncogenic and is responsible for 1% of human cancers. During latent infection, EBV expresses specific sets of proteins according to the given latency type, each of which is associated with specific types of cancers. For example, type III latency, in which the virus expresses its full repertoire of latent proteins, is characteristic of AIDS-associated and posttransplant lymphomas associated with EBV infection. Understanding how viral latency type is regulated at the chromatin level may reveal potential targets for EBV-specific pharmacological intervention in EBV-associated cancers. Epstein Barr virus (EBV) is a potentially oncogenic gammaherpesvirus that establishes a chronic, latent infection in memory B cells. The EBV genome persists in infected host cells as a chromatinized episome and is subject to chromatin-mediated regulation. Binding of the host insulator protein CTCF to the EBV genome has an established role in maintaining viral latency type. CTCF is posttranslationally modified by the host enzyme PARP1. PARP1, or poly(ADP-ribose) polymerase 1, catalyzes the transfer of a poly(ADP-ribose) (PAR) moiety from NAD+ onto acceptor proteins, including itself, histone proteins, and CTCF. PARylation of CTCF by PARP1 can affect CTCF's insulator activity, DNA binding capacity, and ability to form chromatin loops. Both PARP1 and CTCF have been implicated in the regulation of EBV latency and lytic reactivation. Thus, we predicted that pharmacological inhibition with PARP1 inhibitors would affect EBV latency type through a chromatin-specific mechanism. Here, we show that PARP1 and CTCF colocalize at specific sites throughout the EBV genome and provide evidence to suggest that PARP1 acts to stabilize CTCF binding and maintain the open chromatin landscape at the active Cp promoter during type III latency. Further, PARP1 activity is important in maintaining latency type-specific viral gene expression. The data presented here provide a rationale for the use of PARP inhibitors in the treatment of EBV-associated cancers exhibiting type III latency and ultimately could contribute to an EBV-specific treatment strategy for AIDS-related or posttransplant lymphomas. IMPORTANCE EBV is a human gammaherpesvirus that infects more than 95% of individuals worldwide. Upon infection, EBV circularizes as an episome and establishes a chronic, latent infection in B cells. In doing so, the virus utilizes host cell machinery to regulate and maintain the viral genome. In otherwise healthy individuals, EBV infection is typically nonpathological; however, latent infection is potentially oncogenic and is responsible for 1% of human cancers. During latent infection, EBV expresses specific sets of proteins according to the given latency type, each of which is associated with specific types of cancers. For example, type III latency, in which the virus expresses its full repertoire of latent proteins, is characteristic of AIDS-associated and posttransplant lymphomas associated with EBV infection. Understanding how viral latency type is regulated at the chromatin level may reveal potential targets for EBV-specific pharmacological intervention in EBV-associated cancers.
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38
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Pavlaki I, Docquier F, Chernukhin I, Kita G, Gretton S, Clarkson CT, Teif VB, Klenova E. Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:718-730. [PMID: 29981477 PMCID: PMC6074063 DOI: 10.1016/j.bbagrm.2018.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/23/2018] [Accepted: 06/23/2018] [Indexed: 12/11/2022]
Abstract
CTCF is an evolutionarily conserved and ubiquitously expressed architectural protein regulating a plethora of cellular functions via different molecular mechanisms. CTCF can undergo a number of post-translational modifications which change its properties and functions. One such modifications linked to cancer is poly(ADP-ribosyl)ation (PARylation). The highly PARylated CTCF form has an apparent molecular mass of 180 kDa (referred to as CTCF180), which can be distinguished from hypo- and non-PARylated CTCF with the apparent molecular mass of 130 kDa (referred to as CTCF130). The existing data accumulated so far have been mainly related to CTCF130. However, the properties of CTCF180 are not well understood despite its abundance in a number of primary tissues. In this study we performed ChIP-seq and RNA-seq analyses in human breast cells 226LDM, which display predominantly CTCF130 when proliferating, but CTCF180 upon cell cycle arrest. We observed that in the arrested cells the majority of sites lost CTCF, whereas fewer sites gained CTCF or remain bound (i.e. common sites). The classical CTCF binding motif was found in the lost and common, but not in the gained sites. The changes in CTCF occupancies in the lost and common sites were associated with increased chromatin densities and altered expression from the neighboring genes. Based on these results we propose a model integrating the CTCF130/180 transition with CTCF-DNA binding and gene expression changes. This study also issues an important cautionary note concerning the design and interpretation of any experiments using cells and tissues where CTCF180 may be present.
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Affiliation(s)
- Ioanna Pavlaki
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - France Docquier
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Igor Chernukhin
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Georgia Kita
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Svetlana Gretton
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Christopher T Clarkson
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Vladimir B Teif
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Elena Klenova
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
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39
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Moreno-Villanueva M, Bürkle A. Epigenetic and redox biomarkers: Novel insights from the MARK-AGE study. Mech Ageing Dev 2018; 177:128-134. [PMID: 29969595 DOI: 10.1016/j.mad.2018.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/12/2018] [Accepted: 06/29/2018] [Indexed: 02/07/2023]
Abstract
Ageing is a multifactorial process that affects most, if not all, of the body's tissues and organs and can be defined as the accumulation of physical and psychological changes in a human being over time. The rate of ageing differs between individuals of the same chronological age, meaning that 'biological age' of a person may be different from 'chronological age'. Furthermore, ageing represents a very potent risk factor for diseases and disability in humans. Therefore, establishment of markers of biological ageing is important for preventing age-associated diseases and extending health span. MARK-AGE, a large-scale European study, aimed at identifying a set of biomarkers which, as a combination of parameters with appropriate weighting, would measure biological age better than any marker in isolation. But beyond the identification of useful biomarkers, MARK-AGE provided new insights in age-associated specific cellular processes, such as DNA methylation, oxidative stress and the regulation of zinc homeostasis.
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Affiliation(s)
- Maria Moreno-Villanueva
- Molecular Toxicology Group, Dept. of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Alexander Bürkle
- Molecular Toxicology Group, Dept. of Biology, University of Konstanz, D-78457 Konstanz, Germany.
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40
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Shanmugam MK, Arfuso F, Arumugam S, Chinnathambi A, Jinsong B, Warrier S, Wang LZ, Kumar AP, Ahn KS, Sethi G, Lakshmanan M. Role of novel histone modifications in cancer. Oncotarget 2018; 9:11414-11426. [PMID: 29541423 PMCID: PMC5834259 DOI: 10.18632/oncotarget.23356] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/01/2017] [Indexed: 01/02/2023] Open
Abstract
Oncogenesis is a multistep process mediated by a variety of factors including epigenetic modifications. Global epigenetic post-translational modifications have been detected in almost all cancers types. Epigenetic changes appear briefly and do not involve permanent changes to the primary DNA sequence. These epigenetic modifications occur in key oncogenes, tumor suppressor genes, and transcription factors, leading to cancer initiation and progression. The most commonly observed epigenetic changes include DNA methylation, histone lysine methylation and demethylation, histone lysine acetylation and deacetylation. However, there are several other novel post-translational modifications that have been observed in recent times such as neddylation, sumoylation, glycosylation, phosphorylation, poly-ADP ribosylation, ubiquitination as well as transcriptional regulation and these have been briefly discussed in this article. We have also highlighted the diverse epigenetic changes that occur during the process of tumorigenesis and described the role of histone modifications that can occur on tumor suppressor genes as well as oncogenes, which regulate tumorigenesis and can thus form the basis of novel strategies for cancer therapy.
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Affiliation(s)
- Muthu K. Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Surendar Arumugam
- Institute of Molecular and Cell Biology, A*STAR, Biopolis Drive, Proteos, Singapore, Singapore
| | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Bian Jinsong
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, School of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, India
| | - Ling Zhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
- National University Cancer Institute, National University Health System, Singapore, Singapore
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
| | - Kwang Seok Ahn
- College of Korean Medicine, Kyung Hee University, Dongdaemun-gu, Seoul, Korea
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Manikandan Lakshmanan
- Institute of Molecular and Cell Biology, A*STAR, Biopolis Drive, Proteos, Singapore, Singapore
- Department of Pathology, National University Hospital Singapore, Singapore, Singapore
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41
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Liu J, Ding Z, Li G, Tang L, Xu Y, Luo H, Yi J, Lu Y, Mao R, Nan Q, Ren L, Zhang T, Wang K. Identification and validation of colorectal neoplasia-specific methylation biomarkers based on CTCF-binding sites. Oncotarget 2017; 8:114183-114194. [PMID: 29371978 PMCID: PMC5768395 DOI: 10.18632/oncotarget.23172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
To date, the sensitivity of currently available biomarkers based on the methylation of gene promoters is suboptimal for detecting adenomas and early-stage colorectal cancer (CRC). We aimed to develop biomarkers with methylated DNA binding sites of the multifunctional transcriptional factor CTCF for early detection of CRC. Using combined analyses of genome-wide occupation and the methylation profile of CTCF-binding sites, we identified candidate CTCF-binding sites. Then, we applied methylation-sensitive high-resolution melting (MS-HRM) and mass spectrometry analysis to screen and validate these candidate sites in diverse sample sets. We identified a set of colorectal neoplasia-specific biomarkers with robust performance. The top five biomarkers were selected and recommended for early detection of colorectal neoplasia. All of the five novel biomarkers exhibited a more robust discriminatory performance than that by BMP3 and NDRG4, two currently acknowledged robust methylation biomarkers. When the five new biomarkers were considered as a marker panel and tumor-positive was defined as having two or more (of the five) positive biomarkers, the marker panel could achieve a sensitivity of 91.67% for adenomas, 97.44% for Stage I CRC, 94.06% for Stage II CRC, 93.62% for Stage III CRC, and 93.54% for total colorectal tumors with a specificity of 94.05%. To our knowledge, this is the first study for colorectal neoplasia-specific methylation biomarkers based on CTCF-binding sites. Using a similar strategy, CTCF-binding sites could be potentially developed into biomarkers for other tumors. In summary, this study opens a new area in developing biomarkers for tumor prevention and treatment.
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Affiliation(s)
- Jiang Liu
- Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Zhaoli Ding
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650032, Yunnan, China.,Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming 650032, Yunnan, China
| | - Guimei Li
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650032, Yunnan, China.,Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming 650032, Yunnan, China
| | - Li Tang
- Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Yu Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Huayou Luo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Jinhua Yi
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Youwang Lu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Rui Mao
- School of Stomatology, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Qiong Nan
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Li Ren
- The First People's Hospital of Yunnan Province, Kunming 650031, Yunnan, China
| | - Tong Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Kunhua Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
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42
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Christmann M, Kaina B. Epigenetic regulation of DNA repair genes and implications for tumor therapy. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 780:15-28. [PMID: 31395346 DOI: 10.1016/j.mrrev.2017.10.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 12/31/2022]
Abstract
DNA repair represents the first barrier against genotoxic stress causing metabolic changes, inflammation and cancer. Besides its role in preventing cancer, DNA repair needs also to be considered during cancer treatment with radiation and DNA damaging drugs as it impacts therapy outcome. The DNA repair capacity is mainly governed by the expression level of repair genes. Alterations in the expression of repair genes can occur due to mutations in their coding or promoter region, changes in the expression of transcription factors activating or repressing these genes, and/or epigenetic factors changing histone modifications and CpG promoter methylation or demethylation levels. In this review we provide an overview on the epigenetic regulation of DNA repair genes. We summarize the mechanisms underlying CpG methylation and demethylation, with de novo methyltransferases and DNA repair involved in gain and loss of CpG methylation, respectively. We discuss the role of components of the DNA damage response, p53, PARP-1 and GADD45a on the regulation of the DNA (cytosine-5)-methyltransferase DNMT1, the key enzyme responsible for gene silencing. We stress the relevance of epigenetic silencing of DNA repair genes for tumor formation and tumor therapy. A paradigmatic example is provided by the DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT), which is silenced in up to 40% of various cancers through CpG promoter methylation. The CpG methylation status of the MGMT promoter strongly correlates with clinical outcome and, therefore, is used as prognostic marker during glioblastoma therapy. Mismatch repair genes are also subject of epigenetic silencing, which was shown to correlate with colorectal cancer formation. For many other repair genes shown to be epigenetically regulated the clinical outcome is not yet clear. We also address the question of whether genotoxic stress itself can lead to epigenetic alterations of genes encoding proteins involved in the defense against genotoxic stress.
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Affiliation(s)
- Markus Christmann
- Department of Toxicology, University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany.
| | - Bernd Kaina
- Department of Toxicology, University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany.
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43
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Henderson DJP, Miranda JL, Emerson BM. The β-NAD + salvage pathway and PKC-mediated signaling influence localized PARP-1 activity and CTCF Poly(ADP)ribosylation. Oncotarget 2017; 8:64698-64713. [PMID: 29029387 PMCID: PMC5630287 DOI: 10.18632/oncotarget.19841] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/06/2017] [Indexed: 01/03/2023] Open
Abstract
Poly(ADP)ribosylation (PARylation) of the chromatin architectural protein CTCF is critical for CTCF-dependent regulation of chromatin boundary and insulator elements. Loss of CTCF PARylation results in epigenetic silencing of certain tumor suppressor genes through destabilization of nearby chromatin boundaries. We investigated the metabolic and mechanistic processes that regulate PARP-1-mediated CTCF PARylation in human cancer cell lines and discovered a key role for the expression and activity of β-NAD+ salvage enzymes, NAMPT and NMNAT-1. These enzymes are downregulated in cells that exhibit reduced CTCF PARylation, resulting in a decreased concentration of nuclear β-NAD+. In these cells, decreased NMNAT-1 expression is enforced by a proteasome-mediated feedback loop resulting in degradation of NMNAT-1, transcriptional repression of NAMPT, and suppression of PARP-1 activity. Interestingly, dePARylated CTCF is associated in a stable protein complex with PARP-1 and NMNAT-1 in cancer cells harboring silenced tumor suppressor genes. Although the metabolic context in these cells favors suppression of PARP-1 activity, CTCF PARylation can be restored by Protein Kinase C (PKC) signaling. PKC induces dissociation of the catalytically inactive PARP-1/NMNAT-1/CTCF protein complex and phosphorylation of NMNAT-1, which stimulates its proteasome-mediated degradation. Our findings suggest that CTCF PARylation is underpinned by a cellular metabolic context engendered by regulation of the β-NAD+ salvage pathway in which NMNAT-1 acts as a rheostat to control localized β-NAD+ synthesis at CTCF/PARP-1 complexes.
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Affiliation(s)
| | - Jj L Miranda
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
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44
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Rajawat J, Shukla N, Mishra DP. Therapeutic Targeting of Poly(ADP-Ribose) Polymerase-1 (PARP1) in Cancer: Current Developments, Therapeutic Strategies, and Future Opportunities. Med Res Rev 2017; 37:1461-1491. [PMID: 28510338 DOI: 10.1002/med.21442] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/31/2017] [Accepted: 02/16/2017] [Indexed: 12/16/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) plays a central role in numerous cellular processes including DNA repair, replication, and transcription. PARP interacts directly, indirectly or via PARylation with various oncogenic proteins and regulates several transcription factors thereby modulating carcinogenesis. Therapeutic inhibition of PARP is therefore perceived as a promising anticancer strategy and a number of PARP inhibitors (PARPi) are currently under development and clinical evaluation. PARPi inhibit the DNA repair pathway and thus form the concept of synthetic lethality in cancer therapeutics. Preclinical and clinical studies have shown the potential of PARPi as chemopotentiator, radiosensitizer, or as adjuvant therapeutic agents. Recent studies have shown that PARP-1 could be either oncogenic or tumor suppressive in different cancers. PARP inhibitor resistance is also a growing concern in the clinical setting. Recently, changes in the levels of PARP-1 activity or expression in cancer patients have provided the basis for consideration of PARP-1 regulatory proteins as potential biomarkers. This review focuses on the current developments related to the role of PARP in cancer progression, therapeutic strategies targeting PARP-associated oncogenic signaling, and future opportunities in use of PARPi in anticancer therapeutics.
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Affiliation(s)
- Jyotika Rajawat
- Cell Death Research Laboratory, Endocrinology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India
| | - Nidhi Shukla
- Cell Death Research Laboratory, Endocrinology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India
| | - Durga Prasad Mishra
- Cell Death Research Laboratory, Endocrinology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India
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45
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Du Y, Yamaguchi H, Hsu JL, Hung MC. PARP inhibitors as precision medicine for cancer treatment. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwx027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AbstractPersonalized or precision medicine is an emerging treatment approach tailored to individuals or certain groups of patients based on their unique characteristics. These types of therapies guided by biomarkers tend to be more effective than traditional approaches, especially in cancer. The inhibitor against poly (ADP-ribose) polymerase (PARP), olaparib (Lynparza, AstraZeneca), which was approved by the US Food and Drug Administration (FDA) in 2014, demonstrated efficacy specifically for ovarian cancer patients harboring mutations in BRCA genes, which encode proteins in DNA double-strand break repairs. However, the response to PARP inhibitors has been less encouraging in other cancer types that also carry defects in the BRCA genes. Thus, furthering our understanding of the underlying mechanism of PARP inhibitors and resistance is critical to improve their efficacy. In this review, we summarize the results of preclinical studies and the clinical application of PARP inhibitors, and discuss the future direction of PARP inhibitors as a potential marker-guided personalized medicine for cancer treatment.
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Affiliation(s)
- Yi Du
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston 77030
| | - Hirohito Yamaguchi
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston 77030
| | - Jennifer L. Hsu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston 77030
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung 40402
- Department of Biotechnology, Asia University, Taichung 41354
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston 77030
- Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung 40402
- Department of Biotechnology, Asia University, Taichung 41354
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46
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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.
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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.
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47
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Abstract
There is a dynamic interplay between metabolic processes and gene regulation via the remodeling of chromatin. Most chromatin-modifying enzymes use cofactors, which are products of metabolic processes. This article explores the biosynthetic pathways of the cofactors nicotinamide adenine dinucleotide (NAD), acetyl coenzyme A (acetyl-CoA), S-adenosyl methionine (SAM), α-ketoglutarate, and flavin adenine dinucleotide (FAD), and their role in metabolically regulating chromatin processes. A more detailed look at the interaction between chromatin and the metabolic processes of circadian rhythms and aging is described as a paradigm for this emerging interdisciplinary field.
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Affiliation(s)
- Shelley L Berger
- Department of Cell & Developmental Biology, Department of Biology, and Department of Genetics, Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6508
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-4049
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48
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Muvarak NE, Chowdhury K, Xia L, Robert C, Choi EY, Cai Y, Bellani M, Zou Y, Singh ZN, Duong VH, Rutherford T, Nagaria P, Bentzen SM, Seidman MM, Baer MR, Lapidus RG, Baylin SB, Rassool FV. Enhancing the Cytotoxic Effects of PARP Inhibitors with DNA Demethylating Agents - A Potential Therapy for Cancer. Cancer Cell 2016; 30:637-650. [PMID: 27728808 PMCID: PMC5201166 DOI: 10.1016/j.ccell.2016.09.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 03/16/2016] [Accepted: 09/08/2016] [Indexed: 12/20/2022]
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPis) are clinically effective predominantly for BRCA-mutant tumors. We introduce a mechanism-based strategy to enhance PARPi efficacy based on DNA damage-related binding between DNA methyltransferases (DNMTs) and PARP1. In acute myeloid leukemia (AML) and breast cancer cells, DNMT inhibitors (DNMTis) alone covalently bind DNMTs into DNA and increase PARP1 tightly bound into chromatin. Low doses of DNMTis plus PARPis, versus each drug alone, increase PARPi efficacy, increasing amplitude and retention of PARP1 directly at laser-induced DNA damage sites. This correlates with increased DNA damage, synergistic tumor cytotoxicity, blunting of self-renewal, and strong anti-tumor responses, in vivo in unfavorable AML subtypes and BRCA wild-type breast cancer cells. Our combinatorial approach introduces a strategy to enhance efficacy of PARPis in treating cancer.
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MESH Headings
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Cell Line, Tumor
- Chromatin/metabolism
- DNA Breaks, Double-Stranded
- DNA Methylation/drug effects
- Drug Synergism
- Female
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Male
- Mice
- Mice, Inbred NOD
- Mice, Nude
- Phthalazines/pharmacology
- Poly (ADP-Ribose) Polymerase-1/antagonists & inhibitors
- Poly (ADP-Ribose) Polymerase-1/metabolism
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Triple Negative Breast Neoplasms/drug therapy
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Nidal E Muvarak
- Department of Radiation Oncology, University of Maryland, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Khadiza Chowdhury
- Department of Radiation Oncology, University of Maryland, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Limin Xia
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Carine Robert
- Department of Radiation Oncology, University of Maryland, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Eun Yong Choi
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Yi Cai
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Marina Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Ying Zou
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zeba N Singh
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Vu H Duong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | | | - Pratik Nagaria
- Department of Radiation Oncology, University of Maryland, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Søren M Bentzen
- Department of Radiation Oncology, University of Maryland, Baltimore, MD 21201, USA; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD 21224, USA
| | - Maria R Baer
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA; Veterans Affairs Medical Center, Baltimore, MD 21201, USA
| | - Rena G Lapidus
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA; Van Andel Research Institute, Grand Rapids, MI 49503
| | - Feyruz V Rassool
- Department of Radiation Oncology, University of Maryland, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA.
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49
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Rank L, Veith S, Gwosch EC, Demgenski J, Ganz M, Jongmans MC, Vogel C, Fischbach A, Buerger S, Fischer JMF, Zubel T, Stier A, Renner C, Schmalz M, Beneke S, Groettrup M, Kuiper RP, Bürkle A, Ferrando-May E, Mangerich A. Analyzing structure-function relationships of artificial and cancer-associated PARP1 variants by reconstituting TALEN-generated HeLa PARP1 knock-out cells. Nucleic Acids Res 2016; 44:10386-10405. [PMID: 27694308 PMCID: PMC5137445 DOI: 10.1093/nar/gkw859] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 09/05/2016] [Accepted: 09/16/2016] [Indexed: 12/17/2022] Open
Abstract
Genotoxic stress activates PARP1, resulting in the post-translational modification of proteins with poly(ADP-ribose) (PAR). We genetically deleted PARP1 in one of the most widely used human cell systems, i.e. HeLa cells, via TALEN-mediated gene targeting. After comprehensive characterization of these cells during genotoxic stress, we analyzed structure–function relationships of PARP1 by reconstituting PARP1 KO cells with a series of PARP1 variants. Firstly, we verified that the PARP1\E988K mutant exhibits mono-ADP-ribosylation activity and we demonstrate that the PARP1\L713F mutant is constitutively active in cells. Secondly, both mutants exhibit distinct recruitment kinetics to sites of laser-induced DNA damage, which can potentially be attributed to non-covalent PARP1–PAR interaction via several PAR binding motifs. Thirdly, both mutants had distinct functional consequences in cellular patho-physiology, i.e. PARP1\L713F expression triggered apoptosis, whereas PARP1\E988K reconstitution caused a DNA-damage-induced G2 arrest. Importantly, both effects could be rescued by PARP inhibitor treatment, indicating distinct cellular consequences of constitutive PARylation and mono(ADP-ribosyl)ation. Finally, we demonstrate that the cancer-associated PARP1 SNP variant (V762A) as well as a newly identified inherited PARP1 mutation (F304L\V762A) present in a patient with pediatric colorectal carcinoma exhibit altered biochemical and cellular properties, thereby potentially supporting human carcinogenesis. Together, we establish a novel cellular model for PARylation research, by revealing strong structure–function relationships of natural and artificial PARP1 variants.
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Affiliation(s)
- Lisa Rank
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sebastian Veith
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Research Training Group 1331, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Eva C Gwosch
- Bioimaging Center, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Janine Demgenski
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Magdalena Ganz
- Bioimaging Center, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud University Medical Center Nijmegen, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.,Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherland
| | - Christopher Vogel
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Arthur Fischbach
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Stefanie Buerger
- FlowKon FACS Facility, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Jan M F Fischer
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Tabea Zubel
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Anna Stier
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Christina Renner
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Michael Schmalz
- Center of Applied Photonics, Department of Physics, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sascha Beneke
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Ecotoxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marcus Groettrup
- FlowKon FACS Facility, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Immunology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center Nijmegen, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Elisa Ferrando-May
- Bioimaging Center, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Aswin Mangerich
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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50
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Abplanalp J, Hottiger MO. Cell fate regulation by chromatin ADP-ribosylation. Semin Cell Dev Biol 2016; 63:114-122. [PMID: 27693398 DOI: 10.1016/j.semcdb.2016.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/24/2016] [Accepted: 09/16/2016] [Indexed: 11/15/2022]
Abstract
ADP-ribosylation is an evolutionarily conserved complex posttranslational modification that alters protein function and/or interaction. Intracellularly, it is mainly catalyzed by diphtheria toxin-like ADP-ribosyltransferases (ARTDs), which attach one or several ADP-ribose residues onto target proteins. Several specific mono- and poly-ADP-ribosylation binding modules exist; hydrolases reverse the modification. The best-characterized ARTD family member, ARTD1, regulates various DNA-associated processes. Here, we focus on the role of ARTD1-mediated chromatin ADP-ribosylation in development, differentiation, and pluripotency, and the recent development of new methodologies that will enable more insight into these processes.
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Affiliation(s)
- Jeannette Abplanalp
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland.
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