251
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Epigenomic regulation of oncogenesis by chromatin remodeling. Oncogene 2016; 35:4423-36. [PMID: 26804164 DOI: 10.1038/onc.2015.513] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/27/2015] [Accepted: 12/07/2015] [Indexed: 02/08/2023]
Abstract
Disruption of the intricate gene expression program represents one of major driving factors for the development, progression and maintenance of human cancer, and is often associated with acquired therapeutic resistance. At the molecular level, cancerous phenotypes are the outcome of cellular functions of critical genes, regulatory interactions of histones and chromatin remodeling complexes in response to dynamic and persistent upstream signals. A large body of genetic and biochemical evidence suggests that the chromatin remodelers integrate the extracellular and cytoplasmic signals to control gene activity. Consequently, widespread dysregulation of chromatin remodelers and the resulting inappropriate expression of regulatory genes, together, lead to oncogenesis. We summarize the recent developments and current state of the dysregulation of the chromatin remodeling components as the driving mechanism underlying the growth and progression of human tumors. Because chromatin remodelers, modifying enzymes and protein-protein interactions participate in interpreting the epigenetic code, selective chromatin remodelers and bromodomains have emerged as new frontiers for pharmacological intervention to develop future anti-cancer strategies to be used either as single-agent or in combination therapies with chemotherapeutics or radiotherapy.
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252
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Lerrer B, Gertler AA, Cohen HY. The complex role of SIRT6 in carcinogenesis. Carcinogenesis 2015; 37:108-18. [PMID: 26717993 DOI: 10.1093/carcin/bgv167] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 11/25/2015] [Indexed: 12/28/2022] Open
Abstract
SIRT6, a member of the mammalian sirtuins family, functions as a mono-ADP-ribosyl transferase and NAD(+)-dependent deacylase of both acetyl groups and long-chain fatty acyl groups. SIRT6 regulates diverse cellular functions such as transcription, genome stability, telomere integrity, DNA repair, inflammation and metabolic related diseases such as diabetes, obesity and cancer. In this review, we will discuss the implication of SIRT6 in the biology of cancer and the relevance to organism homeostasis and lifespan.
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Affiliation(s)
- Batia Lerrer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Asaf A Gertler
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Haim Y Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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253
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ATM and SIRT6/SNF2H Mediate Transient H2AX Stabilization When DSBs Form by Blocking HUWE1 to Allow Efficient γH2AX Foci Formation. Cell Rep 2015; 13:2728-40. [DOI: 10.1016/j.celrep.2015.11.054] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 11/03/2015] [Accepted: 11/17/2015] [Indexed: 01/07/2023] Open
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254
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Ghosh S, Liu B, Wang Y, Hao Q, Zhou Z. Lamin A Is an Endogenous SIRT6 Activator and Promotes SIRT6-Mediated DNA Repair. Cell Rep 2015; 13:1396-1406. [PMID: 26549451 DOI: 10.1016/j.celrep.2015.10.006] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 07/13/2015] [Accepted: 10/02/2015] [Indexed: 01/08/2023] Open
Abstract
The nuclear lamins are essential for various molecular events in the nucleus, such as chromatin organization, DNA replication, and provision of mechanical support. A specific point mutation in the LMNA gene creates a truncated prelamin A termed progerin, causing Hutchinson-Gilford progeria syndrome (HGPS). SIRT6 deficiency leads to defective genomic maintenance and accelerated aging similar to HGPS, suggesting a potential link between lamin A and SIRT6. Here, we report that lamin A is an endogenous activator of SIRT6 and facilitates chromatin localization of SIRT6 upon DNA damage. Lamin A promotes SIRT6-dependent DNA-PKcs (DNA-PK catalytic subunit) recruitment to chromatin, CtIP deacetylation, and PARP1 mono-ADP ribosylation in response to DNA damage. The presence of progerin jeopardizes SIRT6 activation and compromises SIRT6-mediated molecular events in response to DNA damage. These data reveal a critical role for lamin A in regulating SIRT6 activities, suggesting that defects in SIRT6 functions contribute to impaired DNA repair and accelerated aging in HGPS.
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Affiliation(s)
- Shrestha Ghosh
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong; Shenzhen Institute of Innovation and Research, The University of Hong Kong, Nanshan, Shenzhen 518000, China
| | - Baohua Liu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong; School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Yi Wang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong
| | - Quan Hao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong
| | - Zhongjun Zhou
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, Hong Kong; Shenzhen Institute of Innovation and Research, The University of Hong Kong, Nanshan, Shenzhen 518000, China.
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255
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Abstract
PURPOSE OF REVIEW The circadian clock is an intricate biological timekeeper that is subject to fine-tuning mechanisms in order to maintain synchrony with the surrounding environment. One such mechanism is performed by the mammalian sirtuins that provide plasticity to the circadian clock by sensing cellular metabolic state. The sirtuins modulate the circadian epigenome and subsequent transcriptional control, and alterations to this organized system manifest in metabolic consequences, aging phenotypes and possibly cancer. RECENT FINDINGS New information regarding sirtuin-dependent control of the circadian clock has emerged. In addition to sirtuin (SIRT)1 and SIRT3, SIRT6 has been demonstrated as a critical regulator of circadian transcription that also serves as an interface with metabolic homeostasis. Also, new metabolic functions of SIRT1 have been described in the brain, which are critical to relay nutritional inputs to the central clock. SUMMARY This review focuses on the link between the circadian clock and the sirtuins, with an emphasis on new findings. In addition, speculation on the possible connections at the physiological level will be made that could further link the clock to aging and cancer.
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Affiliation(s)
- Selma Masri
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, California, USA
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256
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Abstract
DNA damage is correlated with and may drive the ageing process. Neurons in the brain are postmitotic and are excluded from many forms of DNA repair; therefore, neurons are vulnerable to various neurodegenerative diseases. The challenges facing the field are to understand how and when neuronal DNA damage accumulates, how this loss of genomic integrity might serve as a 'time keeper' of nerve cell ageing and why this process manifests itself as different diseases in different individuals.
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Affiliation(s)
- Hei-man Chow
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.,Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Karl Herrup
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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257
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Abstract
The sirtuins (SIRTs; of which there are seven in mammals) are NAD(+)-dependent enzymes that regulate a large number of cellular pathways and forestall the progression of ageing and age-associated diseases. In recent years, the role of sirtuins in cancer biology has become increasingly apparent, and growing evidence demonstrates that sirtuins regulate many processes that go awry in cancer cells, such as cellular metabolism, the regulation of chromatin structure and the maintenance of genomic stability. In this article, we review recent advances in our understanding of how sirtuins affect cancer metabolism, DNA repair and the tumour microenvironment and how activating or inhibiting sirtuins may be important in preventing or treating cancer.
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Affiliation(s)
- Angeliki Chalkiadaki
- Department of Biology, The Paul F. Glenn Center for the Science of Aging, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Bldg 68-280 Cambridge, Massachusetts 02139, USA
| | - Leonard Guarente
- Department of Biology, The Paul F. Glenn Center for the Science of Aging, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Bldg 68-280 Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Kendall Square, Cambridge, Massachusetts 02139, USA
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258
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Xu Z, Zhang L, Zhang W, Meng D, Zhang H, Jiang Y, Xu X, Van Meter M, Seluanov A, Gorbunova V, Mao Z. SIRT6 rescues the age related decline in base excision repair in a PARP1-dependent manner. Cell Cycle 2015; 14:269-76. [PMID: 25607651 DOI: 10.4161/15384101.2014.980641] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In principle, a decline in base excision repair (BER) efficiency with age should lead to genomic instability and ultimately contribute to the onset of the aging phenotype. Although multiple studies have indicated a negative link between aging and BER, the change of BER efficiency with age in humans has not been systematically analyzed. Here, with foreskin fibroblasts isolated from 19 donors between 20 and 64 y of age, we report a significant decline of BER efficiency with age using a newly developed GFP reactivation assay. We further observed a very strong negative correlation between age and the expression levels of SIRT6, a factor which is known to maintain genomic integrity by improving DNA double strand break (DSB) repair. Our mechanistic study suggests that, similar to the regulatory role that SIRT6 plays in DNA DSB repair, SIRT6 regulates BER in a PARP1-depdendent manner. Moreover, overexpression of SIRT6 rescues the decline of BER in aged fibroblasts. In summary, our results uncovered the regulatory mechanisms of BER by SIRT6, suggesting that SIRT6 reactivation in aging tissues may help delay the process of aging through improving BER.
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Affiliation(s)
- Zhu Xu
- a Department of Clinical Laboratory Medicine; Shanghai Tenth People's Hospital; School of Life Sciences and Technology; Tongji University ; Shanghai , China
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259
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Simic Z, Weiwad M, Schierhorn A, Steegborn C, Schutkowski M. The ɛ-Amino Group of Protein Lysine Residues Is Highly Susceptible to Nonenzymatic Acylation by Several Physiological Acyl-CoA Thioesters. Chembiochem 2015; 16:2337-47. [PMID: 26382620 DOI: 10.1002/cbic.201500364] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 01/04/2023]
Abstract
Mitochondrial enzymes implicated in the pathophysiology of diabetes, cancer, and metabolic syndrome are highly regulated by acetylation. However, mitochondrial acetyltransferases have not been identified. Here, we show that acetylation and also other acylations are spontaneous processes that depend on pH value, acyl-CoA concentration and the chemical nature of the acyl residue. In the case of a peptide derived from carbamoyl phosphate synthetase 1, the rates of succinylation and glutarylation were up to 150 times than for acetylation. These results were confirmed by using the protein substrate cyclophilin A (CypA). Deacylation experiments revealed that SIRT3 exhibits deacetylase activity but is not able to remove any of the succinyl groups from CypA, whereas SIRT5 is an effective protein desuccinylase. Thus, the acylation landscape on lysine residues might largely depend on the enzymatic activity of specific sirtuins, and the availability and reactivity of acyl-CoA compounds.
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Affiliation(s)
- Zeljko Simic
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Matthias Weiwad
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Angelika Schierhorn
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany.
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260
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Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat Rev Mol Cell Biol 2015; 16:593-610. [PMID: 26373265 DOI: 10.1038/nrm4048] [Citation(s) in RCA: 407] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ageing is affected by both genetic and non-genetic factors. Here, we review the chromatin-based epigenetic changes that occur during ageing, the role of chromatin modifiers in modulating lifespan and the importance of epigenetic signatures as biomarkers of ageing. We also discuss how epigenome remodelling by environmental stimuli affects several aspects of transcription and genomic stability, with important consequences for longevity, and outline epigenetic differences between the 'mortal soma' and the 'immortal germ line'. Finally, we discuss the inheritance of characteristics of ageing and potential chromatin-based strategies to delay or reverse hallmarks of ageing or age-related diseases.
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261
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Abstract
Regulation of chromatin structure is an essential component of the DNA damage response (DDR), which effectively preserves the integrity of DNA by a network of multiple DNA repair and associated signaling pathways. Within the DDR, chromatin is modified and remodeled to facilitate efficient DNA access, to control the activity of repair proteins and to mediate signaling. The mammalian ISWI family has recently emerged as one of the major ATP-dependent chromatin remodeling complex families that function in the DDR, as it is implicated in at least 3 major DNA repair pathways: homologous recombination, non-homologous end-joining and nucleotide excision repair. In this review, we discuss the various manners through which different ISWI complexes regulate DNA repair and how they are targeted to chromatin containing damaged DNA.
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Key Words
- ACF1
- ACF1, ATP-utilizing Chromatin assembly and remodeling Factor 1
- ATP-dependent chromatin remodeling
- BER, Base Excision Repair
- DDR, DNA Damage Response
- DNA damage response
- DSB, Double Strand Break
- GG-NER, Global Genome Nucleotide Excision Repair
- HR, Homologous Recombination
- Homologous Recombination
- ISWI
- ISWI, Imitation SWItch
- MRN, MRE11/Rad50/NBS1
- NER, Nucleotide Excision Repair
- NHEJ, Non-Homologous End Joining
- Non-Homologous End-Joining
- Nucleotide Excision Repair
- PAR, Poly(ADP-Ribose)
- RNApolII, RNA Polymerase II
- RSF1, Remodeling and Spacing Factor 1
- SMARCA, SWI-SNF-related Matrix-associated Actin-dependent Regulator of Chromatin A
- SMARCA5/SNF2H
- TC-NER, Transcription-Coupled Nucleotide Excision Repair
- WSTF
- WSTF, Williams Syndrome Transcription Factor
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Affiliation(s)
- Özge Z Aydin
- a Department of Genetics ; Cancer Genomics Netherlands; Erasmus MC ; Rotterdam , The Netherlands
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262
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Donà M, Mittelsten Scheid O. DNA Damage Repair in the Context of Plant Chromatin. PLANT PHYSIOLOGY 2015; 168:1206-18. [PMID: 26089404 PMCID: PMC4528755 DOI: 10.1104/pp.15.00538] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/17/2015] [Indexed: 05/03/2023]
Abstract
The integrity of DNA molecules is constantly challenged. All organisms have developed mechanisms to detect and repair multiple types of DNA lesions. The basic principles of DNA damage repair (DDR) in prokaryotes and unicellular and multicellular eukaryotes are similar, but the association of DNA with nucleosomes in eukaryotic chromatin requires mechanisms that allow access of repair enzymes to the lesions. This is achieved by chromatin-remodeling factors, and their necessity for efficient DDR has recently been demonstrated for several organisms and repair pathways. Plants share many features of chromatin organization and DNA repair with fungi and animals, but they differ in other, important details, which are both interesting and relevant for our understanding of genome stability and genetic diversity. In this Update, we compare the knowledge of the role of chromatin and chromatin-modifying factors during DDR in plants with equivalent systems in yeast and humans. We emphasize plant-specific elements and discuss possible implications.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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263
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Kato A, Komatsu K. RNF20-SNF2H Pathway of Chromatin Relaxation in DNA Double-Strand Break Repair. Genes (Basel) 2015; 6:592-606. [PMID: 26184323 PMCID: PMC4584319 DOI: 10.3390/genes6030592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/25/2023] Open
Abstract
Rapid progress in the study on the association of histone modifications with chromatin remodeling factors has broadened our understanding of chromatin dynamics in DNA transactions. In DNA double-strand break (DSB) repair, the well-known mark of histones is the phosphorylation of the H2A variant, H2AX, which has been used as a surrogate marker of DSBs. The ubiquitylation of histone H2B by RNF20 E3 ligase was recently found to be a DNA damage-induced histone modification. This modification is required for DSB repair and regulated by a distinctive pathway from that of histone H2AX phosphorylation. Moreover, the connection between H2B ubiquitylation and the chromatin remodeling activity of SNF2H has been elucidated. In this review, we summarize the current knowledge of RNF20-mediated processes and the molecular link to H2AX-mediated processes during DSB repair.
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Affiliation(s)
- Akihiro Kato
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida-konoecho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kenshi Komatsu
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida-konoecho, Sakyo-ku, Kyoto 606-8501, Japan.
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264
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Sebastián C, Mostoslavsky R. The role of mammalian sirtuins in cancer metabolism. Semin Cell Dev Biol 2015; 43:33-42. [DOI: 10.1016/j.semcdb.2015.07.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 07/29/2015] [Indexed: 12/26/2022]
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265
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Chromatin Remodelers: From Function to Dysfunction. Genes (Basel) 2015; 6:299-324. [PMID: 26075616 PMCID: PMC4488666 DOI: 10.3390/genes6020299] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 12/20/2022] Open
Abstract
Chromatin remodelers are key players in the regulation of chromatin accessibility and nucleosome positioning on the eukaryotic DNA, thereby essential for all DNA dependent biological processes. Thus, it is not surprising that upon of deregulation of those molecular machines healthy cells can turn into cancerous cells. Even though the remodeling enzymes are very abundant and a multitude of different enzymes and chromatin remodeling complexes exist in the cell, the particular remodeling complex with its specific nucleosome positioning features must be at the right place at the right time in order to ensure the proper regulation of the DNA dependent processes. To achieve this, chromatin remodeling complexes harbor protein domains that specifically read chromatin targeting signals, such as histone modifications, DNA sequence/structure, non-coding RNAs, histone variants or DNA bound interacting proteins. Recent studies reveal the interaction between non-coding RNAs and chromatin remodeling complexes showing importance of RNA in remodeling enzyme targeting, scaffolding and regulation. In this review, we summarize current understanding of chromatin remodeling enzyme targeting to chromatin and their role in cancer development.
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266
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Hwang BJ, Jin J, Gao Y, Shi G, Madabushi A, Yan A, Guan X, Zalzman M, Nakajima S, Lan L, Lu AL. SIRT6 protein deacetylase interacts with MYH DNA glycosylase, APE1 endonuclease, and Rad9-Rad1-Hus1 checkpoint clamp. BMC Mol Biol 2015; 16:12. [PMID: 26063178 PMCID: PMC4464616 DOI: 10.1186/s12867-015-0041-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/29/2015] [Indexed: 02/07/2023] Open
Abstract
Background SIRT6, a member of the NAD+-dependent histone/protein deacetylase family, regulates genomic stability, metabolism, and lifespan. MYH glycosylase and APE1 are two base excision repair (BER) enzymes involved in mutation avoidance from oxidative DNA damage. Rad9–Rad1–Hus1 (9–1–1) checkpoint clamp promotes cell cycle checkpoint signaling and DNA repair. BER is coordinated with the checkpoint machinery and requires chromatin remodeling for efficient repair. SIRT6 is involved in DNA double-strand break repair and has been implicated in BER. Here we investigate the direct physical and functional interactions between SIRT6 and BER enzymes. Results We show that SIRT6 interacts with and stimulates MYH glycosylase and APE1. In addition, SIRT6 interacts with the 9-1-1 checkpoint clamp. These interactions are enhanced following oxidative stress. The interdomain connector of MYH is important for interactions with SIRT6, APE1, and 9–1–1. Mutagenesis studies indicate that SIRT6, APE1, and Hus1 bind overlapping but different sequence motifs on MYH. However, there is no competition of APE1, Hus1, or SIRT6 binding to MYH. Rather, one MYH partner enhances the association of the other two partners to MYH. Moreover, APE1 and Hus1 act together to stabilize the MYH/SIRT6 complex. Within human cells, MYH and SIRT6 are efficiently recruited to confined oxidative DNA damage sites within transcriptionally active chromatin, but not within repressive chromatin. In addition, Myh foci induced by oxidative stress and Sirt6 depletion are frequently localized on mouse telomeres. Conclusions Although SIRT6, APE1, and 9-1-1 bind to the interdomain connector of MYH, they do not compete for MYH association. Our findings indicate that SIRT6 forms a complex with MYH, APE1, and 9-1-1 to maintain genomic and telomeric integrity in mammalian cells. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0041-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bor-Jang Hwang
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA.
| | - Jin Jin
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA.
| | - Ying Gao
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA. .,School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing, 100084, China.
| | - Guoli Shi
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA. .,University of Maryland School of Nursing, 655 West Lombard Street, Baltimore, MD, 21201, USA.
| | - Amrita Madabushi
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA. .,Department of Natural and Physical Sciences, Life Sciences Institute, Baltimore City Community College, 801 West Baltimore Street, Baltimore, MD, 21201, USA.
| | - Austin Yan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA.
| | - Xin Guan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA.
| | - Michal Zalzman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA. .,Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, 16 South Eutaw Street, Baltimore, MD, 21201, USA.
| | - Satoshi Nakajima
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA. .,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA.
| | - Li Lan
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA. .,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA.
| | - A-Lien Lu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA. .,Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD, 21201, USA.
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267
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Ghosh S, Zhou Z. SIRTain regulators of premature senescence and accelerated aging. Protein Cell 2015; 6:322-33. [PMID: 25907989 PMCID: PMC4417679 DOI: 10.1007/s13238-015-0149-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/28/2015] [Indexed: 12/11/2022] Open
Abstract
The sirtuin proteins constitute class III histone deacetylases (HDACs). These evolutionarily conserved NAD(+)-dependent enzymes form an important component in a variety of cellular and biological processes with highly divergent as well as convergent roles in maintaining metabolic homeostasis, safeguarding genomic integrity, regulating cancer metabolism and also inflammatory responses. Amongst the seven known mammalian sirtuin proteins, SIRT1 has gained much attention due to its widely acknowledged roles in promoting longevity and ameliorating age-associated pathologies. The contributions of other sirtuins in the field of aging are also gradually emerging. Here, we summarize some of the recent discoveries in sirtuins biology which clearly implicate the functions of sirtuin proteins in the regulation of premature cellular senescence and accelerated aging. The roles of sirtuins in various cellular processes have been extrapolated to draw inter-linkage with anti-aging mechanisms. Also, the latest findings on sirtuins which might have potential effects in the process of aging have been reviewed.
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Affiliation(s)
- Shrestha Ghosh
- Department of Biochemistry, The University of Hong Kong, Hong Kong, China
| | - Zhongjun Zhou
- Department of Biochemistry, The University of Hong Kong, Hong Kong, China
- Shenzhen Institute of Innovation and Technology, The University of Hong Kong, Hong Kong, China
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268
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Etchegaray JP, Chavez L, Huang Y, Ross KN, Choi J, Martinez-Pastor B, Walsh RM, Sommer CA, Lienhard M, Kugel S, Silberman DM, Ramaswamy S, Mostoslavsky G, Hochedlinger K, Goren A, Rao A, Mostoslavsky R. The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine. Nat Cell Biol 2015; 17:545-57. [PMID: 25915124 PMCID: PMC4593707 DOI: 10.1038/ncb3147] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 03/03/2015] [Indexed: 02/08/2023]
Abstract
How embryonic stem cells (ESCs) commit to specific cell lineages and yield all cell types of a fully formed organism remains a major question. ESC differentiation is accompanied by large-scale histone and DNA modifications, but the relations between these epigenetic categories are not understood. Here we demonstrate the interplay between the histone deacetylase sirtuin 6 (SIRT6) and the ten-eleven translocation enzymes (TETs). SIRT6 targets acetylated histone H3 at Lys 9 and 56 (H3K9ac and H3K56ac), while TETs convert 5-methylcytosine into 5-hydroxymethylcytosine (5hmC). ESCs derived from Sirt6 knockout (S6KO) mice are skewed towards neuroectoderm development. This phenotype involves derepression of OCT4, SOX2 and NANOG, which causes an upregulation of TET-dependent production of 5hmC. Genome-wide analysis revealed neural genes marked with 5hmC in S6KO ESCs, thereby implicating TET enzymes in the neuroectoderm-skewed differentiation phenotype. We demonstrate that SIRT6 functions as a chromatin regulator safeguarding the balance between pluripotency and differentiation through Tet-mediated production of 5hmC.
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Affiliation(s)
- Jean-Pierre Etchegaray
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Lukas Chavez
- La Jolla Institute for Allergy and Immunology, Sanford Consortium for Regenerative Medicine, UCSD Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA 92037, USA
| | - Yun Huang
- La Jolla Institute for Allergy and Immunology, Sanford Consortium for Regenerative Medicine, UCSD Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA 92037, USA
| | - Kenneth N. Ross
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Jiho Choi
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Barbara Martinez-Pastor
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Ryan M. Walsh
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Cesar A. Sommer
- The Center for Regenerative Medicine (CReM), Boston Medical Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Matthias Lienhard
- La Jolla Institute for Allergy and Immunology, Sanford Consortium for Regenerative Medicine, UCSD Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA 92037, USA
| | - Sita Kugel
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Dafne M. Silberman
- Department of Human Biochemistry, Medical School, CEFyBO-UBA-CONICET, Argentina
| | - Sridhar Ramaswamy
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Gustavo Mostoslavsky
- The Center for Regenerative Medicine (CReM), Boston Medical Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Konrad Hochedlinger
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Alon Goren
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, Sanford Consortium for Regenerative Medicine, UCSD Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA 92037, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114 USA
- The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA
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269
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Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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270
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Helfricht A, van Attikum H. Remodeling and spacing factor 1 (RSF1): a rising star in DNA repair. Epigenomics 2015; 6:261-5. [PMID: 25111480 DOI: 10.2217/epi.14.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Angela Helfricht
- Leiden University Medical Center, Department of Human Genetics, Einsteinweg 20, 2333ZC Leiden, The Netherlands
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271
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Affiliation(s)
- Hui Jing
- Department
of Chemistry and
Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Hening Lin
- Department
of Chemistry and
Chemical Biology, Cornell University, Ithaca, New York 14850, United States
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272
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Fonseca Costa SS, Ripperger JA. Impact of the circadian clock on the aging process. Front Neurol 2015; 6:43. [PMID: 25798127 PMCID: PMC4351613 DOI: 10.3389/fneur.2015.00043] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/19/2015] [Indexed: 12/11/2022] Open
Abstract
The increase of life expectancy and the decline of biological functions with advancing age are impending obstacles for our society. In general, age-related changes can be separated into two processes. Primary aging is based on programs governing gradual changes which are generally not harmful. On the other hand, secondary aging or senescence is more aleatory in nature and it is at this stage that the progressive impairment of metabolic, physiological, and neurological functions increases the risk of death. Exploiting genetic animal models, we obtain more and more information on the underlying regulatory networks. The aim of this review is to identify potential links between the output of the circadian oscillator and secondary aging. The reasons to suspect such links rely on the fact that the mouse models without functional circadian clocks sometimes exhibit reduced life expectancy. This may be due to their inability to properly control and synchronize energy expenditure, affecting, for example, the integrity of neurons in the brain. Hence, it is tempting to speculate that re-synchronization of metabolic and physiological functions by the circadian clock may slow down the aging process.
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Affiliation(s)
- Sara S Fonseca Costa
- Department of Biology/Biochemistry, University of Fribourg , Fribourg , Switzerland
| | - Jürgen A Ripperger
- Department of Biology/Biochemistry, University of Fribourg , Fribourg , Switzerland
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273
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Klement K, Luijsterburg MS, Pinder JB, Cena CS, Del Nero V, Wintersinger CM, Dellaire G, van Attikum H, Goodarzi AA. Opposing ISWI- and CHD-class chromatin remodeling activities orchestrate heterochromatic DNA repair. ACTA ACUST UNITED AC 2015; 207:717-33. [PMID: 25533843 PMCID: PMC4274264 DOI: 10.1083/jcb.201405077] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chromatin compaction mediated by CHD3.1 must be counteracted by ACF1–SNF2H and RNF20 in order to allow DNA double-strand break repair in heterochromatin of postreplicative cells. Heterochromatin is a barrier to DNA repair that correlates strongly with elevated somatic mutation in cancer. CHD class II nucleosome remodeling activity (specifically CHD3.1) retained by KAP-1 increases heterochromatin compaction and impedes DNA double-strand break (DSB) repair requiring Artemis. This obstruction is alleviated by chromatin relaxation via ATM-dependent KAP-1S824 phosphorylation (pKAP-1) and CHD3.1 dispersal from heterochromatic DSBs; however, how heterochromatin compaction is actually adjusted after CHD3.1 dispersal is unknown. In this paper, we demonstrate that Artemis-dependent DSB repair in heterochromatin requires ISWI (imitation switch)-class ACF1–SNF2H nucleosome remodeling. Compacted chromatin generated by CHD3.1 after DNA replication necessitates ACF1–SNF2H–mediated relaxation for DSB repair. ACF1–SNF2H requires RNF20 to bind heterochromatic DSBs, underlies RNF20-mediated chromatin relaxation, and functions downstream of pKAP-1–mediated CHD3.1 dispersal to enable DSB repair. CHD3.1 and ACF1–SNF2H display counteractive activities but similar histone affinities (via the plant homeodomains of CHD3.1 and ACF1), which we suggest necessitates a two-step dispersal and recruitment system regulating these opposing chromatin remodeling activities during DSB repair.
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Affiliation(s)
- Karolin Klement
- Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Centre, 2333 ZC Leiden, Netherlands
| | - Jordan B Pinder
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Chad S Cena
- Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Victor Del Nero
- Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Christopher M Wintersinger
- Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Centre, 2333 ZC Leiden, Netherlands
| | - Aaron A Goodarzi
- Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada Robson DNA Science Centre, Southern Alberta Cancer Research Institute; and Department of Biochemistry and Molecular Biology and Department of Oncology, Cumming School of Medicine; University of Calgary, Calgary, Alberta T2N 4N1, Canada
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274
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Saito Y, Zhou H, Kobayashi J. Chromatin modification and NBS1: their relationship in DNA double-strand break repair. Genes Genet Syst 2015; 90:195-208. [DOI: 10.1266/ggs.15-00010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yuichiro Saito
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University
| | - Hui Zhou
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University
| | - Junya Kobayashi
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University
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275
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Ming M, Han W, Zhao B, Sundaresan NR, Deng CX, Gupta MP, He YY. SIRT6 promotes COX-2 expression and acts as an oncogene in skin cancer. Cancer Res 2014; 74:5925-33. [PMID: 25320180 DOI: 10.1158/0008-5472.can-14-1308] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
SIRT6 is a SIR2 family member that regulates multiple molecular pathways involved in metabolism, genomic stability, and aging. It has been proposed previously that SIRT6 is a tumor suppressor in cancer. Here, we challenge this concept by presenting evidence that skin-specific deletion of SIRT6 in the mouse inhibits skin tumorigenesis. SIRT6 promoted expression of COX-2 by repressing AMPK signaling, thereby increasing cell proliferation and survival in the skin epidermis. SIRT6 expression in skin keratinocytes was increased by exposure to UVB light through activation of the AKT pathway. Clinically, we found that SIRT6 was upregulated in human skin squamous cell carcinoma. Taken together, our results provide evidence that SIRT6 functions as an oncogene in the epidermis and suggest greater complexity to its role in epithelial carcinogenesis.
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Affiliation(s)
- Mei Ming
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois
| | - Weinong Han
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois
| | - Baozhong Zhao
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois
| | - Nagalingam R Sundaresan
- Department of Surgery, Committee on Cellular and Molecular Physiology, University of Chicago, Chicago, Illinois. Division of Biological Sciences, Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Chu-Xia Deng
- National Institute of Diabetes, Digestive and Kidney Diseases, US NIH, Bethesda, Maryland
| | - Mahesh P Gupta
- Department of Surgery, Committee on Cellular and Molecular Physiology, University of Chicago, Chicago, Illinois
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois.
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276
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Li DQ, Yang Y, Kumar R. MTA family of proteins in DNA damage response: mechanistic insights and potential applications. Cancer Metastasis Rev 2014; 33:993-1000. [PMID: 25332144 PMCID: PMC4302735 DOI: 10.1007/s10555-014-9524-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The DNA damage, most notably DNA double-strand breaks, poses a serious threat to the stability of mammalian genome. Maintenance of genomic integrity is largely dependent on an efficient, accurate, and timely DNA damage response in the context of chromatin. Consequently, dysregulation of the DNA damage response machinery is fundamentally linked to the genomic instability and a likely predisposition to cancer. In turn, aberrant activation of DNA damage response pathways in human cancers enables tumor cells to survive DNA damages, thus, leading to the development of resistance of tumor cells to DNA damaging radio- and chemotherapies. A substantial body of experimental evidence has established that ATP-dependent chromatin remodeling and histone modifications play a central role in the DNA damage response. As a component of the nucleosome remodeling and histone deacetylase (NuRD) complex that couples both ATP-dependent chromatin remodeling and histone deacetylase activities, the metastasis-associated protein (MTA) family proteins have been recently shown to participate in the DNA damage response beyond its well-established roles in gene transcription. In this thematic review, we will focus on our current understandings of the role of the MTA family proteins in the DNA damage response and their potential implications in DNA damaging anticancer therapy.
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Affiliation(s)
- Da-Qiang Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China,
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277
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Jeggo PA, Downs JA. Roles of chromatin remodellers in DNA double strand break repair. Exp Cell Res 2014; 329:69-77. [PMID: 25278484 DOI: 10.1016/j.yexcr.2014.09.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 10/24/2022]
Abstract
Now that we have a good understanding of the DNA double strand break (DSB) repair mechanisms and DSB-induced damage signalling, attention is focusing on the changes to the chromatin environment needed for efficient DSB repair. Mutations in chromatin remodelling complexes have been identified in cancers, making it important to evaluate how they impact upon genomic stability. Our current understanding of the DSB repair pathways suggests that each one has distinct requirements for chromatin remodelling. Moreover, restricting the extent of chromatin modifications could be a significant factor regulating the decision of pathway usage. In this review, we evaluate the distinct DSB repair pathways for their potential need for chromatin remodelling and review the roles of ATP-driven chromatin remodellers in the pathways.
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Affiliation(s)
- Penny A Jeggo
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton BN19RQ, UK.
| | - Jessica A Downs
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton BN19RQ, UK.
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278
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Dahlin JL, Chen X, Walters MA, Zhang Z. Histone-modifying enzymes, histone modifications and histone chaperones in nucleosome assembly: Lessons learned from Rtt109 histone acetyltransferases. Crit Rev Biochem Mol Biol 2014; 50:31-53. [PMID: 25365782 DOI: 10.3109/10409238.2014.978975] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During DNA replication, nucleosomes ahead of replication forks are disassembled to accommodate replication machinery. Following DNA replication, nucleosomes are then reassembled onto replicated DNA using both parental and newly synthesized histones. This process, termed DNA replication-coupled nucleosome assembly (RCNA), is critical for maintaining genome integrity and for the propagation of epigenetic information, dysfunctions of which have been implicated in cancers and aging. In recent years, it has been shown that RCNA is carefully orchestrated by a series of histone modifications, histone chaperones and histone-modifying enzymes. Interestingly, many features of RCNA are also found in processes involving DNA replication-independent nucleosome assembly like histone exchange and gene transcription. In yeast, histone H3 lysine K56 acetylation (H3K56ac) is found in newly synthesized histone H3 and is critical for proper nucleosome assembly and for maintaining genomic stability. The histone acetyltransferase (HAT) regulator of Ty1 transposition 109 (Rtt109) is the sole enzyme responsible for H3K56ac in yeast. Much research has centered on this particular histone modification and histone-modifying enzyme. This Critical Review summarizes much of our current understanding of nucleosome assembly and highlights many important insights learned from studying Rtt109 HATs in fungi. We highlight some seminal features in nucleosome assembly conserved in mammalian systems and describe some of the lingering questions in the field. Further studying fungal and mammalian chromatin assembly may have important public health implications, including deeper understandings of human cancers and aging as well as the pursuit of novel anti-fungal therapies.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine , Rochester, MN , USA
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279
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Bosch-Presegué L, Vaquero A. Sirtuin-dependent epigenetic regulation in the maintenance of genome integrity. FEBS J 2014; 282:1745-67. [DOI: 10.1111/febs.13053] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/09/2014] [Accepted: 09/12/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Laia Bosch-Presegué
- Chromatin Biology Laboratory; Cancer Epigenetics and Biology Program; Institut d'Investigació Biomèdica de Bellvitge; Barcelona Spain
| | - Alejandro Vaquero
- Chromatin Biology Laboratory; Cancer Epigenetics and Biology Program; Institut d'Investigació Biomèdica de Bellvitge; Barcelona Spain
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280
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Sonzogni SV, Ogara MF, Castillo DS, Sirkin PF, Radicella JP, Cánepa ET. Nuclear translocation of p19INK4d in response to oxidative DNA damage promotes chromatin relaxation. Mol Cell Biochem 2014; 398:63-72. [DOI: 10.1007/s11010-014-2205-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/30/2014] [Indexed: 12/23/2022]
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281
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Masri S, Sassone-Corsi P. Sirtuins and the circadian clock: bridging chromatin and metabolism. Sci Signal 2014; 7:re6. [PMID: 25205852 DOI: 10.1126/scisignal.2005685] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The circadian clock is a finely tuned system of transcriptional and translational regulation that is required for daily synchrony of organismal physiological processes. Additional layers of complexity that contribute to efficient clock function involve posttranslational modifications and enzymatic feedback loops. SIRT1, the founding member of the sirtuin family of protein deacetylases, was the first sirtuin to be reported to modulate circadian function. SIRT1 affects the circadian clock by its actions in the nucleus. Moreover, recent data implicate SIRT3 and SIRT6 in controlling mitochondrial and nuclear circadian functions, revealing previously unappreciated roles that extend to various subcellular domains, including fatty acid metabolism in the mitochondria. This review focuses on the roles of sirtuins in directing circadian functions in diverse organelles and speculates on the endogenous signals that may mediate the segregated roles of this family of enzymes.
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Affiliation(s)
- Selma Masri
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U904 INSERM, University of California, Irvine, Irvine, CA 92697, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, U904 INSERM, University of California, Irvine, Irvine, CA 92697, USA.
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282
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Yang J, Gupta V, Carroll KS, Liebler DC. Site-specific mapping and quantification of protein S-sulphenylation in cells. Nat Commun 2014; 5:4776. [PMID: 25175731 PMCID: PMC4167403 DOI: 10.1038/ncomms5776] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/22/2014] [Indexed: 02/06/2023] Open
Abstract
Cysteine S-sulphenylation provides redox regulation of protein functions, but the global cellular impact of this transient post-translational modification remains unexplored. We describe a chemoproteomic workflow to map and quantify over 1,000 S-sulphenylation sites on more than 700 proteins in intact cells. Quantitative analysis of human cells stimulated with hydrogen peroxide or epidermal growth factor measured hundreds of site selective redox changes. Different cysteines in the same proteins displayed dramatic differences in susceptibility to S-sulphenylation. Newly discovered S-sulphenylations provided mechanistic support for proposed cysteine redox reactions and suggested novel redox mechanisms, including S-sulphenyl-mediated redox regulation of the transcription factor HIF1A by SIRT6. S-sulphenylation is favored at solvent-exposed protein surfaces and is associated with sequence motifs that are distinct from those for other thiol modifications. S-sulphenylations affect regulators of phosphorylation, acetylation and ubiquitylation, which suggest regulatory crosstalk between redox control and signalling pathways.
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Affiliation(s)
- Jing Yang
- 1] Departmemt of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, USA [2] Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, USA
| | - Vinayak Gupta
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Daniel C Liebler
- 1] Departmemt of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, USA [2] Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, USA
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283
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Pan L, Penney J, Tsai LH. Chromatin regulation of DNA damage repair and genome integrity in the central nervous system. J Mol Biol 2014; 426:3376-88. [PMID: 25128619 DOI: 10.1016/j.jmb.2014.08.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 12/17/2022]
Abstract
With the continued extension of lifespan, aging and age-related diseases have become a major medical challenge to our society. Aging is accompanied by changes in multiple systems. Among these, the aging process in the central nervous system is critically important but very poorly understood. Neurons, as post-mitotic cells, are devoid of replicative associated aging processes, such as senescence and telomere shortening. However, because of the inability to self-replenish, neurons have to withstand challenge from numerous stressors over their lifetime. Many of these stressors can lead to damage of the neurons' DNA. When the accumulation of DNA damage exceeds a neuron's capacity for repair, or when there are deficiencies in DNA repair machinery, genome instability can manifest. The increased mutation load associated with genome instability can lead to neuronal dysfunction and ultimately to neuron degeneration. In this review, we first briefly introduce the sources and types of DNA damage and the relevant repair pathways in the nervous system (summarized in Fig. 1). We then discuss the chromatin regulation of these processes and summarize our understanding of the contribution of genomic instability to neurodegenerative diseases.
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Affiliation(s)
- Ling Pan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jay Penney
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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284
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Zwaans BMM, Lombard DB. Interplay between sirtuins, MYC and hypoxia-inducible factor in cancer-associated metabolic reprogramming. Dis Model Mech 2014; 7:1023-32. [PMID: 25085992 PMCID: PMC4142723 DOI: 10.1242/dmm.016287] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In the early twentieth century, Otto Heinrich Warburg described an elevated rate of glycolysis occurring in cancer cells, even in the presence of atmospheric oxygen (the Warburg effect). Despite the inefficiency of ATP generation through glycolysis, the breakdown of glucose into lactate provides cancer cells with a number of advantages, including the ability to withstand fluctuations in oxygen levels, and the production of intermediates that serve as building blocks to support rapid proliferation. Recent evidence from many cancer types supports the notion that pervasive metabolic reprogramming in cancer and stromal cells is a crucial feature of neoplastic transformation. Two key transcription factors that play major roles in this metabolic reprogramming are hypoxia inducible factor-1 (HIF1) and MYC. Sirtuin-family deacetylases regulate diverse biological processes, including many aspects of tumor biology. Recently, the sirtuin SIRT6 has been shown to inhibit the transcriptional output of both HIF1 and MYC, and to function as a tumor suppressor. In this Review, we highlight the importance of HIF1 and MYC in regulating tumor metabolism and their regulation by sirtuins, with a main focus on SIRT6.
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Affiliation(s)
- Bernadette M M Zwaans
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David B Lombard
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
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285
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Masri S, Rigor P, Cervantes M, Ceglia N, Sebastian C, Xiao C, Roqueta-Rivera M, Deng C, Osborne TF, Mostoslavsky R, Baldi P, Sassone-Corsi P. Partitioning circadian transcription by SIRT6 leads to segregated control of cellular metabolism. Cell 2014; 158:659-72. [PMID: 25083875 PMCID: PMC5472354 DOI: 10.1016/j.cell.2014.06.050] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/29/2014] [Accepted: 06/20/2014] [Indexed: 01/11/2023]
Abstract
Circadian rhythms are intimately linked to cellular metabolism. Specifically, the NAD(+)-dependent deacetylase SIRT1, the founding member of the sirtuin family, contributes to clock function. Whereas SIRT1 exhibits diversity in deacetylation targets and subcellular localization, SIRT6 is the only constitutively chromatin-associated sirtuin and is prominently present at transcriptionally active genomic loci. Comparison of the hepatic circadian transcriptomes reveals that SIRT6 and SIRT1 separately control transcriptional specificity and therefore define distinctly partitioned classes of circadian genes. SIRT6 interacts with CLOCK:BMAL1 and, differently from SIRT1, governs their chromatin recruitment to circadian gene promoters. Moreover, SIRT6 controls circadian chromatin recruitment of SREBP-1, resulting in the cyclic regulation of genes implicated in fatty acid and cholesterol metabolism. This mechanism parallels a phenotypic disruption in fatty acid metabolism in SIRT6 null mice as revealed by circadian metabolome analyses. Thus, genomic partitioning by two independent sirtuins contributes to differential control of circadian metabolism.
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Affiliation(s)
- Selma Masri
- Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Paul Rigor
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Marlene Cervantes
- Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Nicholas Ceglia
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Carlos Sebastian
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Cuiying Xiao
- Genetics of Development and Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Manuel Roqueta-Rivera
- Metabolic Disease Program, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Chuxia Deng
- Genetics of Development and Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timothy F Osborne
- Metabolic Disease Program, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Pierre Baldi
- Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA; INSERM U904, Sprague Hall, University of California, Irvine, Irvine, CA 92697, USA.
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286
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Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells. Nat Commun 2014; 5:4494. [PMID: 25058002 PMCID: PMC4124875 DOI: 10.1038/ncomms5494] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 06/24/2014] [Indexed: 12/17/2022] Open
Abstract
In living cells, most proteins diffuse over distances of micrometres within seconds. Protein translocation is constrained due to the cellular organization into subcompartments that impose diffusion barriers and guide enzymatic activities to their targets. Here, we introduce an approach to retrieve structural features from the scale-dependent mobility of green fluorescent protein monomer and multimers in human cells. We measure protein transport simultaneously between hundreds of positions by multi-scale fluorescence cross-correlation spectroscopy using a line-illuminating confocal microscope. From these data we derive a quantitative model of the intracellular architecture that resembles a random obstacle network for diffusing proteins. This topology partitions the cellular content and increases the dwell time of proteins in their local environment. The accessibility of obstacle surfaces depends on protein size. Our method links multi-scale mobility measurements with a quantitative description of intracellular structure that can be applied to evaluate how drug-induced perturbations affect protein transport and interactions. Numerous obstacles posed by cellular subcompartments and structures constrain protein transport in the cell. Here, Baum et al. map the intracellular topology from a diffusing protein’s point of view by measuring the diffusive movements of fluorescently labelled reporter proteins in living cells on multiple time and length scales.
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287
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Abstract
The integrity of our genetic material is under constant attack from numerous endogenous and exogenous agents. The consequences of a defective DNA damage response are well studied in proliferating cells, especially with regards to the development of cancer, yet its precise roles in the nervous system are relatively poorly understood. Here we attempt to provide a comprehensive overview of the consequences of genomic instability in the nervous system. We highlight the neuropathology of congenital syndromes that result from mutations in DNA repair factors and underscore the importance of the DNA damage response in neural development. In addition, we describe the findings of recent studies, which reveal that a robust DNA damage response is also intimately connected to aging and the manifestation of age-related neurodegenerative disorders such as Alzheimer's disease and amyotrophic lateral sclerosis.
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Affiliation(s)
- Ram Madabhushi
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ling Pan
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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288
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Choi JE, Mostoslavsky R. Sirtuins, metabolism, and DNA repair. Curr Opin Genet Dev 2014; 26:24-32. [PMID: 25005742 DOI: 10.1016/j.gde.2014.05.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/11/2014] [Accepted: 05/26/2014] [Indexed: 12/24/2022]
Abstract
Cells evolve to actively coordinate nutrient availability with cellular activity in order to maintain metabolic homeostasis. In addition, active pathways to repair DNA damage are crucial to avoid deleterious genomic instability. In recent years, it has become increasingly clear that availability of intermediate metabolites may play an important role in DNA repair, suggesting that these two seemingly distant cellular activities may be highly coordinated. The sirtuin family of proteins now described as deacylases (they can also remove acyl groups other than acetyl moieties), it appears to have evolved to control both metabolism and DNA repair. In this review, we discuss recent advances that lay the foundation to understanding the role of sirtuins in these two biological processes, and the potential crosstalk to coordinate them.
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Affiliation(s)
- Jee-Eun Choi
- Biological and Biomedical Sciences Graduate Program, Harvard Medical School, Boston, MA 02115, USA; The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA.
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289
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Aydin ÖZ, Marteijn JA, Ribeiro-Silva C, Rodríguez López A, Wijgers N, Smeenk G, van Attikum H, Poot RA, Vermeulen W, Lans H. Human ISWI complexes are targeted by SMARCA5 ATPase and SLIDE domains to help resolve lesion-stalled transcription. Nucleic Acids Res 2014; 42:8473-85. [PMID: 24990377 PMCID: PMC4117783 DOI: 10.1093/nar/gku565] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chromatin compaction of deoxyribonucleic acid (DNA) presents a major challenge to the detection and removal of DNA damage. Helix-distorting DNA lesions that block transcription are specifically repaired by transcription-coupled nucleotide excision repair, which is initiated by binding of the CSB protein to lesion-stalled RNA polymerase II. Using live cell imaging, we identify a novel function for two distinct mammalian ISWI adenosine triphosphate (ATP)-dependent chromatin remodeling complexes in resolving lesion-stalled transcription. Human ISWI isoform SMARCA5/SNF2H and its binding partners ACF1 and WSTF are rapidly recruited to UV-C induced DNA damage to specifically facilitate CSB binding and to promote transcription recovery. SMARCA5 targeting to UV-C damage depends on transcription and histone modifications and requires functional SWI2/SNF2-ATPase and SLIDE domains. After initial recruitment to UV damage, SMARCA5 re-localizes away from the center of DNA damage, requiring its HAND domain. Our studies support a model in which SMARCA5 targeting to DNA damage-stalled transcription sites is controlled by an ATP-hydrolysis-dependent scanning and proofreading mechanism, highlighting how SWI2/SNF2 chromatin remodelers identify and bind nucleosomes containing damaged DNA.
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Affiliation(s)
- Özge Z Aydin
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Jurgen A Marteijn
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Aida Rodríguez López
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Nils Wijgers
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Godelieve Smeenk
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Haico van Attikum
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Medical Genetics Cluster, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Hannes Lans
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
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290
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Lee N, Kim DK, Kim ES, Park SJ, Kwon JH, Shin J, Park SM, Moon YH, Wang HJ, Gho YS, Choi KY. Comparative interactomes of SIRT6 and SIRT7: Implication of functional links to aging. Proteomics 2014; 14:1610-22. [PMID: 24782448 DOI: 10.1002/pmic.201400001] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 04/01/2014] [Accepted: 04/25/2014] [Indexed: 12/21/2022]
Abstract
Sirtuins are NAD(+) -dependent deacetylases that regulate a range of cellular processes. Although diverse functions of sirtuins have been proposed, those functions of SIRT6 and SIRT7 that are mediated by their interacting proteins remain elusive. In the present study, we identified SIRT6- and SIRT7-interacting proteins, and compared their interactomes to investigate functional links. Our interactomes revealed 136 interacting proteins for SIRT6 and 233 for SIRT7 while confirming seven and 111 proteins identified previously for SIRT6 and SIRT7, respectively. Comparison of SIRT6 and SIRT7 interactomes under the same experimental conditions disclosed 111 shared proteins, implying related functional links. The interaction networks of interactomes indicated biological processes associated with DNA repair, chromatin assembly, and aging. Interactions of two highly acetylated proteins, nucleophosmin (NPM1) and nucleolin, with SIRT6 and SIRT7 were confirmed by co-immunoprecipitation. NPM1 was found to be deacetylated by both SIRT6 and SIRT7. In senescent cells, the acetylation level of NPM1 was increased in conjunction with decreased levels of SIRT6 and SIRT7, suggesting that the acetylation of NPM1 could be regulated by SIRT6 and SIRT7 in the aging process. Our comparative interactomic study of SIRT6 and SIRT7 implies important functional links to aging by their associations with interacting proteins. All MS data have been deposited in the ProteomeXchange with identifiers PXD000159 and PXD000850 (http://proteomecentral.proteomexchange.org/dataset/PXD000159, http://proteomecentral.proteomexchange.org/dataset/PXD000850).
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Affiliation(s)
- Namgyu Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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291
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Abstract
Aging of the hematological system causes anemia, reduced immunity, and increased incidence of hematological malignancies. Hematopoietic stem cells (HSCs) play a crucial role in this process as their functions decline during aging. Sirtuins are a family of protein lysine modifying enzymes that have diverse roles in regulating metabolism, genome stability, cell proliferation, and survival, and have been implicated in mammalian aging and longevity. Here we provide an updated overview of sirtuins in aging research; particularly, how increased activity of SIRT1, SIRT3, or SIRT6 improves several aging parameters, and may possibly increase lifespan in mice. We review the literature on how sirtuins may play a role in HSC aging and hematological malignancies, and how key signaling pathways of HSCs may be affected by sirtuins. Among them, SIRT1 plays a critical role in chronic myelogenous leukemia, an age-dependent malignancy, and inhibition of SIRT1 sensitizes leukemic stem cells to tyrosine kinase inhibitor treatment and blocks acquisition of resistant oncogene mutations. In-depth understanding of sirtuins in HSC aging and malignancy may help design novel strategies to deter hematological aging and improve treatment of hematological malignancies.
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Affiliation(s)
- Mendel Roth
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Zhiqiang Wang
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Wen Yong Chen
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
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292
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Abstract
Cellular proteins are decorated with a wide range of acetyl and other acyl modifications. Many studies have demonstrated regulation of site-specific acetylation by acetyltransferases and deacetylases. Acylation is emerging as a new type of lysine modification, but less is known about its overall regulatory role. Furthermore, the mechanisms of lysine acylation, its overlap with protein acetylation, and how it influences cellular function are major unanswered questions in the field. In this review, we discuss the known roles of acetyltransferases and deacetylases and the sirtuins as a conserved family of a nicotinamide adenine dinucleotide (NAD⁺)-dependent protein deacylases that are important for response to cellular stress and homeostasis. We also consider the evidence for an emerging idea of nonenzymatic protein acylation. Finally, we put forward the hypothesis that protein acylation is a form of protein "carbon stress" that the deacylases evolved to remove as a part of a global protein quality-control network.
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293
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Shetzer Y, Kagan S, Koifman G, Sarig R, Kogan-Sakin I, Charni M, Kaufman T, Zapatka M, Molchadsky A, Rivlin N, Dinowitz N, Levin S, Landan G, Goldstein I, Goldfinger N, Pe'er D, Radlwimmer B, Lichter P, Rotter V, Aloni-Grinstein R. The onset of p53 loss of heterozygosity is differentially induced in various stem cell types and may involve the loss of either allele. Cell Death Differ 2014; 21:1419-31. [PMID: 24832469 DOI: 10.1038/cdd.2014.57] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 02/27/2014] [Accepted: 03/17/2014] [Indexed: 12/12/2022] Open
Abstract
p53 loss of heterozygosity (p53LOH) is frequently observed in Li-Fraumeni syndrome (LFS) patients who carry a mutant (Mut) p53 germ-line mutation. Here, we focused on elucidating the link between p53LOH and tumor development in stem cells (SCs). Although adult mesenchymal stem cells (MSCs) robustly underwent p53LOH, p53LOH in induced embryonic pluripotent stem cells (iPSCs) was significantly attenuated. Only SCs that underwent p53LOH induced malignant tumors in mice. These results may explain why LFS patients develop normally, yet acquire tumors in adulthood. Surprisingly, an analysis of single-cell sub-clones of iPSCs, MSCs and ex vivo bone marrow (BM) progenitors revealed that p53LOH is a bi-directional process, which may result in either the loss of wild-type (WT) or Mut p53 allele. Interestingly, most BM progenitors underwent Mutp53LOH. Our results suggest that the bi-directional p53LOH process may function as a cell-fate checkpoint. The loss of Mutp53 may be regarded as a DNA repair event leading to genome stability. Indeed, gene expression analysis of the p53LOH process revealed upregulation of a specific chromatin remodeler and a burst of DNA repair genes. However, in the case of loss of WTp53, cells are endowed with uncontrolled growth that promotes cancer.
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Affiliation(s)
- Y Shetzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - S Kagan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - G Koifman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - R Sarig
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - I Kogan-Sakin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - M Charni
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - T Kaufman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - M Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - A Molchadsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - N Rivlin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - N Dinowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - S Levin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - G Landan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - I Goldstein
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - N Goldfinger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - D Pe'er
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - B Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - P Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - V Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - R Aloni-Grinstein
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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294
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Vidi PA, Liu J, Salles D, Jayaraman S, Dorfman G, Gray M, Abad P, Moghe PV, Irudayaraj JM, Wiesmüller L, Lelièvre SA. NuMA promotes homologous recombination repair by regulating the accumulation of the ISWI ATPase SNF2h at DNA breaks. Nucleic Acids Res 2014; 42:6365-79. [PMID: 24753406 PMCID: PMC4041463 DOI: 10.1093/nar/gku296] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Chromatin remodeling factors play an active role in the DNA damage response by shaping chromatin to facilitate the repair process. The spatiotemporal regulation of these factors is key to their function, yet poorly understood. We report that the structural nuclear protein NuMA accumulates at sites of DNA damage in a poly[ADP-ribose]ylation-dependent manner and functionally interacts with the ISWI ATPase SNF2h/SMARCA5, a chromatin remodeler that facilitates DNA repair. NuMA coimmunoprecipitates with SNF2h, regulates its diffusion in the nucleoplasm and controls its accumulation at DNA breaks. Consistent with NuMA enabling SNF2h function, cells with silenced NuMA exhibit reduced chromatin decompaction after DNA cleavage, lesser focal recruitment of homologous recombination repair factors, impaired DNA double-strand break repair in chromosomal (but not in episomal) contexts and increased sensitivity to DNA cross-linking agents. These findings reveal a structural basis for the orchestration of chromatin remodeling whereby a scaffold protein promotes genome maintenance by directing a remodeler to DNA breaks.
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Affiliation(s)
- Pierre-Alexandre Vidi
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jing Liu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Daniela Salles
- Department of Obstetrics and Gynecology, University of Ulm, Prittwitzstrasse 43, D-89075 Ulm, Germany
| | - Swaathi Jayaraman
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - George Dorfman
- Department of Biomedical Engineering, and Chemical & Biochemical Engineering, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gray
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Patricia Abad
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Prabhas V Moghe
- Department of Biomedical Engineering, and Chemical & Biochemical Engineering, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph M Irudayaraj
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, University of Ulm, Prittwitzstrasse 43, D-89075 Ulm, Germany
| | - Sophie A Lelièvre
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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295
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53BP1, BRCA1, and the choice between recombination and end joining at DNA double-strand breaks. Mol Cell Biol 2014; 34:1380-8. [PMID: 24469398 DOI: 10.1128/mcb.01639-13] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
When DNA double-strand breaks occur, the cell cycle stage has a major influence on the choice of the repair pathway employed. Specifically, nonhomologous end joining is the predominant mechanism used in the G1 phase of the cell cycle, while homologous recombination becomes fully activated in S phase. Studies over the past 2 decades have revealed that the aberrant joining of replication-associated breaks leads to catastrophic genome rearrangements, revealing an important role of DNA break repair pathway choice in the preservation of genome integrity. 53BP1, first identified as a DNA damage checkpoint protein, and BRCA1, a well-known breast cancer tumor suppressor, are at the center of this choice. Research on how these proteins function at the DNA break site has advanced rapidly in the recent past. Here, we review what is known regarding how the repair pathway choice is made, including the mechanisms that govern the recruitment of each critical factor, and how the cell transitions from end joining in G1 to homologous recombination in S/G2.
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296
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Kugel S, Mostoslavsky R. Chromatin and beyond: the multitasking roles for SIRT6. Trends Biochem Sci 2014; 39:72-81. [PMID: 24438746 DOI: 10.1016/j.tibs.2013.12.002] [Citation(s) in RCA: 288] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/27/2013] [Accepted: 12/06/2013] [Indexed: 12/12/2022]
Abstract
In recent years there has been a large expansion in our understanding of SIRT6 biology including its structure, regulation, biochemical activity, and biological roles. SIRT6 functions as an ADP-ribosylase and NAD(+)-dependent deacylase of both acetyl groups and long-chain fatty-acyl groups. Through these functions SIRT6 impacts upon cellular homeostasis by regulating DNA repair, telomere maintenance, and glucose and lipid metabolism, thus affecting diseases such diabetes, obesity, heart disease, and cancer. Such roles may contribute to the overall longevity and health of the organism. Until recently, the known functions of SIRT6 were largely restricted to the chromatin. In this article we seek to describe and expand this knowledge with recent advances in understanding the mechanisms of SIRT6 action and their implications for human biology and disease.
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Affiliation(s)
- Sita Kugel
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Raul Mostoslavsky
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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297
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Maroschik B, Gürtler A, Krämer A, Rößler U, Gomolka M, Hornhardt S, Mörtl S, Friedl AA. Radiation-induced alterations of histone post-translational modification levels in lymphoblastoid cell lines. Radiat Oncol 2014; 9:15. [PMID: 24406105 PMCID: PMC3903440 DOI: 10.1186/1748-717x-9-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 12/23/2013] [Indexed: 12/22/2022] Open
Abstract
Background Radiation-induced alterations in posttranslational histone modifications (PTMs) may affect the cellular response to radiation damage in the DNA. If not reverted appropriately, altered PTM patterns may cause long-term alterations in gene expression regulation and thus lead to cancer. It is therefore important to characterize radiation-induced alterations in PTM patterns and the factors affecting them. Methods A lymphoblastoid cell line established from a normal donor was used to screen for alterations in methylation levels at H3K4, H3K9, H3K27, and H4K20, as well as acetylation at H3K9, H3K56, H4K5, and H4K16, by quantitative Western Blot analysis at 15 min, 1 h and 24 h after irradiation with 2 Gy and 10 Gy. The variability of alterations in acetylation marks was in addition investigated in a panel of lymphoblastoid cell lines with differing radiosensitivity established from lung cancer patients. Results The screening procedure demonstrated consistent hypomethylation at H3K4me3 and hypoacetylation at all acetylation marks tested. In the panel of lymphoblastoid cell lines, however, a high degree of inter-individual variability became apparent. Radiosensitive cell lines showed more pronounced and longer lasting H4K16 hypoacetylation than radioresistant lines, which correlates with higher levels of residual γ-H2AX foci after 24 h. Conclusion So far, the factors affecting extent and duration of radiation-induced histone alterations are poorly defined. The present work hints at a high degree of inter-individual variability and a potential correlation of DNA damage repair capacity and alterations in PTM levels.
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Affiliation(s)
| | | | | | | | | | | | | | - Anna A Friedl
- Department of Radiation Oncology, Ludwig-Maximilians-University, Munich, Germany.
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298
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299
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Sirbu BM, McDonald WH, Dungrawala H, Badu-Nkansah A, Kavanaugh GM, Chen Y, Tabb DL, Cortez D. Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry. J Biol Chem 2013; 288:31458-67. [PMID: 24047897 DOI: 10.1074/jbc.m113.511337] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Both DNA and chromatin need to be duplicated during each cell division cycle. Replication happens in the context of defects in the DNA template and other forms of replication stress that present challenges to both genetic and epigenetic inheritance. The replication machinery is highly regulated by replication stress responses to accomplish this goal. To identify important replication and stress response proteins, we combined isolation of proteins on nascent DNA (iPOND) with quantitative mass spectrometry. We identified 290 proteins enriched on newly replicated DNA at active, stalled, and collapsed replication forks. Approximately 16% of these proteins are known replication or DNA damage response proteins. Genetic analysis indicates that several of the newly identified proteins are needed to facilitate DNA replication, especially under stressed conditions. Our data provide a useful resource for investigators studying DNA replication and the replication stress response and validate the use of iPOND combined with mass spectrometry as a discovery tool.
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300
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Liu J, Kim J, Oberdoerffer P. Metabolic modulation of chromatin: implications for DNA repair and genomic integrity. Front Genet 2013; 4:182. [PMID: 24065984 PMCID: PMC3779809 DOI: 10.3389/fgene.2013.00182] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/27/2013] [Indexed: 01/06/2023] Open
Abstract
The maintenance of genomic integrity in response to DNA damage is tightly linked to controlled changes in the damage-proximal chromatin environment. Many of the chromatin modifying enzymes involved in DNA repair depend on metabolic intermediates as cofactors, suggesting that changes in cellular metabolism can have direct consequences for repair efficiency and ultimately, genome stability. Here, we discuss how metabolites may contribute to DNA double-strand break repair, and how alterations in cellular metabolism associated with both aging and tumorigenesis may affect the integrity of our genomes.
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Affiliation(s)
- Jinping Liu
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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