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Celona B, Salomonsson SE, Wu H, Dang B, Kratochvil HT, Clelland CD, DeGrado WF, Black BL. Zfp106 binds to G-quadruplex RNAs and inhibits RAN translation and formation of RNA foci caused by G4C2 repeats. Proc Natl Acad Sci U S A 2024; 121:e2220020121. [PMID: 39042693 PMCID: PMC11295049 DOI: 10.1073/pnas.2220020121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/14/2024] [Indexed: 07/25/2024] Open
Abstract
Expansion of intronic GGGGCC repeats in the C9orf72 gene causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Transcription of the expanded repeats results in the formation of RNA-containing nuclear foci and altered RNA metabolism. In addition, repeat-associated non-AUG (RAN) translation of the expanded GGGGCC-repeat sequence results in the production of highly toxic dipeptide-repeat (DPR) proteins. GGGGCC repeat-containing transcripts form G-quadruplexes, which are associated with formation of RNA foci and RAN translation. Zfp106, an RNA-binding protein essential for motor neuron survival in mice, suppresses neurotoxicity in a Drosophila model of C9orf72 ALS. Here, we show that Zfp106 inhibits formation of RNA foci and significantly reduces RAN translation caused by GGGGCC repeats in cultured mammalian cells, and we demonstrate that Zfp106 coexpression reduces the levels of DPRs in C9orf72 patient-derived cells. Further, we show that Zfp106 binds to RNA G-quadruplexes and causes a conformational change in the G-quadruplex structure formed by GGGGCC repeats. Together, these data demonstrate that Zfp106 suppresses the formation of RNA foci and DPRs caused by GGGGCC repeats and suggest that the G-quadruplex RNA-binding function of Zfp106 contributes to its suppression of GGGGCC repeat-mediated cytotoxicity.
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Affiliation(s)
- Barbara Celona
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
| | - Sally E. Salomonsson
- Weill Institute for Neurosciences, University of California, San Francisco, CA94143
- Memory & Aging Center, Department of Neurology, University of California, San Francisco, CA94143
| | - Haifan Wu
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Bobo Dang
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Huong T. Kratochvil
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Claire D. Clelland
- Weill Institute for Neurosciences, University of California, San Francisco, CA94143
- Memory & Aging Center, Department of Neurology, University of California, San Francisco, CA94143
| | - William F. DeGrado
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Brian L. Black
- Cardiovascular Research Institute, University of California, San Francisco, CA94143
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
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2
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Liu Y, McGann CD, Krebs M, Perkins TA, Fields R, Camplisson CK, Nwizugbo DZ, Hsu C, Avanessian SC, Tsue AF, Kania EE, Shechner DM, Beliveau BJ, Schweppe DK. DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604987. [PMID: 39091817 PMCID: PMC11291153 DOI: 10.1101/2024.07.24.604987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition of chromatin and the regulatory proteins that reside there. Understanding these DNA-protein interactions at the level of specific genomic loci has remained challenging due to technical limitations. Here, we introduce a method termed "DNA O-MAP", which uses programmable peroxidase-conjugated oligonucleotide probes to biotinylate nearby proteins. We show that DNA O-MAP can be coupled with sample multiplexed quantitative proteomics and next-generation sequencing to quantify DNA-protein and DNA-DNA interactions at specific genomic loci.
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Affiliation(s)
- Yuzhen Liu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- These authors contributed equally: Yuzhen Liu, Christopher D. McGann
| | - Christopher D. McGann
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- These authors contributed equally: Yuzhen Liu, Christopher D. McGann
| | - Mary Krebs
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Thomas A. Perkins
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Conor K. Camplisson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - David Z. Nwizugbo
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Chris Hsu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Shayan C. Avanessian
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Ashley F. Tsue
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
| | - Evan E. Kania
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
| | - David M. Shechner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
| | - Brian J. Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
| | - Devin K. Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
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3
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Thenin-Houssier S, Machida S, Jahan C, Bonnet-Madin L, Abbou S, Chen HC, Tesfaye R, Cuvier O, Benkirane M. POLE3 is a repressor of unintegrated HIV-1 DNA required for efficient virus integration and escape from innate immune sensing. SCIENCE ADVANCES 2023; 9:eadh3642. [PMID: 37922361 PMCID: PMC10624344 DOI: 10.1126/sciadv.adh3642] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
Abstract
Unintegrated retroviral DNA is transcriptionally silenced by host chromatin silencing factors. Here, we used the proteomics of isolated chromatin segments method to reveal viral and host factors associated with unintegrated HIV-1DNA involved in its silencing. By gene silencing using siRNAs, 46 factors were identified as potential repressors of unintegrated HIV-1DNA. Knockdown and knockout experiments revealed POLE3 as a transcriptional repressor of unintegrated HIV-1DNA. POLE3 maintains unintegrated HIV-1DNA in a repressive chromatin state, preventing RNAPII recruitment to the viral promoter. POLE3 and the recently identified host factors mediating unintegrated HIV-1 DNA silencing, CAF1 and SMC5/SMC6/SLF2, show specificity toward different forms of unintegrated HIV-1DNA. Loss of POLE3 impaired HIV-1 replication, suggesting that repression of unintegrated HIV-1DNA is important for optimal viral replication. POLE3 depletion reduces the integration efficiency of HIV-1. POLE3, by maintaining a repressive chromatin structure of unintegrated HIV-1DNA, ensures HIV-1 escape from innate immune sensing in primary CD4+ T cells.
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Affiliation(s)
- Suzie Thenin-Houssier
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Shinichi Machida
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
- Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Cyprien Jahan
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Lucie Bonnet-Madin
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Scarlette Abbou
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Heng-Chang Chen
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Robel Tesfaye
- Laboratory of Chromatin Dynamics, Centre de Biologie Intégrative (CBI), MCD Unit (UMR5077), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Cuvier
- Laboratory of Chromatin Dynamics, Centre de Biologie Intégrative (CBI), MCD Unit (UMR5077), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Monsef Benkirane
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
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4
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MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
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Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
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5
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Cheng R, Zheng X, Wang Y, Ma X, Liu X, Xu W, Wang M, Gao Y, Xing X, Zhou C, Sun H, Guo Z, Quan F, Liu J, Hua S, Wang Y, Zhang Y, Liu X. Modification of alternative splicing in bovine somatic cell nuclear transfer embryos using engineered CRISPR-Cas13d. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2257-2268. [PMID: 35524909 DOI: 10.1007/s11427-021-2060-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Animal cloning can be achieved by somatic cell nuclear transfer (SCNT), but the resulting live birth rate is relatively low. We previously improved the efficiency of bovine SCNT by exogenous melatonin treatment or by overexpression of lysine-specific demethylase 4D (KDM4D) and 4E (KDM4E). In this study, we revealed abundant alternative splicing (AS) transitions during fertilization and embryonic genome activation, and demonstrated abnormal AS in bovine SCNT embryos compared with in vitro fertilized embryos. We used the CRISPR-Cas13d RNA-targeting system to target cis-elements of ABI2 and ZNF106 pre-mRNA to modify AS, thus reducing the ratio of abnormal-isoform SCNT embryos by nearly 50% and achieving a high survival rate (11%-19%). These results indicate that this system may provide an efficient method for bovine cloning, while also paving the way for further improvements in the efficiency of SCNT.
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Affiliation(s)
- Rui Cheng
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Xiaoman Zheng
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Yingmei Wang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Xing Ma
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Xin Liu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Wenjun Xu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Mengyun Wang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Yuanpeng Gao
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Xupeng Xing
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Chuan Zhou
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Hongzheng Sun
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Fusheng Quan
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China
| | - Jun Liu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
| | - Song Hua
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
| | - Yongsheng Wang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
| | - Xu Liu
- College of Veterinary Medicine, Northwest A&F University, Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, 712100, China.
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6
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Yang K, Feng X, Yu G, Han W, Liu F, Xie Y, Zhang H, Yu Y, Zou G. Single polymeric microfiber waveguide platform for sensitive detection and discrimination of DNA methylation. Analyst 2022; 147:1892-1898. [DOI: 10.1039/d1an02243a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel sensitive detection platform for p16 and p16 methylation based on a single polymeric fluorescent microfiber waveguide with sandwich-structured hybridization designs.
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Affiliation(s)
- Kexin Yang
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Xiaohui Feng
- Division of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Gaoyuan Yu
- Undergraduate major in clinical medicine, grade 2017, class 1, Medical College of Hubei University of Science and Technology, Xianning, Hubei 437100, P. R. China
| | - Wenjie Han
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Funing Liu
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Yifan Xie
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Hongli Zhang
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Yue Yu
- Division of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Gang Zou
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
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7
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Ide S, Sasaki A, Kawamoto Y, Bando T, Sugiyama H, Maeshima K. Telomere-specific chromatin capture using a pyrrole-imidazole polyamide probe for the identification of proteins and non-coding RNAs. Epigenetics Chromatin 2021; 14:46. [PMID: 34627342 PMCID: PMC8502363 DOI: 10.1186/s13072-021-00421-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
Background Knowing chromatin components at a DNA regulatory element at any given time is essential for understanding how the element works during cellular proliferation, differentiation and development. A region-specific chromatin purification is an invaluable approach to dissecting the comprehensive chromatin composition at a particular region. Several methods (e.g., PICh, enChIP, CAPTURE and CLASP) have been developed for isolating and analyzing chromatin components. However, all of them have some shortcomings in identifying non-coding RNA associated with DNA regulatory elements. Results We have developed a new approach for affinity purification of specific chromatin segments employing an N-methyl pyrrole (P)-N-methylimidazole (I) (PI) polyamide probe, which binds to a specific sequence in double-stranded DNA via Watson–Crick base pairing as a minor groove binder. This new technique is called proteomics and RNA-omics of isolated chromatin segments (PI-PRICh). Using PI-PRICh to isolate mouse and human telomeric components, we found enrichments of shelterin proteins, the well-known telomerase RNA component (TERC) and telomeric repeat-containing RNA (TERRA). When PI-PRICh was performed for alternative lengthening of telomere (ALT) cells with highly recombinogenic telomeres, in addition to the conventional telomeric chromatin, we obtained chromatin regions containing telomeric repeat insertions scattered in the genome and their associated RNAs. Conclusion PI-PRICh reproducibly identified both the protein and RNA components of telomeric chromatin when targeting telomere repeats. PI polyamide is a promising alternative to simultaneously isolate associated proteins and RNAs of sequence-specific chromatin regions under native conditions, allowing better understanding of chromatin organization and functions within the cell. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00421-8.
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Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.
| | - Asuka Sasaki
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
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8
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Fujita H, Fujita T, Fujii H. Locus-Specific Genomic DNA Purification Using the CRISPR System: Methods and Applications. CRISPR J 2021; 4:290-300. [PMID: 33876963 DOI: 10.1089/crispr.2020.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A multitude of molecular interactions with chromatin governs various chromosomal functions in cells. Insights into the molecular compositions at specific genomic regions are pivotal to deepen our understanding of regulatory mechanisms and the pathogenesis of disorders caused by the abnormal regulation of genes. The locus-specific purification of genomic DNA using the clustered regularly interspaced short palindromic repeats (CRISPR) system enables the isolation of target genomic regions for identification of bound interacting molecules. This CRISPR-based DNA purification method has many applications. In this study, we present an overview of the CRISPR-based DNA purification methodologies as well as recent applications.
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Affiliation(s)
- Hirotaka Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan
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9
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Knaupp AS, Mohenska M, Larcombe MR, Ford E, Lim SM, Wong K, Chen J, Firas J, Huang C, Liu X, Nguyen T, Sun YBY, Holmes ML, Tripathi P, Pflueger J, Rossello FJ, Schröder J, Davidson KC, Nefzger CM, Das PP, Haigh JJ, Lister R, Schittenhelm RB, Polo JM. TINC- A Method to Dissect Regulatory Complexes at Single-Locus Resolution- Reveals an Extensive Protein Complex at the Nanog Promoter. Stem Cell Reports 2020; 15:1246-1259. [PMID: 33296673 PMCID: PMC7724517 DOI: 10.1016/j.stemcr.2020.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
Cellular identity is ultimately dictated by the interaction of transcription factors with regulatory elements (REs) to control gene expression. Advances in epigenome profiling techniques have significantly increased our understanding of cell-specific utilization of REs. However, it remains difficult to dissect the majority of factors that interact with these REs due to the lack of appropriate techniques. Therefore, we developed TINC: TALE-mediated isolation of nuclear chromatin. Using this new method, we interrogated the protein complex formed at the Nanog promoter in embryonic stem cells (ESCs) and identified many known and previously unknown interactors, including RCOR2. Further interrogation of the role of RCOR2 in ESCs revealed its involvement in the repression of lineage genes and the fine-tuning of pluripotency genes. Consequently, using the Nanog promoter as a paradigm, we demonstrated the power of TINC to provide insight into the molecular makeup of specific transcriptional complexes at individual REs as well as into cellular identity control in general. TINC allows the isolation of a specific locus for molecular analyses TINC identified hundreds of proteins at the Nanog promoter RCOR2 is a component of the pluripotency network in embryonic stem cells RCOR2 is required for efficient differentiation
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Affiliation(s)
- Anja S Knaupp
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Monika Mohenska
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michael R Larcombe
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Sue Mei Lim
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kayla Wong
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jaber Firas
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Xiaodong Liu
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Trung Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Yu B Y Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Melissa L Holmes
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Pratibha Tripathi
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jan Schröder
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kathryn C Davidson
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Partha P Das
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia
| | - Jody J Haigh
- Australian Centre for Blood Diseases, Monash University, Clayton, VIC 3004, Australia; Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB, Canada; Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia.
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10
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Ide S, Imai R, Ochi H, Maeshima K. Transcriptional suppression of ribosomal DNA with phase separation. SCIENCE ADVANCES 2020; 6:6/42/eabb5953. [PMID: 33055158 PMCID: PMC7556839 DOI: 10.1126/sciadv.abb5953] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/25/2020] [Indexed: 05/21/2023]
Abstract
The nucleolus is a nuclear body with multiphase liquid droplets for ribosomal RNA (rRNA) transcription. How rRNA transcription is regulated in the droplets remains unclear. Here, using single-molecule tracking of RNA polymerase I (Pol I) and chromatin-bound upstream binding factor (UBF), we reveal suppression of transcription with phase separation. For transcription, active Pol I formed small clusters/condensates that constrained rDNA chromatin in the nucleolus fibrillar center (FC). Treatment with a transcription inhibitor induced Pol I to dissociate from rDNA chromatin and to move like a liquid within the nucleolar cap that transformed from the FC. Expression of a Pol I mutant associated with a craniofacial disorder inhibited transcription by competing with wild-type Pol I clusters and transforming the FC into the nucleolar cap. The cap droplet excluded an initiation factor, ensuring robust silencing. Our findings suggest a mechanism of rRNA transcription suppression via phase separation of intranucleolar molecules governed by Pol I.
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Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
| | - Ryosuke Imai
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
| | - Hiroko Ochi
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
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11
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Scott WA, Campos EI. Interactions With Histone H3 & Tools to Study Them. Front Cell Dev Biol 2020; 8:701. [PMID: 32850821 PMCID: PMC7411163 DOI: 10.3389/fcell.2020.00701] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/10/2020] [Indexed: 01/12/2023] Open
Abstract
Histones are an integral part of chromatin and thereby influence its structure, dynamics, and functions. The effects of histone variants, posttranslational modifications, and binding proteins is therefore of great interest. From the moment that they are deposited on chromatin, nucleosomal histones undergo dynamic changes in function of the cell cycle, and as DNA is transcribed and replicated. In the process, histones are not only modified and bound by various proteins, but also shuffled, evicted, or replaced. Technologies and tools to study such dynamic events continue to evolve and better our understanding of chromatin and of histone proteins proper. Here, we provide an overview of H3.1 and H3.3 histone dynamics throughout the cell cycle, while highlighting some of the tools used to study their protein–protein interactions. We specifically discuss how histones are chaperoned, modified, and bound by various proteins at different stages of the cell cycle. Established and select emerging technologies that furthered (or have a high potential of furthering) our understanding of the dynamic histone–protein interactions are emphasized. This includes experimental tools to investigate spatiotemporal changes on chromatin, the role of histone chaperones, histone posttranslational modifications, and histone-binding effector proteins.
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Affiliation(s)
- William A Scott
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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12
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Purification and enrichment of specific chromatin loci. Nat Methods 2020; 17:380-389. [PMID: 32152500 DOI: 10.1038/s41592-020-0765-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then describe the published strategies and discuss their advantages and limitations. We conclude by discussing why significant technology developments are required to unambiguously describe the composition of small single loci.
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13
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Vermeulen M, Déjardin J. Locus-specific chromatin isolation. Nat Rev Mol Cell Biol 2020; 21:249-250. [PMID: 31996790 DOI: 10.1038/s41580-020-0217-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands.
| | - Jérôme Déjardin
- Institute of Human Genetics, CNRS-Université de Montpellier, Montpellier, France.
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14
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Abstract
Identification of the protein complexes associated with defined DNA sequence elements is essential to understand the numerous transactions in which DNA is involved, such as replication, repair, transcription, and chromatin dynamics. Here we describe two protocols, IDAP (Isolation of DNA Associated Proteins) and CoIFI (Chromatin-of-Interest Fragment Isolation), that allow for isolating DNA/protein complexes (i.e., nucleoprotein elements) by means of a DNA capture tool based on DNA triple helix (triplex) formation. Typically, IDAP is used to capture proteins that bind to a given DNA element of interest (e.g., a specific DNA sequence, an unusual DNA structure, a DNA lesion) that can be introduced at will into plasmids. The plasmids are immobilized by means of a triplex-forming probe on magnetic beads and incubated in nuclear extracts; by using in parallel a control plasmid (that lacks the DNA element of interest), proteins that preferentially bind to the DNA element of interest are captured and identified by mass spectrometry. Similarly, CoIFI also uses a triplex-forming probe to capture a specific chromatin fragment from a cultured cell line that has been engineered to contain multiple copies of the DNA element of interest.
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Affiliation(s)
- Asako Isogawa
- DNA Damage Tolerance, CNRS, Marseille, France
- Inserm, CRCM, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Aix-Marseille University, Marseille, France
| | - Robert P Fuchs
- Marseille Medical Genetics, Aix-Marseille University, Inserm, Marseille, France.
| | - Shingo Fujii
- DNA Damage Tolerance, CNRS, Marseille, France.
- Inserm, CRCM, Marseille, France.
- Institut Paoli-Calmettes, Marseille, France.
- Aix-Marseille University, Marseille, France.
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15
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Jensen IS, Yuan J, He J, Lin L, Sander B, Golas MM. The FlpTRAP system for purification of specific, endogenous chromatin regions. Anal Biochem 2019; 587:113418. [PMID: 31520595 DOI: 10.1016/j.ab.2019.113418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/07/2019] [Accepted: 09/08/2019] [Indexed: 10/26/2022]
Abstract
The repressor element 1-silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) binds to repressor element 1/neuron-restrictive silencer element (RE1/NRSE) sites in the genome and recruits effector proteins to repress its target genes. Here, we developed the FlpTRAP system to isolate endogenously assembled DNA-protein complexes such as the REST/NRSF complex. In the FlpTRAP system, we take advantage of the step-arrest variant of the Flp recombinase, FlpH305L, which, in the presence of Flp recognition target (FRT) DNA, accumulates as FRT DNA-protein adduct. The FlpTRAP system consists of three elements: (i) FlpH305L-containing cell extracts or isolates, (ii) a cell line engineered to harbor the DNA motif of interest flanked by FRT sites, and (iii) affinity selection steps to isolate the target chromatin. Specifically, 3×FLAG-tagged FlpH305L was expressed in insect cell cultures infected with baculovirus, and cell lysates were prepared. The lysate was used to capture the FRT-SNAP25 RE1/NRSE-FRT chromatin from a human medulloblastoma cell line, and the target RE1/NRSE chromatin was isolated by anti-FLAG immunoaffinity chromatography. Using electrophoretic mobility shift assays (EMSAs) and chromatin immunopurification (ChIP), we show that FlpH305L recognized and bound to the FRT sites. Overall, we suggest the FlpTRAP system as a tool to purify endogenous, specific chromatin loci from eukaryotic cells.
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Affiliation(s)
- Ida S Jensen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Juan Yuan
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Jin He
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Bjoern Sander
- Centre for Stochastic Geometry and Advanced Bioimaging, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark
| | - Monika M Golas
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Building 1233, 8000, Aarhus C, Denmark.
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16
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A distinct isoform of ZNF207 controls self-renewal and pluripotency of human embryonic stem cells. Nat Commun 2018; 9:4384. [PMID: 30349051 PMCID: PMC6197280 DOI: 10.1038/s41467-018-06908-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 09/21/2018] [Indexed: 01/08/2023] Open
Abstract
Self-renewal and pluripotency in human embryonic stem cells (hESCs) depends upon the function of a remarkably small number of master transcription factors (TFs) that include OCT4, SOX2, and NANOG. Endogenous factors that regulate and maintain the expression of master TFs in hESCs remain largely unknown and/or uncharacterized. Here, we use a genome-wide, proteomics approach to identify proteins associated with the OCT4 enhancer. We identify known OCT4 regulators, plus a subset of potential regulators including a zinc finger protein, ZNF207, that plays diverse roles during development. In hESCs, ZNF207 partners with master pluripotency TFs to govern self-renewal and pluripotency while simultaneously controlling commitment of cells towards ectoderm through direct regulation of neuronal TFs, including OTX2. The distinct roles of ZNF207 during differentiation occur via isoform switching. Thus, a distinct isoform of ZNF207 functions in hESCs at the nexus that balances pluripotency and differentiation to ectoderm.
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17
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Isogawa A, Fuchs RP, Fujii S. Versatile and efficient chromatin pull-down methodology based on DNA triple helix formation. Sci Rep 2018; 8:5925. [PMID: 29651103 PMCID: PMC5897567 DOI: 10.1038/s41598-018-24417-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 03/23/2018] [Indexed: 11/09/2022] Open
Abstract
The goal of present paper is to develop a reliable DNA-based method for isolation of protein complexes bound to DNA (Isolation of DNA Associated Proteins: IDAP). We describe a robust and versatile procedure to pull-down chromatinized DNA sequences-of-interest by formation of a triple helix between a sequence tag present in the DNA and a complementary triple helix forming oligonucleotide (TFO) coupled to a desthiobiotin residue. Following optimization to insure efficient recovery of native plasmids via TFO probe in vitro, the procedure is shown to work under various experimental situations. For instance, it allows capture proteins associated to plasmids hosted in E. coli, and is also successfully applied to recovering nucleosomes in vitro opening many possibilities to study post translational modifications of histones in a genuine nucleosome context. Incubation in human nuclear extracts of a plasmid carrying a NF-κB model promoter is shown to pull-down a specific transcription factor. Finally, isolation of a specific locus from human genomic chromatin has been successfully achieved (Chromatin-of-Interest Fragment Isolation: CoIFI). In conclusion, the methodology can be implemented for capturing proteins that specifically bind to any sequence-of-interest, DNA adduct or secondary structure provided a short sequence tag for triple helix formation is located nearby.
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Affiliation(s)
- Asako Isogawa
- DNA Damage Tolerance CNRS, UMR7258, Marseille, F-13009, France.,Inserm, U1068, CRCM, Marseille, F-13009, France.,Institut Paoli-Calmettes, Marseille, F-13009, France.,Aix-Marseille University, UM 105, F-13284, Marseille, France
| | - Robert P Fuchs
- DNA Damage Tolerance CNRS, UMR7258, Marseille, F-13009, France. .,Inserm, U1068, CRCM, Marseille, F-13009, France. .,Institut Paoli-Calmettes, Marseille, F-13009, France. .,Aix-Marseille University, UM 105, F-13284, Marseille, France. .,Harvard Medical School, Boston, MA, 02115, USA.
| | - Shingo Fujii
- DNA Damage Tolerance CNRS, UMR7258, Marseille, F-13009, France. .,Inserm, U1068, CRCM, Marseille, F-13009, France. .,Institut Paoli-Calmettes, Marseille, F-13009, France. .,Aix-Marseille University, UM 105, F-13284, Marseille, France.
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18
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Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R. dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Proc Natl Acad Sci U S A 2018; 115:E2734-E2741. [PMID: 29507191 PMCID: PMC5866577 DOI: 10.1073/pnas.1718844115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic gene regulation is a complex process, often coordinated by the action of tens to hundreds of proteins. Although previous biochemical studies have identified many components of the basal machinery and various ancillary factors involved in gene regulation, numerous gene-specific regulators remain undiscovered. To comprehensively survey the proteome directing gene expression at a specific genomic locus of interest, we developed an in vitro nuclease-deficient Cas9 (dCas9)-targeted chromatin-based purification strategy, called "CLASP" (Cas9 locus-associated proteome), to identify and functionally test associated gene-regulatory factors. Our CLASP method, coupled to mass spectrometry and functional screens, can be efficiently adapted for isolating associated regulatory factors in an unbiased manner targeting multiple genomic loci across different cell types. Here, we applied our method to isolate the Drosophila melanogaster histone cluster in S2 cells to identify several factors including Vig and Vig2, two proteins that bind and regulate core histone H2A and H3 mRNA via interaction with their 3' UTRs.
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Affiliation(s)
- Chiahao Tsui
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Carla Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Andrew Lu
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720;
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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19
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Hermans N, Huisman JJ, Brouwer TB, Schächner C, van Heusden GPH, Griesenbeck J, van Noort J. Toehold-enhanced LNA probes for selective pull down and single-molecule analysis of native chromatin. Sci Rep 2017; 7:16721. [PMID: 29196662 PMCID: PMC5711847 DOI: 10.1038/s41598-017-16864-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022] Open
Abstract
The organization of DNA into chromatin is thought to regulate gene expression in eukaryotes. To study its structure in vitro, there is a need for techniques that can isolate specific chromosomal loci of natively assembled chromatin. Current purification methods often involve chemical cross-linking to preserve the chromatin composition. However, such cross-linking may affect the native structure. It also impedes single molecule force spectroscopy experiments, which have been instrumental to probe chromatin folding. Here we present a method for the incorporation of affinity tags, such as biotin, into native nucleoprotein fragments based on their DNA sequence, and subsequent single molecule analysis by magnetic tweezers. DNA oligos with several Locked Nucleic Acid (LNA) nucleotides are shown to selectively bind to target DNA at room temperature, mediated by a toehold end in the target, allowing for selective purification of DNA fragments. The stability of the probe-target hybrid is sufficient to withstand over 65 pN of force. We employ these probes to obtain force-extension curves of native chromatin fragments of the 18S ribosomal DNA from the yeast Saccharomyces cerevisiae. These experiments yield valuable insights in the heterogeneity in structure and composition of natively assembled chromatin at the single-molecule level.
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Affiliation(s)
- Nicolaas Hermans
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Niels Bohrweg, 2 2333 CA, Leiden, The Netherlands
| | - Juriën Jori Huisman
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Niels Bohrweg, 2 2333 CA, Leiden, The Netherlands
| | - Thomas Bauke Brouwer
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Niels Bohrweg, 2 2333 CA, Leiden, The Netherlands
| | - Christopher Schächner
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Institut für Biochemie, Genetik und Mikrobiologie, Lehrstuhl Biochemie III, 93053, Regensburg, Germany
| | - G Paul H van Heusden
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Joachim Griesenbeck
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Institut für Biochemie, Genetik und Mikrobiologie, Lehrstuhl Biochemie III, 93053, Regensburg, Germany
| | - John van Noort
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Niels Bohrweg, 2 2333 CA, Leiden, The Netherlands.
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20
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Feng N, Wang Y, Zheng M, Yu X, Lin H, Ma RN, Shi O, Zheng X, Gao M, Yu H, Garmire L, Qian B. Genome-wide analysis of DNA methylation and their associations with long noncoding RNA/mRNA expression in non-small-cell lung cancer. Epigenomics 2017; 9:137-153. [PMID: 28111977 DOI: 10.2217/epi-2016-0120] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIM The goal of this study is to identify differentially methylated (DM) loci associated with long noncoding RNA (lncRNA)/mRNA expression in non-small-cell lung cancer (NSCLC). MATERIALS & METHODS Microarrays were used to interrogate genome-wide methylation and expression of lncRNA/mRNA in NSCLC. RESULTS We identified 113,644 DM loci between tumors and adjacent tissues. Among them, 26,310 DM loci were associated with 1685 differentially expressed genes, and 839 genes had significant correlations between methylation and expression, of which 26 hypermethylated loci in transcription start site 200 were correlated with low gene expression. We validated the correlations between methylation and expression in five genes (CDO1, C2orf40, SCARF1, ZFP106 and IFFO1) using pyrosequencing and quantitative polymerase chain reaction. We also found significant correlations between lncRNAs and mRNAs, and validated four of the correlations with quantitative polymerase chain reaction. CONCLUSION Integrated analysis of genome-wide DNA methylation and lncRNA/mRNA expression allows us to identify new DM loci-correlated with gene expression in NSCLC.
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Affiliation(s)
- Nannan Feng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Min Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao Yu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hongyan Lin
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Rong-Na Ma
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Oumin Shi
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiangqian Zheng
- Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Ming Gao
- Tianjin Key Laboratory of Cancer Prevention & Therapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI 96813, USA
| | - Lana Garmire
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI 96813, USA
| | - Biyun Qian
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital & Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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21
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Nishibuchi G, Déjardin J. The molecular basis of the organization of repetitive DNA-containing constitutive heterochromatin in mammals. Chromosome Res 2017; 25:77-87. [PMID: 28078514 DOI: 10.1007/s10577-016-9547-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 12/19/2016] [Indexed: 12/31/2022]
Abstract
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes. Genetic and biochemical studies have revealed that histone methylation at H3K9 and its recognition by heterochromatin protein 1 represent the fundamental mechanism by which heterochromatin forms. Although this molecular mechanism is highly conserved from yeast to human cells, its detailed epigenetic regulation is more complex and dynamic for each distinct constitutive heterochromatin structure in higher eukaryotes. It can also vary according to the developmental stage. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis is a powerful tool to investigate the epigenetic regulation of eukaryote genomes, but non-unique reads are usually discarded during standard ChIP-seq data alignment to reference genome databases. Therefore, specific methods to obtain global epigenetic information concerning repetitive elements are needed. In this review, we focus on such approaches and we summarize the latest molecular models for distinct constitutive heterochromatin types in mammals.
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Affiliation(s)
- Gohei Nishibuchi
- Biology of Repetitive Sequences, CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France
| | - Jérôme Déjardin
- Biology of Repetitive Sequences, CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France.
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22
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Celona B, Dollen JV, Vatsavayai SC, Kashima R, Johnson JR, Tang AA, Hata A, Miller BL, Huang EJ, Krogan NJ, Seeley WW, Black BL. Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106. eLife 2017; 6. [PMID: 28072389 PMCID: PMC5283830 DOI: 10.7554/elife.19032] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 01/02/2017] [Indexed: 12/13/2022] Open
Abstract
Expanded GGGGCC repeats in the first intron of the C9orf72 gene represent the most common cause of familial amyotrophic lateral sclerosis (ALS), but the mechanisms underlying repeat-induced disease remain incompletely resolved. One proposed gain-of-function mechanism is that repeat-containing RNA forms aggregates that sequester RNA binding proteins, leading to altered RNA metabolism in motor neurons. Here, we identify the zinc finger protein Zfp106 as a specific GGGGCC RNA repeat-binding protein, and using affinity purification-mass spectrometry, we show that Zfp106 interacts with multiple other RNA binding proteins, including the ALS-associated factors TDP-43 and FUS. We also show that Zfp106 knockout mice develop severe motor neuron degeneration, which can be suppressed by transgenic restoration of Zfp106 specifically in motor neurons. Finally, we show that Zfp106 potently suppresses neurotoxicity in a Drosophila model of C9orf72 ALS. Thus, these studies identify Zfp106 as an RNA binding protein with important implications for ALS. DOI:http://dx.doi.org/10.7554/eLife.19032.001 Molecules of ribonucleic acid (or RNA for short) have many roles in cells, including acting as templates to make proteins. RNA is made of building blocks called nucleotides that are assembled to form strands. The precise order of the nucleotides in an RNA molecule can have a dramatic effect on the role that RNA plays in the body. For example, amyotrophic lateral sclerosis (ALS) is a deadly disease caused by the gradual loss of the nerve cells that control muscle (known as motor neurons). The most common cause of inherited ALS is a genetic mutation that results in some RNA molecules having many more copies of a simple six nucleotide sequence known as GGGGCC than normal cells. RNA molecules with these “GGGGCC repeats” form clumps in motor neurons. The clumps of RNA molecules also contain proteins, but the identities of these RNA-binding proteins and the roles they play in ALS remain largely unknown. Celona et al. have now identified a new RNA-binding protein called Zfp106, which binds specifically to GGGGCC repeats in mice and fruit flies. Removing the gene that encodes Zfp106 from mice causes the mice to develop ALS. On the other hand, restoring Zfp106 only to the motor neurons of these mutant mice prevents the mice from developing disease. This suggests that Zfp106’s role is specific to motor neurons. Indeed, fruit flies that have too many copies of GGGGCC develop severe symptoms reminiscent of ALS. Introducing a mammalian version of Zfp106 into these flies prevents them from developing the disease. The findings of Celona et al. suggest that Zfp106 might be a potential new drug target for treating ALS in humans. The next step following this work will be to find out exactly how Zfp106 regulates normal cellular processes by binding to RNA and how it suppresses ALS-like disease by binding to GGGGCC RNA-repeats. DOI:http://dx.doi.org/10.7554/eLife.19032.002
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Affiliation(s)
- Barbara Celona
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - John von Dollen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Sarat C Vatsavayai
- Department of Neurology, University of California, San Francisco, San Francisco, United States
| | - Risa Kashima
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Amy A Tang
- Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Bruce L Miller
- Department of Neurology, University of California, San Francisco, San Francisco, United States
| | - Eric J Huang
- Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - William W Seeley
- Department of Neurology, University of California, San Francisco, San Francisco, United States.,Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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Kan SL, Saksouk N, Déjardin J. Proteome Characterization of a Chromatin Locus Using the Proteomics of Isolated Chromatin Segments Approach. Methods Mol Biol 2017; 1550:19-33. [PMID: 28188520 DOI: 10.1007/978-1-4939-6747-6_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The biological functions of given genomic regions are ruled by the local chromatin composition. The Proteomics of Isolated Chromatin segments approach (PICh) is a powerful and unbiased method to analyze the composition of chosen chromatin segments, provided they are abundant (repeated) or that the organism studied has a small genome. PICh can be used to identify novel and unexpected regulatory factors, or when combined with quantitative mass spectrometric approaches, to characterize the function of a defined factor at the chosen locus, by quantifying composition changes at the locus upon removal/addition of that factor.
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Affiliation(s)
- Sophie L Kan
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France
| | - Nehmé Saksouk
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France
| | - Jérome Déjardin
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France.
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24
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Fraser R, Lin CJ. Epigenetic reprogramming of the zygote in mice and men: on your marks, get set, go! Reproduction 2016; 152:R211-R222. [PMID: 27601712 PMCID: PMC5097126 DOI: 10.1530/rep-16-0376] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/02/2016] [Indexed: 12/19/2022]
Abstract
Gametogenesis (spermatogenesis and oogenesis) is accompanied by the acquisition of gender-specific epigenetic marks, such as DNA methylation, histone modifications and regulation by small RNAs, to form highly differentiated, but transcriptionally silent cell-types in preparation for fertilisation. Upon fertilisation, extensive global epigenetic reprogramming takes place to remove the previously acquired epigenetic marks and produce totipotent zygotic states. It is the aim of this review to delineate the cellular and molecular events involved in maternal, paternal and zygotic epigenetic reprogramming from the time of gametogenesis, through fertilisation, to the initiation of zygotic genome activation for preimplantation embryonic development. Recent studies have begun to uncover the indispensable functions of epigenetic players during gametogenesis, fertilisation and preimplantation embryo development, and a more comprehensive understanding of these early events will be informative for increasing pregnancy success rates, adding particular value to assisted fertility programmes.
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Affiliation(s)
- Rupsha Fraser
- The University of EdinburghMRC Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Chih-Jen Lin
- The University of EdinburghMRC Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
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25
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Severe muscle wasting and denervation in mice lacking the RNA-binding protein ZFP106. Proc Natl Acad Sci U S A 2016; 113:E4494-503. [PMID: 27418600 PMCID: PMC4978283 DOI: 10.1073/pnas.1608423113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Innervation of skeletal muscle by motor neurons occurs through the neuromuscular junction, a cholinergic synapse essential for normal muscle growth and function. Defects in nerve-muscle signaling cause a variety of neuromuscular disorders with features of ataxia, paralysis, skeletal muscle wasting, and degeneration. Here we show that the nuclear zinc finger protein ZFP106 is highly enriched in skeletal muscle and is required for postnatal maintenance of myofiber innervation by motor neurons. Genetic disruption of Zfp106 in mice results in progressive ataxia and hindlimb paralysis associated with motor neuron degeneration, severe muscle wasting, and premature death by 6 mo of age. We show that ZFP106 is an RNA-binding protein that associates with the core splicing factor RNA binding motif protein 39 (RBM39) and localizes to nuclear speckles adjacent to spliceosomes. Upon inhibition of pre-mRNA synthesis, ZFP106 translocates with other splicing factors to the nucleolus. Muscle and spinal cord of Zfp106 knockout mice displayed a gene expression signature of neuromuscular degeneration. Strikingly, altered splicing of the Nogo (Rtn4) gene locus in skeletal muscle of Zfp106 knockout mice resulted in ectopic expression of NOGO-A, the neurite outgrowth factor that inhibits nerve regeneration and destabilizes neuromuscular junctions. These findings reveal a central role for Zfp106 in the maintenance of nerve-muscle signaling, and highlight the involvement of aberrant RNA processing in neuromuscular disease pathogenesis.
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26
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Abstract
Hundreds of distinct chemical modifications to DNA and histone amino acids have been described. Regulation exerted by these so-called epigenetic marks is vital to normal development, stability of cell identity through mitosis, and nongenetic transmission of traits between generations through meiosis. Loss of this regulation contributes to many diseases. Evidence indicates epigenetic marks function in combinations, whereby a given modification has distinct effects on local genome control, depending on which additional modifications are locally present. This review summarizes emerging methods for assessing combinatorial epigenomic states, as well as challenges and opportunities for their refinement.
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Affiliation(s)
- Paul D. Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States
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27
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Joyce PI, Fratta P, Landman AS, Mcgoldrick P, Wackerhage H, Groves M, Busam BS, Galino J, Corrochano S, Beskina OA, Esapa C, Ryder E, Carter S, Stewart M, Codner G, Hilton H, Teboul L, Tucker J, Lionikas A, Estabel J, Ramirez-Solis R, White JK, Brandner S, Plagnol V, Bennet DLH, Abramov AY, Greensmith L, Fisher EMC, Acevedo-Arozena A. Deficiency of the zinc finger protein ZFP106 causes motor and sensory neurodegeneration. Hum Mol Genet 2015; 25:291-307. [PMID: 26604141 PMCID: PMC4706115 DOI: 10.1093/hmg/ddv471] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/11/2015] [Indexed: 12/12/2022] Open
Abstract
Zinc finger motifs are distributed amongst many eukaryotic protein families, directing nucleic acid–protein and protein–protein interactions. Zinc finger protein 106 (ZFP106) has previously been associated with roles in immune response, muscle differentiation, testes development and DNA damage, although little is known about its specific function. To further investigate the function of ZFP106, we performed an in-depth characterization of Zfp106 deficient mice (Zfp106−/−), and we report a novel role for ZFP106 in motor and sensory neuronal maintenance and survival. Zfp106−/− mice develop severe motor abnormalities, major deficits in muscle strength and histopathological changes in muscle. Intriguingly, despite being highly expressed throughout the central nervous system, Zfp106−/− mice undergo selective motor and sensory neuronal and axonal degeneration specific to the spinal cord and peripheral nervous system. Neurodegeneration does not occur during development of Zfp106−/− mice, suggesting that ZFP106 is likely required for the maintenance of mature peripheral motor and sensory neurons. Analysis of embryonic Zfp106−/− motor neurons revealed deficits in mitochondrial function, with an inhibition of Complex I within the mitochondrial electron transport chain. Our results highlight a vital role for ZFP106 in sensory and motor neuron maintenance and reveal a novel player in mitochondrial dysfunction and neurodegeneration.
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Affiliation(s)
- Peter I Joyce
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Pietro Fratta
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Philip Mcgoldrick
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Michael Groves
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Jorge Galino
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | | | - Olga A Beskina
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Edward Ryder
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Sarah Carter
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | | | - Gemma Codner
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Helen Hilton
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Lydia Teboul
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Jennifer Tucker
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | | | - Jeanne Estabel
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Ramiro Ramirez-Solis
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Jacqueline K White
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Sebastian Brandner
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - David L H Bennet
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Andrey Y Abramov
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | - Linda Greensmith
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK,
| | - Elizabeth M C Fisher
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK,
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