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For: Ide S, Dejardin J. End-targeting proteomics of isolated chromatin segments of a mammalian ribosomal RNA gene promoter. Nat Commun 2015;6:6674. [PMID: 25812914 DOI: 10.1038/ncomms7674] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/18/2015] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
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
2
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]
3
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]
4
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
5
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]
6
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]
7
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
8
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
9
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
10
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]
11
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
12
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]
13
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]
14
Isogawa A, Fuchs RP, Fujii S. Chromatin Pull-Down Methodology Based on DNA Triple Helix Formation. Methods Mol Biol 2020;2119:183-199. [PMID: 31989525 DOI: 10.1007/978-1-0716-0323-9_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
15
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]
16
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
17
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
18
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
19
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
20
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
21
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]
22
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
23
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]
24
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]
25
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
26
Soloway PD. Analysis of Combinatorial Epigenomic States. ACS Chem Biol 2016;11:621-31. [PMID: 26555135 DOI: 10.1021/acschembio.5b00833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
27
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
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