Reverse Chromatin Immunoprecipitation (R-ChIP).

Chromatin Immunoprecipitation / methods Chromatin / metabolism DNA / metabolism Humans DNA-Binding Proteins / metabolism Mass Spectrometry / methods Protein Binding DNA Probes / genetics
Biotin-streptavidin system Chromatin immunoprecipitation DNA probe DNA-associated proteins Gene-centered approach Hybridization Mass spectrometry Upstream regulators

Journal

Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969

Informations de publication

Date de publication:
2024
Historique:
medline: 14 8 2024
pubmed: 14 8 2024
entrez: 14 8 2024
Statut: ppublish

Résumé

DNA-protein interactions play fundamental roles in diverse biological functions. The gene-centered method is used to identify the upstream regulators of defined genes. In this study, we developed a novel method for capturing the proteins that bind to certain chromatin fragments or DNA sequences, which is called reverse chromatin immunoprecipitation (R-ChIP). This technology uses a set of specific DNA probes labeled with biotin to isolate chromatin or DNA fragments, and the DNA-associated proteins are then analyzed using mass spectrometry. This method can capture DNA-associated proteins with sufficient quantity and purity for identification.

Identifiants

DOI: 10.1007/978-1-0716-4071-5_8 PMID: 39141233
pubmed: 39141233
doi: 10.1007/978-1-0716-4071-5_8
doi:

Substances chimiques

Chromatin 0
DNA 9007-49-2
DNA-Binding Proteins 0
DNA Probes 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

123-132

Informations de copyright

© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Références

Chang TC, Lin JJ, Lin KC et al (2002) Investigation of DNA–protein recognition by satellite hole spectra of labeling dye. J Lumin 98(1):149–152
doi: 10.1016/S0022-2313(02)00263-6
Malonga H, Neault JF, Arakawa H et al (2006) DNA interaction with human serum albumin studied by affinity capillary electrophoresis and FTIR spectroscopy. DNA Cell Biol 25(1):63–68
doi: 10.1089/dna.2006.25.63 pubmed: 16405401
Walhout AJM (2006) Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res 16(12):1445–1454
doi: 10.1101/gr.5321506 pubmed: 17053092
Reece-Hoyes JS, Barutcu AR, McCord RP et al (2011) Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods 8(12):1050–1052
doi: 10.1038/nmeth.1764 pubmed: 22037702 pmcid: 3263363
Kim TH, Ren B (2006) Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet 7(1):81–102
doi: 10.1146/annurev.genom.7.080505.115634 pubmed: 16722805
Déjardin J, Kingston RE (2009) Purification of proteins associated with specific genomic loci. Cell 136(1):175–186
doi: 10.1016/j.cell.2008.11.045 pubmed: 19135898 pmcid: 3395431
Chu C, Zhang Qiangfeng C, da Rocha Simão T et al (2015) Systematic discovery of Xist RNA binding proteins. Cell 161(2):404–416
doi: 10.1016/j.cell.2015.03.025 pubmed: 25843628 pmcid: 4425988
Tamburino AM, Kaymak E, Shrestha S et al (2017) PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. Translation 5(1):e1295130
doi: 10.1080/21690731.2017.1295130 pubmed: 28702278 pmcid: 5501385
Murarka P, Srivastava P (2018) An improved method for the isolation and identification of unknown proteins that bind to known DNA sequences by affinity capture and mass spectrometry. PLoS One 13(8):e0202602
doi: 10.1371/journal.pone.0202602 pubmed: 30138440 pmcid: 6107227

Auteurs

Xuejing Wen (X)

State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.
Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.

Yucheng Wang (Y)

State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China. wangyucheng@ms.xjb.ac.cn.
Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China. wangyucheng@ms.xjb.ac.cn.
College of Forestry, Shenyang Agricultural University, Shenyang, China. wangyucheng@ms.xjb.ac.cn.

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Classifications MeSH

questionsmedicales.fr › Techniques d'investigation › Techniques immunologiques › Immunoprécipitation › Immunoprécipitation de la chromatine › Reverse Chromatin Immunoprecipitation (R-ChIP).
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Reverse Chromatin Immunoprecipitation (R-ChIP).
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Reverse Chromatin Immunoprecipitation (R-ChIP).
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Reverse Chromatin Immunoprecipitation (R-ChIP).
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines de liaison à l'ADN › Reverse Chromatin Immunoprecipitation (R-ChIP).
questionsmedicales.fr › Techniques d'investigation › Techniques de chimie analytique › Spectrométrie de masse › Reverse Chromatin Immunoprecipitation (R-ChIP).
questionsmedicales.fr › Métabolisme › Liaison aux protéines › Reverse Chromatin Immunoprecipitation (R-ChIP).
questionsmedicales.fr › Actions chimiques et utilisations › Utilisations spécialisées de produits chimiques › Produits chimiques de laboratoire › Sondes moléculaires › Sondes d'acide nucléique › Sondes d'ADN › Reverse Chromatin Immunoprecipitation (R-ChIP).