Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).

Binding Sites Chromatin / genetics Chromatin Immunoprecipitation Sequencing / methods Protein Binding Transcription Factors / metabolism
3D genome Chromatin immunoprecipitation Hi-C Long-range chromatin interaction PLAC-Seq

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:
2021
Historique:
entrez: 12 8 2021
pubmed: 13 8 2021
medline: 2 9 2021
Statut: ppublish

Résumé

Proximity ligation-assisted ChIP-Seq (PLAC-Seq), also known as HiChIP, is a method to detect and quantify chromatin contacts anchored at genomic regions bound by specific proteins or histone modifications. By combining in situ Hi-C and chromatin immunoprecipitation (ChIP) using antibodies against transcription factors (TFs) or histone marks of interest, the method achieves targeted interrogation of chromatin organization at a subset of genomic regions. PLAC-Seq is able to identify long-range chromatin interactions at kilobase-scale resolution with significantly reduced sequencing cost.

Identifiants

DOI: 10.1007/978-1-0716-1597-3_10 PMID: 34382190
pubmed: 34382190
doi: 10.1007/978-1-0716-1597-3_10
doi:

Substances chimiques

Chromatin 0
Transcription Factors 0

Types de publication

Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

181-199

Subventions

Organisme : NIDDK NIH HHS
ID : U54 DK107977
Pays : United States

Informations de copyright

© 2021. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Références

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Dekker J, Marti-Renom MA, Mirny LA (2013) Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 14:390–403. https://doi.org/10.1038/nrg3454
doi: 10.1038/nrg3454 pubmed: 23657480 pmcid: 3874835
Denker A, de Laat W (2016) The second decade of 3C technologies: detailed insights into nuclear organization. Genes Dev 30:1357–1382. https://doi.org/10.1101/gad.281964.116
doi: 10.1101/gad.281964.116 pubmed: 27340173 pmcid: 4926860
Schmitt AD, Hu M, Ren B (2016) Genome-wide mapping and analysis of chromosome architecture. Nat Rev Mol Cell Biol 17(12):743–755. https://doi.org/10.1038/nrm.2016.104
doi: 10.1038/nrm.2016.104 pubmed: 27580841 pmcid: 5763923
Lieberman-Aiden E, van Berkum NL, Williams L et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293. https://doi.org/10.1126/science.1181369
doi: 10.1126/science.1181369 pubmed: 19815776 pmcid: 2858594
Rao SSP, Huntley MH, Durand NC et al (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665–1680. https://doi.org/10.1016/j.cell.2014.11.021
doi: 10.1016/j.cell.2014.11.021 pubmed: 25497547 pmcid: 5635824
Fullwood MJ, Liu MH, Pan YF et al (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58–64. https://doi.org/10.1038/nature08497
doi: 10.1038/nature08497 pubmed: 19890323 pmcid: 2774924
Dryden NH, Broome LR, Dudbridge F et al (2014) Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res 24:1854–1868. https://doi.org/10.1101/gr.175034.114
doi: 10.1101/gr.175034.114 pubmed: 25122612 pmcid: 4216926
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doi: 10.1038/ng.2871 pubmed: 24413732
Mumbach MR, Rubin AJ, Flynn RA et al (2016) HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods 13:919–922. https://doi.org/10.1038/nmeth.3999
doi: 10.1038/nmeth.3999 pubmed: 27643841 pmcid: 5501173
Fang R, Yu M, Li G et al (2016) Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res 26:1345–1348. https://doi.org/10.1038/cr.2016.137
doi: 10.1038/cr.2016.137 pubmed: 27886167 pmcid: 5143423
Juric I, Yu M, Abnousi A et al (2019) MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS Comput Biol 15:e1006982. https://doi.org/10.1371/journal.pcbi.1006982
doi: 10.1371/journal.pcbi.1006982 pubmed: 30986246 pmcid: 6483256
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Auteurs

Miao Yu (M)

Ludwig Institute for Cancer Research, La Jolla, CA, USA.
State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.

Ivan Juric (I)

Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.

Armen Abnousi (A)

Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.

Ming Hu (M)

Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.

Bing Ren (B)

Ludwig Institute for Cancer Research, La Jolla, CA, USA. biren@health.ucsd.edu.
Center for Epigenomics, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA. biren@health.ucsd.edu.

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Classifications MeSH

questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Sites de fixation › Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).
questionsmedicales.fr › Techniques d'investigation › Techniques immunologiques › Immunoprécipitation › Immunoprécipitation de la chromatine › Séquençage après immunoprécipitation de la chromatine › Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).
questionsmedicales.fr › Métabolisme › Liaison aux protéines › Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).