Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9

The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CA...

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Autores principales: Liu, Xin, Chen, Yong, Zhang, Yuannyu, Liu, Yuxuan, Liu, Nan, Botten, Giovanni A., Cao, Hui, Orkin, Stuart H., Zhang, Michael Q., Xu, Jian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059722/
https://www.ncbi.nlm.nih.gov/pubmed/32138752
http://dx.doi.org/10.1186/s13059-020-01973-w
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author Liu, Xin
Chen, Yong
Zhang, Yuannyu
Liu, Yuxuan
Liu, Nan
Botten, Giovanni A.
Cao, Hui
Orkin, Stuart H.
Zhang, Michael Q.
Xu, Jian
author_facet Liu, Xin
Chen, Yong
Zhang, Yuannyu
Liu, Yuxuan
Liu, Nan
Botten, Giovanni A.
Cao, Hui
Orkin, Stuart H.
Zhang, Michael Q.
Xu, Jian
author_sort Liu, Xin
collection PubMed
description The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CAPTURE method for multiplexed analysis of locus-specific chromatin interactions. The redesigned system allows for quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling comparisons across CREs within and between gene clusters. Multiplexed analyses of the spatiotemporal configuration of erythroid super-enhancers and promoter-centric interactions reveal organizational principles of genome structure and function.
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spelling pubmed-70597222020-03-12 Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9 Liu, Xin Chen, Yong Zhang, Yuannyu Liu, Yuxuan Liu, Nan Botten, Giovanni A. Cao, Hui Orkin, Stuart H. Zhang, Michael Q. Xu, Jian Genome Biol Method The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CAPTURE method for multiplexed analysis of locus-specific chromatin interactions. The redesigned system allows for quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling comparisons across CREs within and between gene clusters. Multiplexed analyses of the spatiotemporal configuration of erythroid super-enhancers and promoter-centric interactions reveal organizational principles of genome structure and function. BioMed Central 2020-03-05 /pmc/articles/PMC7059722/ /pubmed/32138752 http://dx.doi.org/10.1186/s13059-020-01973-w Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Liu, Xin
Chen, Yong
Zhang, Yuannyu
Liu, Yuxuan
Liu, Nan
Botten, Giovanni A.
Cao, Hui
Orkin, Stuart H.
Zhang, Michael Q.
Xu, Jian
Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
title Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
title_full Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
title_fullStr Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
title_full_unstemmed Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
title_short Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
title_sort multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3d chromatin by biotinylated dcas9
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059722/
https://www.ncbi.nlm.nih.gov/pubmed/32138752
http://dx.doi.org/10.1186/s13059-020-01973-w
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