Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
Abstract 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...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2020-03-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-020-01973-w |
| _version_ | 1818015279416868864 |
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| author | Xin Liu Yong Chen Yuannyu Zhang Yuxuan Liu Nan Liu Giovanni A. Botten Hui Cao Stuart H. Orkin Michael Q. Zhang Jian Xu |
| author_facet | Xin Liu Yong Chen Yuannyu Zhang Yuxuan Liu Nan Liu Giovanni A. Botten Hui Cao Stuart H. Orkin Michael Q. Zhang Jian Xu |
| author_sort | Xin Liu |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-14T06:54:53Z |
| format | Article |
| id | doaj.art-072cb7b4ebb547e5ae6f74fbfc386c3c |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-14T06:54:53Z |
| publishDate | 2020-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-072cb7b4ebb547e5ae6f74fbfc386c3c2022-12-22T02:06:55ZengBMCGenome Biology1474-760X2020-03-0121112010.1186/s13059-020-01973-wMultiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9Xin Liu0Yong Chen1Yuannyu Zhang2Yuxuan Liu3Nan Liu4Giovanni A. Botten5Hui Cao6Stuart H. Orkin7Michael Q. Zhang8Jian Xu9Children’s Medical Center Research Institute, University of Texas Southwestern Medical CenterDepartment of Biological Sciences, Center for Systems Biology, University of Texas at DallasChildren’s Medical Center Research Institute, University of Texas Southwestern Medical CenterChildren’s Medical Center Research Institute, University of Texas Southwestern Medical CenterDivision of Hematology/Oncology, Boston Children’s Hospital, Dana-Farber Cancer Institute and Harvard Stem Cell Institute, Harvard Medical SchoolChildren’s Medical Center Research Institute, University of Texas Southwestern Medical CenterChildren’s Medical Center Research Institute, University of Texas Southwestern Medical CenterDivision of Hematology/Oncology, Boston Children’s Hospital, Dana-Farber Cancer Institute and Harvard Stem Cell Institute, Harvard Medical SchoolDepartment of Biological Sciences, Center for Systems Biology, University of Texas at DallasChildren’s Medical Center Research Institute, University of Texas Southwestern Medical CenterAbstract 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.http://link.springer.com/article/10.1186/s13059-020-01973-wCRISPR/Cas9ChromatinEpigenetics3D genomeEnhancers |
| spellingShingle | Xin Liu Yong Chen Yuannyu Zhang Yuxuan Liu Nan Liu Giovanni A. Botten Hui Cao Stuart H. Orkin Michael Q. Zhang Jian Xu Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9 Genome Biology CRISPR/Cas9 Chromatin Epigenetics 3D genome Enhancers |
| 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 | CRISPR/Cas9 Chromatin Epigenetics 3D genome Enhancers |
| url | http://link.springer.com/article/10.1186/s13059-020-01973-w |
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