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Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
Long noncoding RNAs (lncRNAs) can regulate the activity of target genes by participating in the organization of chromatin architecture. We have devised a “chromatin-RNA in situ reverse transcription sequencing” (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory element...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724666/ https://www.ncbi.nlm.nih.gov/pubmed/31315906 http://dx.doi.org/10.1101/gr.244996.118 |
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author | Zhang, Shilin Wang, Yichen Jia, Lin Wen, Xue Du, Zhonghua Wang, Cong Hao, Yajing Yu, Dehai Zhou, Lei Chen, Naifei Chen, Jingcheng Chen, Huiling Zhang, Hui Celik, Ilkay Gülsoy, Günhan Luo, Jianjun Qin, Baoming Cui, Xueling Liu, Zhonghui Zhang, Songling Esteban, Miguel A. Ay, Ferhat Xu, Wei Chen, Runsheng Li, Wei Hoffman, Andrew R. Hu, Ji-Fan Cui, Jiuwei |
author_facet | Zhang, Shilin Wang, Yichen Jia, Lin Wen, Xue Du, Zhonghua Wang, Cong Hao, Yajing Yu, Dehai Zhou, Lei Chen, Naifei Chen, Jingcheng Chen, Huiling Zhang, Hui Celik, Ilkay Gülsoy, Günhan Luo, Jianjun Qin, Baoming Cui, Xueling Liu, Zhonghui Zhang, Songling Esteban, Miguel A. Ay, Ferhat Xu, Wei Chen, Runsheng Li, Wei Hoffman, Andrew R. Hu, Ji-Fan Cui, Jiuwei |
author_sort | Zhang, Shilin |
collection | PubMed |
description | Long noncoding RNAs (lncRNAs) can regulate the activity of target genes by participating in the organization of chromatin architecture. We have devised a “chromatin-RNA in situ reverse transcription sequencing” (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory elements by combining the simplicity of RNA biotin labeling with the specificity of the CRISPR/Cas9 system. Using gene-specific gRNAs, we describe a pluripotency-specific lncRNA interacting network in the promoters of Sox2 and Pou5f1, two critical stem cell factors that are required for the maintenance of pluripotency. The promoter-interacting lncRNAs were specifically activated during reprogramming into pluripotency. Knockdown of these lncRNAs caused the stem cells to exit from pluripotency. In contrast, overexpression of the pluripotency-associated lncRNA activated the promoters of core stem cell factor genes and enhanced fibroblast reprogramming into pluripotency. These CRIST-seq data suggest that the Sox2 and Pou5f1 promoters are organized within a unique lncRNA interaction network that determines the fate of pluripotency during reprogramming. This CRIST approach may be broadly used to map lncRNA interaction networks at target loci across the genome. |
format | Online Article Text |
id | pubmed-6724666 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-67246662019-09-17 Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing Zhang, Shilin Wang, Yichen Jia, Lin Wen, Xue Du, Zhonghua Wang, Cong Hao, Yajing Yu, Dehai Zhou, Lei Chen, Naifei Chen, Jingcheng Chen, Huiling Zhang, Hui Celik, Ilkay Gülsoy, Günhan Luo, Jianjun Qin, Baoming Cui, Xueling Liu, Zhonghui Zhang, Songling Esteban, Miguel A. Ay, Ferhat Xu, Wei Chen, Runsheng Li, Wei Hoffman, Andrew R. Hu, Ji-Fan Cui, Jiuwei Genome Res Method Long noncoding RNAs (lncRNAs) can regulate the activity of target genes by participating in the organization of chromatin architecture. We have devised a “chromatin-RNA in situ reverse transcription sequencing” (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory elements by combining the simplicity of RNA biotin labeling with the specificity of the CRISPR/Cas9 system. Using gene-specific gRNAs, we describe a pluripotency-specific lncRNA interacting network in the promoters of Sox2 and Pou5f1, two critical stem cell factors that are required for the maintenance of pluripotency. The promoter-interacting lncRNAs were specifically activated during reprogramming into pluripotency. Knockdown of these lncRNAs caused the stem cells to exit from pluripotency. In contrast, overexpression of the pluripotency-associated lncRNA activated the promoters of core stem cell factor genes and enhanced fibroblast reprogramming into pluripotency. These CRIST-seq data suggest that the Sox2 and Pou5f1 promoters are organized within a unique lncRNA interaction network that determines the fate of pluripotency during reprogramming. This CRIST approach may be broadly used to map lncRNA interaction networks at target loci across the genome. Cold Spring Harbor Laboratory Press 2019-09 /pmc/articles/PMC6724666/ /pubmed/31315906 http://dx.doi.org/10.1101/gr.244996.118 Text en © 2019 Zhang et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Method Zhang, Shilin Wang, Yichen Jia, Lin Wen, Xue Du, Zhonghua Wang, Cong Hao, Yajing Yu, Dehai Zhou, Lei Chen, Naifei Chen, Jingcheng Chen, Huiling Zhang, Hui Celik, Ilkay Gülsoy, Günhan Luo, Jianjun Qin, Baoming Cui, Xueling Liu, Zhonghui Zhang, Songling Esteban, Miguel A. Ay, Ferhat Xu, Wei Chen, Runsheng Li, Wei Hoffman, Andrew R. Hu, Ji-Fan Cui, Jiuwei Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing |
title | Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing |
title_full | Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing |
title_fullStr | Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing |
title_full_unstemmed | Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing |
title_short | Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing |
title_sort | profiling the long noncoding rna interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724666/ https://www.ncbi.nlm.nih.gov/pubmed/31315906 http://dx.doi.org/10.1101/gr.244996.118 |
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