Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2019
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
_version_ 1783449031984283648
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
work_keys_str_mv AT zhangshilin profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT wangyichen profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT jialin profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT wenxue profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT duzhonghua profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT wangcong profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT haoyajing profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT yudehai profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT zhoulei profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT chennaifei profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT chenjingcheng profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT chenhuiling profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT zhanghui profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT celikilkay profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT gulsoygunhan profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT luojianjun profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT qinbaoming profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT cuixueling profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT liuzhonghui profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT zhangsongling profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT estebanmiguela profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT ayferhat profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT xuwei profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT chenrunsheng profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT liwei profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT hoffmanandrewr profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT hujifan profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing
AT cuijiuwei profilingthelongnoncodingrnainteractionnetworkintheregulatoryelementsoftargetgenesbychromatininsitureversetranscriptionsequencing