RT Journal
A1 Zhang, Shilin
A1 Wang, Yichen
A1 Jia, Lin
A1 Wen, Xue
A1 Du, Zhonghua
A1 Wang, Cong
A1 Hao, Yajing
A1 Yu, Dehai
A1 Zhou, Lei
A1 Chen, Naifei
A1 Chen, Jingcheng
A1 Chen, Huiling
A1 Zhang, Hui
A1 Celik, Ilkay
A1 Gülsoy, Günhan
A1 Luo, Jianjun
A1 Qin, Baoming
A1 Cui, Xueling
A1 Liu, Zhonghui
A1 Zhang, Songling
A1 Esteban, Miguel A.
A1 Ay, Ferhat
A1 Xu, Wei
A1 Chen, Runsheng
A1 Li, Wei
A1 Hoffman, Andrew R.
A1 Hu, Ji-Fan
A1 Cui, Jiuwei
T1 Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
JF Genome Research 
JO Genome Research 
YR 2019 
FD September 01 
VO 29 
IS 9 
SP 1521 
OP 1532 
DO 10.1101/gr.244996.118 
UL http://genome.cshlp.org/content/29/9/1521.abstract 
AB 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.