Journal
GENOME RESEARCH
Volume 29, Issue 9, Pages 1521-1532Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.244996.118
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Funding
- National Key R&D Program of China [2018YFA0106902]
- Research on Chronic Noncommunicable Diseases Prevention and Control of the National Ministry of Science and Technology [2016YFC1303804]
- National Natural Science Foundation of China [31430021, 81874052, 81672275, 31871297, 81372835, 81670143]
- Key Project of Chinese Ministry of Education [311015]
- National Basic Research Program of China (973 Program) [2015CB943303]
- National Key Research and Development Program of China [2016YFC13038000]
- Natural Science Foundation of Jilin Province [20190303146SF, 20150101176JC, 20180101117JC, 2013041301 0GH]
- Provincial Science Fund of Jilin Province Development and Reform Commission [2017J064, 2014N147, 2017C022]
- Jilin Provincial Key Laboratory of Biological Therapy [20170622011JC]
- California Institute of Regenerative Medicine (CIRM) [RT2-01942]
- Biomedical Research Service of the U.S. Department of Veterans Affairs [BX002905]
- National Health Development Planning Commission Major Disease Prevention and Control of Science and Technology Plan of Action, Cancer Prevention and Control [ZX-07-C2016004]
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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.
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