Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
- Shilin Zhang1,9,
- Yichen Wang1,9,
- Lin Jia1,9,
- Xue Wen1,9,
- Zhonghua Du1,9,
- Cong Wang1,2,
- Yajing Hao3,
- Dehai Yu1,
- Lei Zhou1,
- Naifei Chen1,
- Jingcheng Chen1,2,
- Huiling Chen4,
- Hui Zhang5,
- Ilkay Celik2,
- Günhan Gülsoy6,
- Jianjun Luo3,
- Baoming Qin5,
- Xueling Cui7,
- Zhonghui Liu7,
- Songling Zhang1,10,
- Miguel A. Esteban5,10,
- Ferhat Ay8,10,
- Wei Xu1,10,
- Runsheng Chen3,10,
- Wei Li1,10,
- Andrew R. Hoffman2,10,
- Ji-Fan Hu1,2,10 and
- Jiuwei Cui1,10
- 1Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China;
- 2Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California 94304, USA;
- 3CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China;
- 4Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China;
- 5Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China;
- 6Google Incorporated, Mountain View, California 94043, USA;
- 7Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China;
- 8La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
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↵9 These authors contributed equally to this work.
Abstract
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.
Footnotes
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↵10 These authors are the senior authors of this work.
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.244996.118.
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Freely available online through the Genome Research Open Access option.
- Received October 10, 2018.
- Accepted July 10, 2019.
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/.
