Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
Year: 2019
Type: preprint
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.
Source: Genome Research
Authors: Shilin Zhang, Yichen Wang, Lin Jia, Xue Wen, Zhonghua Du, Cong Wang, Yajing Hao, Dehai Yu, Lei Zhou, Naifei Chen, Jingcheng Chen, Huiling Chen, Hui Zhang, Ilkay Celik, Günhan Gülsoy, Jianjun Luo, Baoming Qin, Xueling Cui, Zhonghui Liu, Songling Zhang, Miguel A. Esteban, Ferhat Ay, Wei Xu, Runsheng Chen, Wei Li, Andrew R. Hoffman, Ji-Fan Hu, Jiuwei Cui
Institutions: First Hospital of Jilin University, VA Palo Alto Health Care System, Stanford University, Chinese Academy of Sciences, Institute of Biophysics, Central South University, Xiangya Hospital Central South University, Guangzhou Institutes of Biomedicine and Health, Google (United States), Jilin University, La Jolla Institute for Immunology
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: bronze
Funders: U.S. Department of Veterans Affairs, California Institute of Regenerative Medicine, Natural Science Foundation of Jilin Province, Jilin Province Development and Reform Commission, National Natural Science Foundation of China, People's Government of Jilin Province, National Key Research and Development Program of China
Awards: G1061010473, G1066976473, G115530167, G1828425977, G187430994, G2193155630, G2413030836, G2690432849, G3175914102, G3200901369, G338883960, G3595248122, 遗传印迹长非编码RNA-IRAIN在乳腺癌干细胞中的抑癌机理研究, G4322551861, G443485259, G5649765087, G5697908871, G5794144238, 利用CRISPR/Cas9靶向表观遗传学修饰技术研究IGF2在白血病干细胞中基因印记异常的机制, G605605435, G6397467787, G6628922209, G6774107620, G7214886494, G7225058542, G7574632262, G781309531, G7898354511, G8240331401, G8630018183, G8922106909, G8966560539
OpenAlex ID: W2973199536