TY - JOUR T1 - Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen JF - bioRxiv DO - 10.1101/839316 SP - 839316 AU - Hao Fei Wang AU - Tushar Warrier AU - Chadi EL Farran AU - Zheng Zihao AU - Qiao Rui Xing AU - Melissa J Fullwood AU - Li-Feng Zhang AU - Hu Li AU - Jian Xu AU - Tit-Meng Lim AU - Yuin-Han Loh Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/11/12/839316.abstract N2 - Cis Regulatory Elements (CREs) regulate the expression of the genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of its target genes in the cellular native environment. In this study, we performed a Features Oriented CRISPR Utilized Systematic (FOCUS) screen of OCT4-bound CREs using CRISPR/Cas9 to identify functional enhancers important for pluripotency maintenance in mouse ES cells. From the initial 235 candidates tested, 16 CREs were identified to be essential stem cell enhancers. Using RNA-seq and genomic 4C-seq, we further uncovered a complex network of candidate CREs and their downstream target genes, which supports the growth and self-renewal of mESCs. Notably, an essential enhancer, CRE111, and its target, Lrrc31, form the important switch to modulate the LIF-JAK1-STAT3 signaling pathway. ER -