PT  - JOURNAL ARTICLE
AU  - Adam J. Litterman
AU  - Wandi S. Zhu
AU  - Robin Kageyama
AU  - Wenxue Zhao
AU  - Noah Zaitlen
AU  - David J. Erle
AU  - K. Mark Ansel
TI  - A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome
AID  - 10.1101/448654
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 448654
4099  - http://biorxiv.org/content/early/2018/10/22/448654.short
4100  - http://biorxiv.org/content/early/2018/10/22/448654.full
AB  - RNA binding proteins (RBPs) mediate constitutive RNA metabolism and gene specific regulatory interactions. To identify RNA cis-regulatory elements, we developed GCLiPP, a biochemical technique for detecting RBP occupancy transcriptome-wide. GCLiPP sequence tags corresponded with known RBP binding sites, specifically correlating to abundant cytosolic RBPs. To demonstrate the utility of our occupancy profiles, we performed functional dissection of 3′ UTRs with CRISPR/Cas9 genome editing. Two RBP occupied sites in the CD69 3′ UTR destabilized the transcript of this key regulator of lymphocyte tissue egress. Comparing human Jurkat T cells and mouse primary T cells uncovered hundreds of biochemically shared peaks of GCLiPP signal across homologous regions of human and mouse 3′ UTRs, including a cis-regulatory element that governs the stability of the mRNA that encodes the proto-oncogene PIM3 in both species. Our GCLiPP datasets provide a rich resource for investigation of post-transcriptional regulation in the immune system.