RT Journal Article
SR Electronic
T1 A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 448654
DO 10.1101/448654
A1 Litterman, Adam J.
A1 Zhu, Wandi S.
A1 Kageyama, Robin
A1 Zhao, Wenxue
A1 Zaitlen, Noah
A1 Erle, David J.
A1 Ansel, K. Mark
YR 2018
UL http://biorxiv.org/content/early/2018/10/22/448654.abstract
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.