Resources for the comprehensive discovery of functional RNA elements

Abstract

Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell-lines, tissues and developmental stages, is the availability of validated IP-quality antibodies. Using IP followed by immunoblot assays, we have developed a validated repository of 438 commercially available antibodies that interrogate 365 unique RBPs. In parallel, 362 short-hairpin RNA (shRNA) constructs against 276 unique RBPs were also used to confirm specificity of these antibodies. These antibodies can characterize subcellular RBP localization. With the burgeoning interest in the roles of RBPs in cancer, neurobiology and development, these resources are invaluable to the broad scientific community. Detailed information about these resources is publicly available at the ENCODE portal (https://www.encodeproject.org/).\n\nHighlightsO_LIAntibodies against 365 unique RBPs successfully immunoprecipitate the RBPs\nC_LIO_LIShort-hairpin RNAs against 276 unique RBPs confirm the specificity of RBP antibodies\nC_LIO_LIAntibodies characterize subcellular localization of RBPs\nC_LIO_LIAntibody and hairpin RNA information are provided at https://www.encodeproject.org/\nC_LI