Resources for the Comprehensive Discovery of Functional RNA Elements

Mol Cell. 2016 Mar 17;61(6):903-13. doi: 10.1016/j.molcel.2016.02.012.

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/).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Databases, Genetic*
  • Humans
  • Protein Binding
  • RNA / genetics
  • RNA / metabolism*
  • RNA, Small Interfering / classification
  • RNA, Small Interfering / genetics
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism
  • Transcriptome / genetics*

Substances

  • RNA, Small Interfering
  • RNA-Binding Proteins
  • RNA