Comprehensive identification of RNA-binding domains in human cells

Journal article

Mammalian cells harbor more than a thousand RNA-binding proteins (RBPs), with half of these employing unknown modes of RNA binding. We developed RBDmap to determine the RNA-binding sites of native RBPs on a proteome-wide scale. We identified 1,174 binding sites within 529 HeLa cell RBPs, discovering numerous RNA-binding domains (RBDs). Catalytic centers or protein-protein interaction domains are in close relationship with RNA-binding sites, invoking possible effector roles of RNA in the control of protein function. Nearly half of the RNA-binding sites map to intrinsically disordered regions, uncovering unstructured domains as prevalent partners in protein-RNA interactions. RNA-binding sites represent hot spots for defined posttranslational modifications such as lysine acetylation and tyrosine phosphorylation, suggesting metabolic and signal-dependent regulation of RBP function. RBDs display a high degree of evolutionary conservation and incidence of Mendelian mutations, suggestive of important functional roles. RBDmap thus yields profound insights into native protein-RNA interactions in living cells.

Authors: Castello, A; Fischer, B; Frese, CK; Horos, R; Alleaume, A-M

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Cell Press
• Journal: Molecular Cell
• Volume: 63
• Issue: 4
• Pages: 696-710
• Publication date: 2016-07-21
• Acceptance date: 2016-06-20
• DOI: 10.1016/j.molcel.2016.06.029
• EISSN: 1097-4164
• ISSN: 1097-2765
• Language: English
• Keywords: RNA binding domain; RNA; RNA binding protein