Genome-wide survey of putative RNA-binding proteins encoded in the human proteome

Abstract

RNA-binding proteins (RBPs) are involved in various post-transcriptional gene regulatory processes and are also functionally important members of the ribosome and the spliceosome. However, RBPs and their interactions with RNA are less well-studied in comparison to DNA-binding proteins. We have classified the existing RBP structures, available in complexes with RNA and RNA/DNA hybrids, into different structural families and created Hidden Markov Models (HMMs). These structure-centric family HMMs, along with the sequence-centric family HMMs, were used as a primary database to systematically search the human proteome for the presence of putative RBPs. We have found more than 2600 gene products with RBP signatures in humans, of which around 28% are likely to bind to RNA but not DNA, whereas 9% might bind to both RNA and DNA. 11% of them do not contain an explicit functional annotation yet. Nearly 30% of the putative RBPs are exclusively nuclear, 15% have known disease associations and around 30% are enzymes. Around 40% of the proteins identified in this study are novel and have not been reported by recent large-scale studies on human RBPs.

EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins

“…All the data presented in this database were obtained from our previous study [9], in which genome-wide survey (GWS) of RBPs were performed for 166 complete E. coli proteomes, retrieved from the RefSeq database (May 2016) (please see Additional File 1 for further details on the search method). The start-points for such search methods, were known sequence and structure signatures of RBPs, organised as structure-centric and sequence-centric family Hidden Markov Models (HMMs) [5]. 8464 putative RBPs could be identified from 166 E. coli proteomes studied ( Table 1).…”

“…The complete RBP repertoire of a few model organisms have now been identified by various research groups, including ours [2][3][4][5], but the data is not conveniently available to the users due to the lack of proper organisation. The most widely used of the RBP repositories, RBPDB [6], reports experimentally observed RNA-binding sites that have been manually curated from literature, but was last updated in 2012.…”

The role of Trim25 in development, disease and RNA metabolism

“…A recent genome-wide bioinformatic screen of the human proteome identified more than 2600 proteins with RBP signatures [51]. Around 30% of these are enzymes.…”

hRBPome: a central repository of all known human RNA-binding proteins

“…RBP-RNA associations are dynamic in nature and defines the rate of translation of mRNA cellular localisation, as well as the lifetime and processing of different kinds of RNA [2]. Our previous work has identified the complete RBP repertoire (or RBPome) in humans [3], but in the process of studying the same, we had realised the differences exist in the size of the human RBPome as reported by different groups [3][4][5][6][7][8]. To assemble all the known human RBPs, and their related information in one platform, we present hRBPomea comprehensive database of human RBPs.…”