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Nucleic Acids Res. 2016 Jan 4;44(D1):D154-63. doi: 10.1093/nar/gkv1308. Epub 2015 Dec 3.

RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins.

Author information

1
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China.
2
Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China.
3
State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410078, China.
4
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
5
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China sunzsbiols@126.com.
6
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China sunzsbiols@126.com.

Abstract

Transcription factors bind to the genome by forming specific contacts with the primary DNA sequence; however, RNA-binding proteins (RBPs) have greater scope to achieve binding specificity through the RNA secondary structure. It has been revealed that single nucleotide variants (SNVs) that alter RNA structure, also known as RiboSNitches, exhibit 3-fold greater local structure changes than replicates of the same DNA sequence, demonstrated by the fact that depletion of RiboSNitches could result in the alteration of specific RNA shapes at thousands of sites, including 3' UTRs, binding sites of microRNAs and RBPs. However, the network between SNVs and post-transcriptional regulation remains unclear. Here, we developed RBP-Var, a database freely available at http://www.rbp-var.biols.ac.cn/, which provides annotation of functional variants involved in post-transcriptional interaction and regulation. RBP-Var provides an easy-to-use web interface that allows users to rapidly find whether SNVs of interest can transform the secondary structure of RNA and identify RBPs whose binding may be subsequently disrupted. RBP-Var integrates DNA and RNA biology to understand how various genetic variants and post-transcriptional mechanisms cooperate to orchestrate gene expression. In summary, RBP-Var is useful in selecting candidate SNVs for further functional studies and exploring causal SNVs underlying human diseases.

PMID:
26635394
PMCID:
PMC4702914
DOI:
10.1093/nar/gkv1308
[Indexed for MEDLINE]
Free PMC Article

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