RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins

Abstract

RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation and disease. Their binding sites cover more of the genome than coding exons; nevertheless, most noncoding variant-prioritization methods only focus on transcriptional regulation. Here, we integrate the portfolio of ENCODE-RBP experiments to develop RADAR, a variant-scoring framework. RADAR uses conservation, RNA structure, network centrality, and motifs to provide an overall impact score. Then it further incorporates tissuespecific inputs to highlight disease-specific variants. Our results demonstrate RADAR can successfully pinpoint variants, both somatic and germline, associated with RBP-function dysregulation, that cannot be found by most current prioritization methods, for example variants affecting splicing. KeywordsRNA binding protein, post-transcriptional regulation, variant prioritization, variant functional impact 3 Background Dysregulation of gene expression is a hallmark of many diseases, including cancer [1]. In recent years, the accumulation of transcription-level functional characterization data, such as transcriptional factor binding, chromatin accessibility, histone modification, and methylation, has brought great success to annotating and pinpointing deleterious variants. However, beyond transcriptional processing, genes also experience various delicately controlled steps, including the conversion of premature RNA to mature RNA, and then the transportation, translation, and degradation of RNA in the cell. Dysregulation in any one of these steps can alter the final fate of gene products and result in abnormal phenotypes [2][3][4]. Furthermore, the posttranscriptional regulome covers an even larger amount of the genome than coding exons and demonstrates significantly higher cross-population and cross-species conservation. Unfortunately, variant impact in the post-transcriptional regulome has been barely investigated, partially due to the lack of large-scale functional mapping.RNA binding proteins (RBPs) have been reported to play essential roles in both co-and post-transcriptional regulation [5][6][7]. RBPs bind to thousands of genes in the cell through multiple processes, including splicing, cleavage and polyadenylation, editing, localization, stability, and translation [8][9][10][11][12]. Recently, scientists have made efforts to complete these post-or co-transcriptional regulome by synthesizing public RBP binding profiles [13][14][15][16], which have greatly expanded our understanding of RBP regulation. Since 2016, the Encyclopedia of DNA Elements (ENCODE) consortium started to release data from various types of assays on matched cell types to map the functional elements in post-transcriptional regulome. For instance, ENCODE has released large-scale enhanced crosslinking and immunoprecipitation (eCLIP) experiments for hundreds of RBPs [17]. This methodology provides high-quality RBP binding profiles with strict quality control and uniform peak calling to accurately catalog the RBP binding sites at a single nucleotide re...

DECODE: ADeep-learning Framework forCondensing Enhancers and Refining Boundaries with Large-scale Functional Assays

“…Disease-causal variant mapping is one of the most important applications of distal regulatory element mapping. Lines of evidence have demonstrated that accurate and compact annotations can significantly increase the statistical power for both somatic and germline variant mapping in disease studies (Fu et al ., 2014; Zhang, Liu, et al ., 2020; Zhang, Lee, et al ., 2020). Therefore, we further tested whether our condensed enhancer definitions can benefit variant prioritization and interpretations.…”

“…We further evaluated the quality of our compact enhancer annotation from DECODE via the enrichment of rare variants with a simple but validated assumption -key functional regions in the genome are under strong negative selection and hence are depleted in common variants (Fu et al, 2014;Zhang, Liu, et al, 2020). Therefore, we compared the rare variant enrichment in the refined and original positive enhancer regions.…”

DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays

“…We further evaluated the quality of our compact enhancer annotation from DECODE via the enrichment of rare variants with a simple but validated assumption—key functional regions in the genome are under strong negative selection and hence are depleted in common variants ( Fu et al, 2014 ; Zhang et al, 2020b ). Therefore, we compared the rare variant enrichment in the refined and original positive enhancer regions (and against ENCODE NPC cCREs, FANTOM human enhancers, FANTOM neuronal stem cell enhancers in Supplementary Fig.…”

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins

“…We have made this RNA variant annotation and prioritization tool available as an open-source software at https://github.com/gersteinlab/RADAR [46]. The source code is released under MIT License.…”