POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

Abstract

RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation. Accurate identification of RBP binding sites in multiple cell lines and tissue types from diverse species is a fundamental endeavor towards understanding the regulatory mechanisms of RBPs under both physiological and pathological conditions. Our POSTAR annotation processes make use of publicly available large-scale CLIP-seq datasets and external functional genomic annotations to generate a comprehensive map of RBP binding sites and their association with other regulatory events as well as functional variants. Here, we present POSTAR3, an updated database with improvements in data collection, annotation infrastructure, and analysis that support the annotation of post-transcriptional regulation in multiple species including: we made a comprehensive update on the CLIP-seq and Ribo-seq datasets which cover more biological conditions, technologies, and species; we added RNA secondary structure profiling for RBP binding sites; we provided miRNA-mediated degradation events validated by degradome-seq; we included RBP binding sites at circRNA junction regions; we expanded the annotation of RBP binding sites, particularly using updated genomic variants and mutations associated with diseases. POSTAR3 is freely available at http://postar.ncrnalab.org.

Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty

“…3 can be found in Table 2 . This table provides substantial scientific information that has been extracted from other highly valuable databases such as NPInter 136 – 139 , BioGRID 140 and POSTAR3 141 which rigorously report data from Affinity Capture-Mass Spectrometry (BioGRID terminology) 142 , UV Cross-Linking and Immunoprecipitation (CLIP) / CLIP-seq / HITS-CLIP 143 – 149 , Photoactivatable Ribonucleoside-enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) 150 – 153 , Enhanced CLIP (eCLIP) 154 , 155 , Individual-nucleotide resolution UV Crosslinking and Immunoprecipitation (iCLIP), Capture Hybridization Analysis of RNA Targets (CHART-seq) 156 , Affinity Chromatography 157 , as well as other methods such as RNA Immunoprecipitation (RIP), Affinity Capture-RNA (BioGRID terminology) 158 – 161 and other “Protein-RNA” methods (BioGRID terminology) 162 – 164 which may also include a combination of Immunocytochemistry (ICC), In Situ Hybridization, Northern Blot and/or RT-PCR 165 , 166 .

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“…PAR-CLIP; HITS-CLIP; iCLIP (POSTAR3) AGO2, ELAVL1. PAR-CLIP Affinity Capture - RNA (POSTAR3, BioGRID) 159 Information extracted from several databases including NPInter 136 – 139 , BioGRID 140 , lncRNome 134 and POSTAR3 141 . CLIP UV Cross-Linking and Immunoprecipitation, PAR-CLIP Photoactivatable Ribonucleoside-enhanced Crosslinking and Immunoprecipitation, eCLIP Enhanced CLIP, iCLIP Individual-nucleotide resolution UV Crosslinking and Immunoprecipitation, CHART-seq Capture Hybridization Analysis of RNA Targets, RIP RNA Immunoprecipitation.…”

“…Given the relatively high frequency of recruitment of eIF4A3, FUS and related RNA-binding proteins (RBPs) by cancer-associated lncRNAs and their known roles in tumorigenesis, we here provide in Fig. 4 the putative consensus motifs that enable lncRNAs to specifically bind these RBPs, as this may help investigators to identify novel interactions between their lncRNA of interest and these tumorigenic RBPs (consensus motifs extracted from POSTAR3 database which reports CLIP-seq data 141 ).

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“… Data extracted from POSTAR3 database (CLIPseq-based) 141 and processed by HOMER and MEME algorithms that are commonly used for motif discovery and next-generation sequencing (NGS) data analysis. Square boxes highlight similar patterns identified in the motifs provided by both algorithms.…”

CD47 is correlated with immune infiltration and is a prognostic biomarker in colorectal cancer

“…Construction of mRNA-TF, mRNA-RBP, mRNA-Drug, and mRNA-miRNA network Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRRUST) [13](https://www.grnpedia.org/trrust/), a manually curated database of human transcriptional regulatory networks, contains not only the target gene of transcription factors but also potential interactions between transcription factors. Post-transcriptional regulation(POSTAR)3 [14](http://111.198.139.65/) is a database that uses public large-scale crosslinking immunoprecipitation (CLIP)-seq data and external functional genome annotations, which provides binding sites for RNA-binding proteins, their functional variants, and regulatory mechanisms. The starBase database [15]contains more than 700 CLIP-seq datasets, current degradome data, multiple types of omics data assisted miRNA target prediction, many visualizations of miRNA target interfaces, and analyzed interactions between lncRNA, circRNA, protein and mRNA, or ceRNA mechanism of 23 species.…”