Poster abstracts

Poster number 115 submitted by Rajneesh Srivastava

SliceIt: RNA-Binding Protein (RBP) centric genome-wide in silico library of sgRNAs for CRISPR/Cas9 screens

Sasank Vemuri (BioHealth Informatics, IUPUI), Rajneesh Srivastava (BioHealth Informatics, IUPUI), Seyedsasan Hashemikhabir (BioHealth Informatics, IUPUI), Sarath Chandra Janga (BioHealth Informatics, IUPUI)

Abstract:
Several UV cross linking protocols such as eCLIP have been established to delineate the molecular interaction of RNA Binding Protein (RBP) and their target RNAs. CRISPR/ Cas9 system has been employed to verify such localized interactions in cells. With the advancement of pooled CRISPR/Cas9 screens, it is possible to study the global impact of these proteins in human cells. Here, we present SliceIt, a database of in silico sgRNA (or guideRNA) library that helps the researchers to conduct such high throughput screens. We used CRISPR-DO to design ~4.8 million unique sgRNAs targeting all possible RBP binding sites from the eCLIP experiment of 123 RBP in HepG2 and K562 cell lines from ENCODE. SliceIt provides a user friendly environment, developed in highly advanced search engine framework called Elasticsearch. It is available in both table and genome browser view that facilitates the easy navigation of RBP binding sites, sgRNAs, SNPs and GWAS. It also provides the exon expression profile across 53 tissues from GTEx to examine the locus specific changes proximal to the binding sites. User can also upload custom tracks of various file formats (in browser) to navigate additional genomic features in hg38 genome and cross compare with our profiling. All the binding site centric information is dynamically accessible via “search by gene”, “search by coordinate” and “search by RBP” and readily available to download. Finally, SliceIt is a one-stop repertoire of guideRNA library, RBP binding sites along with several layer of functional information to design the high throughput CRISPR cas9 screens for studying the phenotypes and diseases associated to RBP centric post transcriptional regulation.

URL: https://sliceit.soic.iupui.edu/

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Keywords: RNA binding proteins, in silico library, CRISPRCas9 pooled screens