Quantitative evaluation of all hexamers as exonic splicing elements

• DOI: 10.1101/gr.119628.110
• Publication Date: 2011-06-10T08:48:24Z
• Authors: Shengdong Ke; Shulian Shang; Sergey M. Kalachikov; Irina Morozova; Lin Yu; James J. Russo; Jingyue Ju; Lawrence A. Chasin
• Keywords: 0301 basic medicine; 03 medical and health sciences; RNA Splicing; Humans; Nucleic Acid Conformation; RNA; Exons; RNA Splice Sites; Regulatory Sequences, Ribonucleic Acid; Chromatin

We describe a comprehensive quantitative measure of the splicing impact complete set RNA 6-mer sequences by deep sequencing successfully spliced transcripts. All 4096 6-mers were substituted at five positions within two different internal exons in 3-exon minigene, and millions transcripts sequenced after transfection human cells. The results allowed assignment relative strength score to each mutant molecule. effect on often depended their location; much this context could be ascribed creation overlapping site. Taking these overlaps into account, quantified, designated as enhancers (ESEseqs) silencers (ESSseqs), with an ESRseq indicating strength. Some exhibited positional bias splice sites. distribution conservation ESRseqs around supported classification. Predicted secondary structure effects also seen: Effective enhancers, 3′ sites tend single stranded, effective 5′ double stranded. that may form positive or negative synergy another identified. Chromatin influence enhancement observed, good correspondence was found between performance predicted nucleosome occupancy scores 6-mers. This approach prove general use defining nucleic acid regulatory motifs, substitute for functional SELEX most cases, provide insights about mechanisms.