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Merilla's Current Project

3’ Untranslated Regions (3’UTRs) influence gene function by controlling transcript stability, translational efficiency and mRNA transport. These functions are coordinated by 3’UTR interaction with specific cisinteracting molecules, including microRNAs and RNA-Binding Proteins (RBPs). The recent surge of highthroughput transcriptome sequencing has revealed a surprising diversity of 3’UTR isoforms. 3’UTR isoforms are regulated in a tissue-type and cell-type specific manner, and the longest 3’UTRs transcripts are expressed in the nervous system. To profile 3’UTR isoform diversity in Human DRG neurons, we performed Pacific Biosciences (PacBio) IsoSeq whole-transcript sequencing of RNA pooled from seven Human DRG samples. Limitations of the IsoSeq methodology are 1) it is cost-prohibitive for use with larger comparative experiments and 2) the resulting data is not quantitative across conditions. Therefore, we developed a pipeline employing an in-house developed algorithm - CSI-UTR - to analyze 3’UTR isoform expression in DRG neurons using standard mRNA libraries sequenced with Illumina technology.

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