Transcriptomics,Genomics

Dataset Information

152

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA editing targets in transcript 3'UTRs


ABSTRACT: Apolipoprotein B-editing enzyme, catalytic polypeptide-1 (APOBEC1) is a cytidine deaminase, initially identified by its activity in converting a specific cytidine (C) to uridine (U) in apolipoprotein B (apoB) mRNA transcripts in the small intestine. Editing results in translation of a truncated apoB isoform with distinct functions in lipid transport. To address the possibility that APOBEC1 edits additional mRNAs, we developed a transcriptome-wide comparative RNA-Seq screen. We identified and validated 32 previously undescribed mRNA targets of APOBEC1 editing, all of which are located in AU-rich segments of transcript 3′ untranslated regions (3′ UTRs). Further analysis revealed several characteristic sequence features of editing targets, which were predictive for the identification of additional APOBEC1 substrates. The identification of multiple mRNA editing substrates for APOBEC1 suggests additional functions for this cytidine deaminase beyond its characterized role in lipid absorption. Overall design: Poly(A)+ RNA-Seq libraries were prepared from C57Bl6 Wild-type and congenic Apobec1-/- murine small intestinal epithelial cells (2 samples total).

INSTRUMENT(S): Illumina Genome Analyzer II (Mus musculus)

SUBMITTER: Brad Rosenberg 

PROVIDER: GSE24958 | GEO | 2011-01-23

SECONDARY ACCESSION(S): PRJNA131999

REPOSITORIES: GEO

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Publications

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs.

Rosenberg Brad R BR   Hamilton Claire E CE   Mwangi Michael M MM   Dewell Scott S   Papavasiliou F Nina FN  

Nature structural & molecular biology 20110123 2


Apolipoprotein B-editing enzyme, catalytic polypeptide-1 (APOBEC1) is a cytidine deaminase initially identified by its activity in converting a specific cytidine (C) to uridine (U) in apolipoprotein B (apoB) mRNA transcripts in the small intestine. Editing results in the translation of a truncated apoB isoform with distinct functions in lipid transport. To address the possibility that APOBEC1 edits additional mRNAs, we developed a transcriptome-wide comparative RNA sequencing (RNA-Seq) screen. W  ...[more]

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