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Series GSE24958 Query DataSets for GSE24958
Status Public on Jan 23, 2011
Title Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA editing targets in transcript 3'UTRs
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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).
Contributor(s) Rosenberg BR, Hamilton CE, Dewell S, Papavasiliou FN
Citation(s) 21258325
Submission date Oct 27, 2010
Last update date May 15, 2019
Contact name Brad Rosenberg
Organization name Icahn School of Medicine at Mount Sinai
Department Microbiology
Street address 1 Gustave L Levy Place
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (2)
GSM613387 IntestineEpi_WT
GSM613388 IntestineEpi_APOBEC1
SRA SRP004025
BioProject PRJNA131999

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Supplementary file Size Download File type/resource
GSE24958_RAW.tar 2.4 Gb (http)(custom) TAR (of BAM)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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