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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 23, 2014 |
| Title |
Genome-wide identification and functional analysis of Apobec-1 mediated C-to-U RNA editing in mouse small intestine and liver |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
The genome-wide identification, tissue-specificity and functional implications of Apobec-1 mediated C-to-U RNA editing remains incomplete. Deep sequencing, data filtering and validation from wild-type and Apobec-1 deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs (74-81% true-positive), all within 3' untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites were unique to liver. Changes in RNA editing led to corresponding changes in intestinal mRNA and protein levels in 11 genes. We found distinctive polysome profiles for several editing targets and demonstrated nuclear but not cytoplasmic editing of novel exonic sites in intestinal (but not hepatic) apoB RNA. RNA editing was validated using cell-free extracts from wild-type but not Apobec-1 deficient mice. These studies define selective, tissue-specific targets of Apobec-1 dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.
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| Overall design |
Examination of C-to-U RNA editing in mouse liver and intestine
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| Contributor(s) |
Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Hamidane HB, Graumann J, Mortazavi A, Nadeau JH, Davidson NO |
| Citation(s) |
24946870 |
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| Submission date |
May 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Eddie Park |
| E-mail(s) |
eddiep@uci.edu
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| Phone |
9498248393
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| Organization name |
UCI
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| Department |
DevCell
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| Lab |
Mortazavi
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| Street address |
2300 Biological Sciences 3
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| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA248400 |
| SRA |
SRP042200 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57910_intestine.bed.gz |
522 b |
(ftp)(http) |
BED |
| GSE57910_liver.bed.gz |
232 b |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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