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| Status |
Public on Jan 05, 2012 |
| Title |
Widespread regulated alternative splicing of single codons accelerates proteome evolution |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Thousands of human genes contain introns ending in NAGNAG motifs (N any nucleotide), where both NAGs can function as 3' splice sites, yielding isoforms differing by inclusion/exclusion of just three bases. However, the functional importance of NAGNAG alternative splicing is highly controversial. Using very deep RNA-Seq data from sixteen human and eight mouse tissues, we found that approximately half of alternatively spliced NAGNAGs undergo tissue-specific regulation and that regulated events have been selectively retained: alternative splicing of strongly tissue-specific NAGNAGs was ten times as likely to be conserved between species as for non-tissue-specific events. Further, alternative splicing of human NAGNAGs was associated with an order of magnitude increase in the frequency of exon length changes at orthologous mouse/rat exon boundaries, suggesting that NAGNAGs accelerate exon evolution. Together, our analyses show that NAGNAG alternative splicing constitutes a major generator of tissue-specific proteome diversity and accelerates evolution of proteins at exon-exon boundaries.
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| |
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| Overall design |
mRNA-Seq of sixteen human and eight mouse tissues.
Supplementary files:
human.nagnag.junctions.gff and mouse.nagnag.junctions.gff are the annotation files (in GFF3 format) corresponding to the 'bwtout' mapped reads files linked to the Sample records.
Raw data files provided for Samples GSM742937-GSM742952 only.
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| |
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| Contributor(s) |
Bradley RK, Merkin J, Burge CB |
| Citation(s) |
22235189 |
| |
| Submission date |
Jun 16, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert K Bradley |
| Organization name |
MIT
|
| Department |
Biology
|
| Street address |
77 Massachusetts Avenue, 68-223A
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (48)
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| Relations |
| SRA |
SRP007338 |
| BioProject |
PRJNA143693 |
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