Transcriptomics,Genomics

Dataset Information

47

Mouse Alt-Splice Tissue Panel (Brain vs Non-Brain)


ABSTRACT: 22 Normal adult mouse tissues on custom alternative transcript sensitive Affymetrix microarray used to address differeneces in tissue specific alternative splicing. Abstract: Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe expression of RNA containing at least two alternative splice junctions for about a third of the 3200 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues, and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif strikingly similar to the branchpoint consensus, but which is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase (MAGUK) genes reveals that each contains a paralogous tissue regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families. Keywords: Alternative splicing isoform specific, adult mouse tissues Overall design: 22 Normal tissues with at least 3 replicates each. Custom Affymetrix microarrays with probes specific to different alternative splicing events, including splice junction probes. Perfect match probes only.

INSTRUMENT(S): ares_ucsc_mouse_59198_affyMouseA

SUBMITTER: Charles Sugnet  

PROVIDER: GSE3063 | GEO | 2006-01-19

SECONDARY ACCESSION(S): PRJNA93153

REPOSITORIES: GEO

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Publications

Unusual intron conservation near tissue-regulated exons found by splicing microarrays.

Sugnet Charles W CW   Srinivasan Karpagam K   Clark Tyson A TA   O'Brien Georgeann G   Cline Melissa S MS   Wang Hui H   Williams Alan A   Kulp David D   Blume John E JE   Haussler David D   Ares Manuel M  

PLoS computational biology 20060120 1


Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect.  ...[more]

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