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E-GEOD-69656 - An Alternative Splicing Event Amplifies Evolutionary Differences Between Vertebrates

Status
Released on 1 September 2015, last updated on 5 September 2015
Organism
Gallus gallus, Homo sapiens
Samples (14)
Protocols (6)
Description
Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here, we show that mammalian-specific skipping of exon 9 of PTBP1 alters its splicing regulatory activities and affects the inclusion levels of numerous exons. During neurogenesis, skipping of exon 9 reduces PTBP1 repressive activity so as to facilitate activation of a brain-specific AS program. Engineered skipping of the orthologous exon in chicken cells induces a large number of mammalian-like AS changes in PTBP1 target exons. These results thus reveal that a single exon skipping event in an RNA binding regulator directs numerous AS changes between species. The results further suggest that these changes contributed to evolutionary differences in the formation of vertebrate nervous systems. This study contains two sets of samples: (Set 1) mRNA profiling of human 293 cells subjected to four different conditions in two biological replicates: non-targetting control siRNA, PTBP1 and PTBP2 siRNA, PTBP1 and PTBP2 siRNA with overexpression of full-length human PTBP1, PTBP1 and PTBP2 siRNA with overexpression of exon-excluded human PTBP1. (Set 2) mRNA profiling of chicken DT40 cells with 3 genotypes in two bioligcal replicates: wildtype cells, cells with PTBP1 exon 8 (orthologous to human PTBP1 exon 9) deleted in one allele, and cells with PTBP1 exon 8 deleted in both alleles.
Experiment type
RNA-seq of coding RNA 
Contacts
Benjamin J Blencowe, Manuel Irimia, Serge Gueroussov
Citation
RNA SPLICING. An alternative splicing event amplifies evolutionary differences between vertebrates. Gueroussov S, Gonatopoulos-Pournatzis T, Irimia M, Raj B, Lin ZY, Gingras AC, Blencowe BJ.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-69656.idf.txt
Sample and data relationshipE-GEOD-69656.sdrf.txt
Additional data (1)E-GEOD-69656.additional.1.zip
Links