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| Status |
Public on Sep 13, 2009 |
| Title |
Illumina mRNA-Seq of control and hnRNP H knockdown in 293T cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Pre-mRNA splicing is regulated through combinatorial activity of RNA motifs including splice sites and splicing regulatory elements (SREs). Here, we show that the activity of a major class of mammalian SREs is highly sensitive to the strength of the adjacent 5' splice site (5'ss) sequence, and that this has important functional and evolutionary implications. Activity of G-run SREs was higher for intermediate strength 5'ss by ~4-fold relative to weak 5'ss, and by ~1.3-fold relative to strong 5'ss. The dependence on 5'ss strength was supported both by comparative genomics and by microarray and Illumina mRNA-Seq analyses of splicing changes following RNAi against the splicing factor heterogeneous nuclear ribonucleoprotein (hnRNP) H, which binds G-runs. This dependence implies that the responsiveness of exons to changes in hnRNP H levels is a bivariate function of both SRE abundance and 5'ss strength; this relationship may hold also for other splicing factors. This pattern of activity enables G-runs and hnRNP H to buffer the effects of 5'ss mutations, augmenting both the frequency of 5'ss polymorphism and the evolution of new splicing patterns.
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| Overall design |
Examine mRNA expression in 293T cells following hnRNP H or control siRNA knockdown
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| Contributor(s) |
Xiao X, Wang Z, Jang M, Nutiu R, Wang ET, Burge CB |
| Citation(s) |
19749754 |
| Submission date |
Jun 16, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinshu Xiao |
| E-mail(s) |
gxxiao@ucla.edu
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| Organization name |
MIT
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| Department |
Biology
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| Lab |
Chris Burge Lab
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| Street address |
77 Mass Ave. MIT, 68-211
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (2) |
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| Relations |
| SRA |
SRP001349 |
| BioProject |
PRJNA116223 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE16642_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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