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| Status |
Public on Dec 01, 2013 |
| Title |
RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins |
| Organisms |
Drosophila melanogaster; Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Background: Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of Sm RNPs is critical for understanding their functions.
Results: We developed a multi-targeting RNA-immunoprecipitation sequencing (RIP-seq) strategy to reliably identify Sm-associated RNAs from Drosophila ovaries and cultured human cells. Using this method, we discovered three major categories of Sm-associated transcripts: small nuclear (sn)RNAs, small Cajal body (sca)RNAs and mRNAs. Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-independent function for Sm RNPs.
Conclusions: This study represents the first comprehensive analysis of eukaryotic Sm-containing RNPs, and provides a basis for additional functional analyses of Sm proteins and their associated snRNPs outside of the context of pre-mRNA splicing. Our findings expand the repertoire of eukaryotic Sm-containing RNPs and suggest new functions for snRNPs in mRNA metabolism.
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| Overall design |
RNA-Immunoprecipitation sequencing of RNA-Sm protein complexes.
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| Contributor(s) |
Lu Z, Guan X, Schmidt CA, Matera AG |
| Citation(s) |
24393626 |
| Submission date |
Feb 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhipeng Lu |
| E-mail(s) |
zhipengluchina@gmail.com
|
| Organization name |
Stanford University
|
| Department |
Department of Dermatology
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| Lab |
Howard Chang
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (28)
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| Relations |
| SRA |
SRP010944 |
| BioProject |
PRJNA151853 |
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