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| Status |
Public on Nov 18, 2014 |
| Title |
Dissecting non-coding and pathogen RNA-protein interactomes |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
RNA-protein interactions are central to biological regulation. Cross-linking immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA-protein interactomes, but current CLIP methods are limited by challenging biochemical steps and fail to detect many classes of noncoding and non-human RNAs. Here we present FAST-iCLIP, an integrated pipeline with improved CLIP biochemistry and an automated informatic pipeline for comprehensive analysis across protein coding, noncoding, repetitive, retroviral, and non-human transcriptomes. FAST-iCLIP of Poly-C binding protein 2 (PCBP2) showed that PCBP2 bound CU-rich motifs in different topologies to recognize mRNAs and noncoding RNAs with distinct biological functions. FAST-iCLIP of PCBP2 in hepatitis C virus-infected cells enabled a joint analysis of the PCBP2 interactome with host and viral RNAs and their interplay. These results show that FAST-iCLIP can be used to rapidly discover and decipher mechanisms of RNA-protein recognition across the diversity of human and pathogen RNAs.
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| Overall design |
Characterization of non-coding and pathogen RNA-protein interactions using an automated computational pipeline and improved iCLIP biochemistry
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| Contributor(s) |
Martin L, Flynn RA, Chang HY |
| Citation(s) |
25411354 |
| Submission date |
Jul 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
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| Organization name |
Stanford University
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| Street address |
380 Roth Way, Room 265
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA256335 |
| SRA |
SRP044951 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE59840_RAW.tar |
1.8 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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