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Series GSE131210 Query DataSets for GSE131210
Status Public on May 17, 2019
Title easyCLIP Quantifies RNA-Protein Interactions and Characterizes Recurrent PCBP1 Mutations in Cancer
Organism Homo sapiens
Experiment type Other
Summary RNA-protein interactions mediate a host of cellular processes, underscoring the need for methods to quantify their occurrence in living cells. RNA interaction frequencies for the average cellular protein are undefined, however, and there is no quantitative threshold to define a protein as an RNA-binding protein (RBP). Ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing, an effective widely used means of characterizing RNA-protein interactions, would particularly benefit from the capacity to quantitate the number of RNA cross-links per protein per cell. In addition, CLIP-seq methods are difficult, have high experimental failure rates and many ambiguous analytical decisions. To address these issues, the easyCLIP method was developed and used to quantify RNA-protein interactions for a panel of known RBPs as well as a spectrum of random non-RBP proteins. easyCLIP provides the advantages of good efficiency compared to current standards, a simple protocol with a very low failure rate, troubleshooting information that includes direct visualization of prepared libraries without amplification, and a new form of analysis. easyCLIP, which uses sequential on-bead ligation of 5’ and 3’ adaptors tagged with different infrared dyes, classified non-RBPs as those with a per protein RNA cross-link rate of <0.1%, with most RBPs substantially above this threshold, including Rbfox1 (18%), hnRNPC (22%), CELF1 (11%), FBL (2%), and STAU1 (1%). easyCLIP with the PCBP1L100 RBP mutant recurrently seen in cancer quantified increased RNA binding compared to wild-type PCBP1 and suggested a potential mechanism for this RBP mutant in cancer. easyCLIP provides a simple, efficient and robust method to both obtain both traditional CLIP-seq information and to define actual RNA interaction frequencies for a given protein, enabling quantitative cross-RBP comparisons as well as insight into RBP mechanisms.
 
Overall design RNA-binding landscapes of 8 RBPs and 10 non-RBPs, with 1-3 replicates,
 
Contributor(s) Porter DF, Miao W, Khavari PA
Citation(s) 33692367
NIH grant(s)
Grant ID Grant title Affiliation Name
F32 AR072504 Mechanisms of lncRNA-mediated control of epidermal proliferation and differentiation STANFORD UNIVERSITY Douglas F Porter
R01 AR045192 Regulators of Epidermal Gene Expression STANFORD UNIVERSITY PAUL KHAVARI
R01 AR049737 Epidermal Signaling Regulators STANFORD UNIVERSITY PAUL KHAVARI
T32 AR007422 Postgraduate Training Program in Epithelial Biology STANFORD UNIVERSITY PAUL KHAVARI
Submission date May 14, 2019
Last update date Oct 11, 2022
Contact name Douglas Porter
Organization name Stanford
Department Dermatology
Lab Khavari
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (3)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (50)
GSM3767627 easyCLIP CCIN Replicate 1 [Exp56_CCIN_tcCTGATC_TCA]
GSM3767628 easyCLIP CCIN Replicate 2 [Exp56_CCIN_tcCTGATC_AGT]
GSM3767629 easyCLIP CDK4 Replicate 1 [Exp31_CDK4_05GCCATG_AAC]
Relations
BioProject PRJNA542907
SRA SRP198401

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE131210_ann_counts.txt.gz 1.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
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