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Series GSE106476 Query DataSets for GSE106476
Status Public on Apr 30, 2018
Title RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary G-quadruplexes (rG4s) are recognized as key structures involved in RNA biology and are linked to neurodegenerative disease and cancer. However, detailed knowledge of rG4s and their binding partners is lacking. Here, a systematic, unbiased affinity proteomics approach identified 80 potential high-confidence interactors of the rG4 structure in the 5’UTR of the NRAS oncogene. Using epitope-tagged protein expression, we validated a subset of interactions including DDX3X, DDX5, DDX17, DHX9, DHX36, FXR1, FXR2, GRSF1 and NSUN5. More than half of the identified rG4 interactors were enriched in glycine-arginine (GAR) domains, and for DDX3X and DDX17, we show that the GAR domain is required for rG4 interaction. Transcriptome-wide binding analysis using DDX3X iCLIP revealed a striking association with rG4s in 5’UTRs that was lacking in the GAR-domain mutant. Overall, our work highlights a hitherto unrecognized complexity in rG4 structure-protein interactions that should be considered for the understanding of rG4 function.
 
Overall design 6 libraries for Flp-In T-Rex 293 cell line iCLIP experiment: 3 for mutant-DDX3X and 3 for WT-DDX3X; 11 libraries for Flp-In T-Rex 293 cell line RNA-seq experiment: 4 for WT-DDX3X, 4 for mutant-DDX3X and 3 for no expression (negative).
 
Contributor(s) Meyer C, Herdy B, Varshney D, Marsico G, Taylor C, D'Santos C, Tannahill D, Balasubramanian S
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 02, 2017
Last update date May 15, 2019
Contact name Giovanni Marsico
E-mail(s) persego@gmail.com
Organization name CRUK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (18)
GSM2838581 All_reads
GSM2838582 mRG1
GSM2838583 mRG2
Relations
BioProject PRJNA417119
SRA SRP123630

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
GSE106476_RAW.tar 13.4 Mb (http)(custom) TAR (of BED, BEDGRAPH, TXT)
GSE106476_README.txt 1.3 Kb (ftp)(http) TXT
GSE106476_WT.norm.sum.bedGraph.gz 5.7 Mb (ftp)(http) BEDGRAPH
GSE106476_WT_NO_mRG.multi2.middle_100.bed.gz 20.0 Kb (ftp)(http) BED
GSE106476_WT_all.multi2.middle_100.bed.gz 33.2 Kb (ftp)(http) BED
GSE106476_WT_and_mRG_all.multi2.middle_100.bed.gz 14.6 Kb (ftp)(http) BED
GSE106476_gencode.v19.pc_lncRNA_transcripts.expr.fa.gz 16.4 Mb (ftp)(http) FA
GSE106476_mRG.norm.sum.bedGraph.gz 6.7 Mb (ftp)(http) BEDGRAPH
GSE106476_mRG_4_WT_4_Neg_3.htseq.txt.gz 401.6 Kb (ftp)(http) TXT
GSE106476_mRG_NO_WT.multi2.middle_100.bed.gz 16.2 Kb (ftp)(http) BED
GSE106476_mRG_all.multi2.middle_100.bed.gz 28.8 Kb (ftp)(http) BED
GSE106476_transcripts.norm.sum.WT_mRG_sig.bed.gz 671.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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