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Series GSE44615 Query DataSets for GSE44615
Status Public on Feb 26, 2013
Title Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition [PAR-CLIP]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3,000 mRNAs at ~9,500 sites located in the 3’UTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines, and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell-cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some, but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors.
 
Overall design LIN28 protein PAR-CLIP
 
Contributor(s) Markus H, Thomas T
Citation(s) 23481595
Submission date Feb 25, 2013
Last update date May 15, 2019
Contact name Miguel Brown
E-mail(s) miguel.a.brown@gmail.com
Organization name The Rockefeller University
Street address 1230 York Ave Box 186
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (4)
GSM1087848 LIN28A PAR-CLIP
GSM1087849 LIN28B_rep1 PAR-CLIP
GSM1087850 LIN28B_rep2 PAR-CLIP
This SubSeries is part of SuperSeries:
GSE44616 Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
Relations
BioProject PRJNA190657
SRA SRP018837

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Supplementary file Size Download File type/resource
GSE44615_LIN28A.xlsx.gz 3.7 Mb (ftp)(http) XLSX
GSE44615_LIN28B.xlsx.gz 4.0 Mb (ftp)(http) XLSX
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Processed data are available on Series record
Raw data are available in SRA

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