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Series GSE124735 Query DataSets for GSE124735
Status Public on Feb 27, 2019
Title ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways [iCLIP-seq]
Organism Homo sapiens
Experiment type Other
Summary we try to investigate the binding of ALYREF and NXF1 on histone mRNA when the cell treated with indicated siRNAs.
ALYREF plays key roles in nuclear export of polyadenylated mRNAs and also modulates their 3' processing, but whether it is involved in regulating RNAs beyond polyadenylated mRNAs is unknown. The replication-dependent (RD) histone mRNAs are not polyadenylated, but end in a stem-loop (SL) structure. Here we demonstrate that ALYREF prevalently binds a region next to the SL on RD histone mRNAs. SL-binding protein (SLBP) directly interacts with ALYREF and ensures this binding. To examine how SLBP KD impact ALYREF distribution on the histone mRNA, we carried out ALYREF iCLIP in control and SLBP KD cells. To investigate the functional consequence for ALYREF binding on histone mRNAs, we isolated polyA+ and polyA- RNAs from control and ALYREF KD cells, and carried out RNA-seq separately.
 
Overall design The ALYREF-iCLIP assay was performed in control and SLBP knock down cells using ALYREF antibody. The NXF1-iCLIP experiments were carried out in Flag-NXF1 stable expressed cells treated with control, ALYREF and SLBP siRNAs for 72 hr using Flag antibody.
 
Contributor(s) Fan J, Du X, Zhou Y, Cheng H
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Submission date Jan 07, 2019
Last update date Mar 20, 2019
Contact name Hong Cheng
E-mail(s) hcheng@sibcb.ac.cn
Organization name Shanghai Institutes for Biological Sciences
Department Shanghai Institute of Biochemistry and Cell Biology
Lab StateKey Laboratory of Molecular Biology
Street address 320 YueYang Road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (10)
GSM3544653 ALYREF-iCLIP Luc KD-1
GSM3544654 ALYREF-iCLIP Luc KD-2
GSM3544655 ALYREF-iCLIP SLBP KD-1
This SubSeries is part of SuperSeries:
GSE125005 ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways
Relations
BioProject PRJNA513300
SRA SRP176432

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Supplementary file Size Download File type/resource
GSE124735_RAW.tar 829.2 Mb (http)(custom) TAR (of BED12)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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