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Series GSE90650 Query DataSets for GSE90650
Status Public on Jul 26, 2017
Title The LncRNA NEAT1 Nests RNA Binding Proteins and the Microprocessor to Globally Enhance Pri-miRNA Processing
Organism Homo sapiens
Experiment type Other
Non-coding RNA profiling by high throughput sequencing
Summary MicroRNA biogenesis is known to be modulated by a variety of RNA binding proteins (RBPs), but in most cases, individual RBPs appear to influence the processing of a small number of selective targets. We herein report binding of the NONO/PSF heterodimer to hundreds of expressed pri-miRNAs in HeLa cells to globally enhance pri-miRNA processing by the Drosha/DGCR8 Microprocessor. As NONO/PSF are key components of paraspeckles organized by the lncRNA NEAT1, we find that NEAT1 also has profound effects on global pri-miRNA processing. Mechanistic dissection reveals that NEAT1 broadly interacts with NONO/PSF as well as many other RBPs, and that multiple RNA segments in NEAT1, including a “pseudo pri-miRNA” near its 3’ end, help attract the Microprocessor. These findings suggest a bird nest model for a large lncRNA to orchestrate efficient processing of an entire class of small RNAs in the nucleus.we used small RNA-seq to identify miRNA level in response to secific knockdowns relative to siGFP treatment control
 
Overall design We profiled the miRNAs expression levels under conditions including siGFP(control), siNEAT1, siNEAT1_V2, siNONO, siPSF and siPSPC1 through small RNA-seq respectively. And we also examined the in vivo interactions between NONO/PSF and RNA through CLIP-seq.
 
Contributor(s) Jiang L, Shao C, Zhou Y, Fu X
Citation(s) 28846091
Submission date Nov 29, 2016
Last update date May 15, 2019
Contact name Xiang-Dong Fu
Organization name UC San Diego
Department CMM
Lab George Palade Laboratories
Street address 9500 Gilman Drive, Room 231
City La Jolla
State/province CA
ZIP/Postal code 92093-0651
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (16)
GSM2409885 siGFP-1
GSM2409886 siGFP-2
GSM2409887 siNEAT1-1
Relations
BioProject PRJNA355281
SRA SRP094056

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Supplementary file Size Download File type/resource
GSE90650_RAW.tar 253.9 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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