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Series GSE35800 Query DataSets for GSE35800
Status Public on Feb 28, 2012
Title Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Decoding post-transcriptional regulatory programs underlying gene expression is a crucial step toward a predictive dynamical understanding of cellular state transitions. Despite recent systematic efforts, the sequence determinants of such mechanisms remain largely uncharacterized. An important obstacle in revealing these elements stems from the contribution of local secondary structures in defining interaction partners in a variety of regulatory contexts, including but not limited to transcript stability, alternative splicing and localization. There are many documented instances where the presence of a structural regulatory element dictates alternative splicing patterns (e.g. human cardiac troponin T) or affects other aspects of RNA biology. Thus, a full characterization of post-transcriptional regulatory programs requires capturing information provided by both local secondary structures and the underlying sequence. We have developed a computational framework based on context-free grammars and mutual information that systematically explores the immense space of structural elements and reveals motifs that are significantly informative of genome-wide measurements of RNA behavior. The application of this framework to genome-wide mammalian mRNA stability data revealed eight highly significant elements with substantial structural information, for the strongest of which we showed a major role in global mRNA regulation. Through biochemistry, mass-spectrometry, and in vivo binding studies, we identified HNRPA2B1 as the key regulator that binds this element and stabilizes a large number of its target genes. Ultimately, we created a global post-transcriptional regulatory map based on the identity of the discovered linear and structural cis-regulatory elements, their regulatory interactions and their target pathways. This approach can also be employed to reveal the structural elements that modulate other aspects of RNA behavior.

This SuperSeries is composed of the SubSeries listed below.
Overall design Refer to individual Series
Citation(s) 22495308
Submission date Feb 14, 2012
Last update date May 15, 2019
Contact name Hani Goodarzi
Organization name UCSF
Department Biochemistry and Biophysics
Street address 600 16th St, GH S312D
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (2)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (43)
GSM874406 decoy_vs_scrambled_1_1
GSM874407 decoy_vs_scrambled_1_2
GSM874408 decoy_vs_scrambled_2_1
This SuperSeries is composed of the following SubSeries:
GSE35749 sRSM1 synthetic decoy vs. scrambled transfections in MDA-MB-231 cells
GSE35753 HNRPA2B1 RIP-chip
GSE35756 Whole-genome decay rate measurements in MDA-MB-231 cells transfected with HNRPA2B1 siRNAs versus controls
BioProject PRJNA152199

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
GSE35800_RAW.tar 433.2 Mb (http)(custom) TAR (of FA, TXT)
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