Yoon et al. 2014 (PRJNA230610)

General Details

Title Integrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (Ribosome)
Organism
Number of Samples 3
Release Date 2013/12/04 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP033503
ENA SRP033503
GEO GSE52976
BioProject PRJNA230610

Publication

Title
Authors Yoon JH,De S,Srikantan S,Abdelmohsen K,Grammatikakis I,Kim J,Kim KM,Noh JH,White EJ,Martindale JL,Yang X,Kang MJ,Wood WH 3rd,Noren Hooten N,Evans MK,Becker KG,Tripathi V,Prasanth KV,Wilson GM,Tuschl T,Ingolia NT,Hafner M,Gorospe M
Journal Nature communications
Publication Date 2014 Nov 4
Abstract Post-transcriptional gene regulation is robustly regulated by RNA-binding proteins (RBPs). Here we describe the collection of RNAs regulated by AUF1 (AU-binding factor 1), an RBP linked to cancer, inflammation and aging. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis reveals that AUF1 primarily recognizes U-/GU-rich sequences in mRNAs and noncoding RNAs and influences target transcript fate in three main directions. First, AUF1 lowers the steady-state levels of numerous target RNAs, including long noncoding RNA NEAT1, in turn affecting the organization of nuclear paraspeckles. Second, AUF1 does not change the abundance of many target RNAs, but ribosome profiling reveals that AUF1 promotes the translation of numerous mRNAs in this group. Third, AUF1 unexpectedly enhances the steady-state levels of several target mRNAs encoding DNA-maintenance proteins. Through its actions on target RNAs, AUF1 preserves genomic integrity, in agreement with the AUF1-elicited prevention of premature cellular senescence.
PMC PMC4291169
PMID 25366541
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1042900 PRJNA230610 Homo sapiens Ribo-Seq
SRR1042901 PRJNA230610 Homo sapiens Ribo-Seq
SRR1042902 PRJNA230610 Homo sapiens Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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