Project description:Purpose: We performed RNA-Immunoprecipitation in Tandem (RIPiT) experiments against human Staufen1 (Stau1) to identify its precise RNA binding sites in a transcriptome-wide manner. To monitor the consequences of Stau1 binding in terms of target mRNA levels and ribosome occupancy, we modified the levels of endogenous Stau1 in cells by siRNA or overexpression and performed RNA-sequencing and ribosome-footprinting experiments. Staufen1 (Stau1) is a double-stranded RNA (dsRNA) binding protein implicated in mRNA transport, regulation of translation, mRNA decay and stress granule homeostasis. Here we combined RNA-Immunoprecipitation in Tandem (RIPiT) with RNase footprinting, formaldehyde crosslinking, sonication-mediated RNA fragmentation and deep sequencing to map Staufen1 binding sites transcriptome-wide. We find that Stau1 binds complex secondary structures containing multiple short helices, many of which are formed by inverted Alu elements in annotated 3'UTRs or in "strongly distal" 3'UTRs extending far beyond the canonical polyadenylation signal. Stau1 also interacts with both actively translating ribosomes and with mRNA coding sequences (CDS) and 3'UTRs in proportion to their GC-content and internal secondary structure-forming propensity. On mRNAs with high CDS GC-content, higher Stau1 levels lead to greater ribosome densities, suggesting a general role for Stau1 in modulating the ability of ribosomes to elongate through secondary structures located in CDS regions.

2013-11-25 | GSE52447 | GEO

Transcriptome-wide mapping of human Staufen1 binding sites

2013-11-25 | E-GEOD-52447 | biostudies-arrayexpress

Genome-wide mapping sites of Ulp2 chromatin binding

Project description:Genome-wide mapping sites of Ulp2 chromatin binding

| PRJNA540826 | ENA

Genome-wide binding sites for Arabidopsis ATH1

Project description:The Arabidopsis thaliana ATH1 encodes a BEL1-like TALE homeodomain (BLH) transcription factor that controls the development of shoot organ boundaries. As part of a screen for genes that mediate the function of ATH1 in shoot development, we performed ChIP-seq to identify genome-wide ATH1 binding sites in developing seedlings.

2021-03-31 | GSE157332 | GEO

Genome-wide mapping sites of Ulp2 chromatin binding

Project description:To map Ulp2 binding sites on a genome-wide scale, we carried out ChIP experiment combined with sequencing assay

2019-07-07 | GSE130623 | GEO

Genome-wide mapping of OsHOX24-binding sites in rice

Project description:Genome-wide mapping of OsHOX24-binding sites in rice

| PRJNA603582 | ENA

iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

Project description:iCLIP transcriptome-wide mapping of UNR (CSDE1) binding sites

| PRJEB10303 | ENA