E-GEOD-6679 - siRNA of human HeLa cells reveals Staufen1 regulates a variety of mammalian transcripts

Status
Released on 15 June 2008, last updated on 27 March 2012
Organism
Homo sapiens
Samples (6)
Array (1)
Protocols (8)
Description
It is currently unknown how extensively the double-stranded RNA binding protein Staufen (Stau)1 is utilized by mammalian cells to regulate gene expression. To date, Stau1 binding to the 3’ untranslated region (3’UTR) of ARF1 mRNA has been shown to target ARF1 mRNA for Stau1-mediated mRNA decay (SMD). ARF1 SMD depends on translation and recruitment of the nonsense-mediated mRNA decay factor Upf1 to the ARF1 3’UTR by Stau1. Here, we use microarray analyses to examine changes in the abundance of cellular mRNAs that occur when Stau1 is depleted. Results indicate that 1.1% and 1.0% of the 11,569 HeLa-cell transcripts that were analyzed are, respectively, upregulated and downregulated at least two-fold in three independently performed experiments. Additionally, we localize the Stau1 binding site to the 3’UTR of four mRNAs that we define as natural SMD targets. Together, these and substantiating results suggest that Stau1 influences the expression of a wide variety of physiologic transcripts and metabolic pathways. Experiment Overall Design: We report the results of three independently performed microarray analyses that examined changes in the abundance of transcripts from HeLa-cell genes upon Stau1 depletion. HeLa cells were transiently transfected with either a nonspecific Control small interfering (si)RNA or Stau1 siRNA. Stau1 siRNA reduced the level of cellular Stau1 to as little as 4% of normal, where normal is defined as the level in the presence of Control siRNA (data not shown). RNA from three independently performed transfections was separately hybridized to microarrays.
Experiment types
RNAi profiling by array, unknown experiment type
Contact
Citation
Staufen1 regulates diverse classes of mammalian transcripts. Yoon Ki Kim, Luc Furic, Marc Parisien, François Major, Luc DesGroseillers, Lynne E Maquat.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-6679.idf.txt
Sample and data relationshipE-GEOD-6679.sdrf.txt
Raw data (1)E-GEOD-6679.raw.1.zip
Processed data (1)E-GEOD-6679.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-6679.eSet.r
Links