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Series GSE41785 Query DataSets for GSE41785
Status Public on Jun 12, 2013
Title Global analysis of Upf1 in mESCs reveals expanded scope of nonsense-mediated mRNA decay
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Nonsense-mediated mRNA decay (NMD) is a conserved RNA surveillance pathway that is an important modulator of disease pathology and is required for embryonic development. Despite significant research effort, the rules that govern NMD remain incompletely understood. Here we used a combined¬¨ approach, integrating RNA-Seq, ribosome footprinting, and CLIP-Seq analysis of the essential NMD factor Upf1, to provide a more complete picture of the role of NMD in modulating gene expression in murine embryonic stem cells (mESCs). We show that presence of an exon-exon junction ‚Č•50 nucleotides (nt) downstream of a termination codon (dEJ) contributes to NMD independently of 3' UTR length, but has stronger effects in genes with shorter 3' UTRs. We also map translated upstream open reading frames (uORFs) in mESCs and show that they are associated with NMD regulation, especially of genes encoding transcription factors, and we find that lowly translated mRNAs can escape NMD. Finally, we identify over 200 direct binding targets of Upf1 and describe a pathway of Upf1-dependent gene regulation reliant on Upf1 binding to the 3' UTR and independent of presence of a dEJ. Together, these analyses characterize known and discover novel determinants of NMD and establish a broader role in mESC gene regulation for Upf1.
Overall design mRNA-Seq analysis of wildtype (2 samples), translationally inhibited (by cycloheximide treatment, 2 samples), control-depleted (2 samples), and Upf1-depleted (4 samples) mouse embryonic stem cells (mESCs); CLIP-Seq analysis of Upf1 (5 samples, and 5 samples of IgG control CLIP-Seq); Ribosome footprint profiling of wildtype (1 sample), control-depleted (1 sample), and Upf1-depleted (1 sample) mESCs
Contributor(s) Hurt JA, Robertson AD, Burge CB
Citation(s) 23766421
Submission date Oct 23, 2012
Last update date May 15, 2019
Contact name Jessica Hurt
Organization name Massachusetts Institute of Technology
Department Biology
Lab Christopher Burge
Street address 77 Massachusetts Avenue
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (23)
GSM1024291 GFP_2.4_mRNASeq
GSM1024292 GFP_2.6_mRNASeq
GSM1024293 Upf1-1_4.4_mRNASeq
BioProject PRJNA178171
SRA SRP016625

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE41785_GFP_merge_genes.fpkm_tracking.gz 741.5 Kb (ftp)(http) FPKM_TRACKING
GSE41785_GFP_merge_isoforms.fpkm_tracking.gz 3.0 Mb (ftp)(http) FPKM_TRACKING
GSE41785_RAW.tar 9.4 Mb (http)(custom) TAR (of BED, FPKM_TRACKING)
GSE41785_Upf1.1_merge_genes.fpkm_tracking.gz 737.1 Kb (ftp)(http) FPKM_TRACKING
GSE41785_Upf1.1_merge_isoforms.fpkm_tracking.gz 2.9 Mb (ftp)(http) FPKM_TRACKING
GSE41785_Upf1.2_merge_genes.fpkm_tracking.gz 727.1 Kb (ftp)(http) FPKM_TRACKING
GSE41785_Upf1.2_merge_isoforms.fpkm_tracking.gz 2.9 Mb (ftp)(http) FPKM_TRACKING
GSE41785_v6.5_CHX_merge_genes.fpkm_tracking.gz 740.6 Kb (ftp)(http) FPKM_TRACKING
GSE41785_v6.5_CHX_merge_isoforms.fpkm_tracking.gz 3.0 Mb (ftp)(http) FPKM_TRACKING
GSE41785_v6.5_NoCHX_merge_genes.fpkm_tracking.gz 739.7 Kb (ftp)(http) FPKM_TRACKING
GSE41785_v6.5_NoCHX_merge_isoforms.fpkm_tracking.gz 3.0 Mb (ftp)(http) FPKM_TRACKING
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Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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