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Series GSE134020 Query DataSets for GSE134020
Status Public on Jan 29, 2020
Title Mammalian RNA decay pathways are highly specialized and widely linked to translation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary RNA decay is crucial for RNA turnover and surveillance, and misregulated in many diseases. This complex system is challenging to study, particularly in mammals, where it remains unclear whether decay pathways perform specialized or redundant roles. Cytoplasmic pathways, and links to translation, are particularly enigmatic. By directly profiling targets of decay factors (XRN1, SKIV2L and MTR4) and normal/aberrant translation events in mouse embryonic stem cells, we uncovered extensive specialization between decay pathways and crosstalk with translation. XRN1 (5’-3’) mediated cytoplasmic bulk mRNA turnover whereas SKIV2L (3’-5’) was universally recruited by ribosomes, tackling aberrant translation and sometimes modulating mRNA abundance. Further exploring translation surveillance, we identified AVEN and FOCAD as SKIV2L interactors. AVEN prevented ribosome stalls at structured regions, which otherwise required SKIV2L for clearance. This pathway was crucial for histone translation, uORF regulation and counteracting spurious non-coding RNA translation. In summary, we identified key targets, components and functions of mammalian RNA decay pathways, and uncovered extensive coupling to translation.
Overall design mESCs with endogenously 3xFLAG-Avi-tagged decay factors (either MTR4, SKIV2L, XRN1 or AVEN) were used for crosslinking and analysis of cDNAs (CRAC), to identify transcriptome-wide direct RNA binding sites. Various WT or knockout cell lines were also profiled by RNA-seq, and some CRAC experiments were repeated in knockout backgrounds.
Contributor(s) Tuck A, Rankova A, Arpat AB
Citation(s) 32048998
Submission date Jul 09, 2019
Last update date Mar 30, 2020
Contact name Alex Charles Tuck
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (183)
GSM3933414 CRAC_Aven_CHX30
GSM3933415 CRAC_Aven_1
GSM3933416 CRAC_Aven_2
BioProject PRJNA553494
SRA SRP213860

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE134020_CRAC_Aven_merged_fw.bigWig 1.5 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Aven_merged_rev.bigWig 1.5 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Mtr4_merged_fw.bigWig 12.5 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Mtr4_merged_rev.bigWig 12.3 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Rps10_merged_fw.bigWig 3.5 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Rps10_merged_rev.bigWig 3.4 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_Aven_KO_4F_merged_fw.bigWig 2.4 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_Aven_KO_4F_merged_rev.bigWig 2.3 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_Aven_KO_6G_merged_fw.bigWig 1.8 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_Aven_KO_6G_merged_rev.bigWig 1.8 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_CHX30_merged_fw.bigWig 607.3 Kb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_CHX30_merged_rev.bigWig 612.1 Kb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_CHX5_merged_fw.bigWig 485.2 Kb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_CHX5_merged_rev.bigWig 489.5 Kb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_Focad_KO_merged_fw.bigWig 1.2 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_Focad_KO_merged_rev.bigWig 1.2 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_HAR30_merged_fw.bigWig 398.6 Kb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_HAR30_merged_rev.bigWig 399.5 Kb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_HAR5_merged_fw.bigWig 386.6 Kb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_HAR5_merged_rev.bigWig 383.6 Kb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_merged_fw.bigWig 2.0 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Skiv2l_merged_rev.bigWig 2.0 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Xrn1_merged_fw.bigWig 1.9 Mb (ftp)(http) BIGWIG
GSE134020_CRAC_Xrn1_merged_rev.bigWig 1.9 Mb (ftp)(http) BIGWIG
GSE134020_Counts_for_half_life_analysis.txt.gz 1.7 Mb (ftp)(http) TXT
GSE134020_Di_selective_AVEN_KO_rep1.wig.gz 647.9 Kb (ftp)(http) WIG
GSE134020_Di_selective_AVEN_KO_rep1_2.wig.gz 1.2 Mb (ftp)(http) WIG
GSE134020_Di_selective_AVEN_KO_rep2.wig.gz 540.8 Kb (ftp)(http) WIG
GSE134020_Di_selective_WT_rep1.wig.gz 589.3 Kb (ftp)(http) WIG
GSE134020_Di_selective_WT_rep1_2.wig.gz 1.7 Mb (ftp)(http) WIG
GSE134020_Di_selective_WT_rep2.wig.gz 1.0 Mb (ftp)(http) WIG
GSE134020_Mono_default_AVEN_KO_rep1.wig.gz 6.3 Mb (ftp)(http) WIG
GSE134020_Mono_default_AVEN_KO_rep1_2.wig.gz 13.2 Mb (ftp)(http) WIG
GSE134020_Mono_default_AVEN_KO_rep2.wig.gz 6.9 Mb (ftp)(http) WIG
GSE134020_Mono_default_WT_rep1.wig.gz 7.2 Mb (ftp)(http) WIG
GSE134020_Mono_default_WT_rep1_2.wig.gz 13.3 Mb (ftp)(http) WIG
GSE134020_Mono_default_WT_rep2.wig.gz 6.5 Mb (ftp)(http) WIG
GSE134020_Supplementary_table_3.txt.gz 2.0 Mb (ftp)(http) TXT
GSE134020_half_lives_231019.txt.gz 1.7 Mb (ftp)(http) TXT
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