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| Status |
Public on Jan 09, 2020 |
| Title |
Translation is required for miRNA-dependent decay of endogenous transcripts. |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Posttranscriptional repression by microRNA (miRNA) occurs through transcript destabilization or translation inhibition. Whereas RNA degradation explains most miRNA-dependent repression, transcript decay occurs co-translationally, raising questions regarding the requirement of target translation to miRNA-dependent transcript destabilization. To assess the contribution of translation to miRNA-mediated RNA destabilization, we decoupled these two molecular processes by dissecting the impact of miRNA loss of function on cytosolic long noncoding RNAs (lncRNAs). We show, that despite interacting with miRNA loaded RNA-induced silencing complex (miRISC), the steady state abundance and degradation rates of these endogenously expressed non-translated transcripts are minimally impacted by miRNA loss. To validate the requirement of translation to miRNA-dependent decay, we fused a miRISC bound lncRNA, whose levels are unaffected by miRNAs, to the 3’end of a protein-coding gene reporter and shown that this results in its miRNA-dependent transcript destabilization. Furthermore, analysis of the few lncRNAs whose levels are regulated by miRNAs revealed these tend to associate with translating ribosomes and are likely misannotated micropeptides, further substantiating the necessity of target translation to miRNA-dependent transcript decay. Our analyses revealed the strict requirement of translation for miRNA-dependent transcript destabilization and demonstrates that the levels of coding and noncoding transcripts are differently affected by miRNAs.
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| Overall design |
Conditional loss of dicer function was induced in mESCs and small RNA sequencing as well as mRNA metabolic labelling was performed to assess changes in transcript degradation and miRNA loss, between wild-type and Dicer depleted mESCs.
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| Contributor(s) |
Biasini A, de Pretis S, Tan JY, Abdulkarim B, Wischnewski H, Dreos R, Pelizzola M, Ciaudo C, Marques AC |
| Citation(s) |
33300180, 35459101 |
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| Submission date |
Jan 08, 2020 |
| Last update date |
May 05, 2022 |
| Contact name |
Ana Marques |
| E-mail(s) |
anaclaudia.marques@unil.ch
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| Organization name |
University of Lausanne
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| Department |
Department of Computational Biology
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| Street address |
Rue du Bugnon 27
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| City |
Lausanne |
| ZIP/Postal code |
1005 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (31)
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| GSM4255949 |
mESCs, smallRNA_KO_d4_1 |
| GSM4255950 |
mESCs, smallRNA_KO_d4_2 |
| GSM4255951 |
mESCs, smallRNA_KO_d4_3 |
| GSM4255952 |
mESCs, smallRNA_KO_d8_1 |
| GSM4255953 |
mESCs, smallRNA_KO_d8_2 |
| GSM4255954 |
mESCs, smallRNA_KO_d8_3 |
| GSM4255955 |
mESCs, smallRNA_KO_d10_1 |
| GSM4255956 |
mESCs, smallRNA_KO_d10_2 |
| GSM4255957 |
mESCs, smallRNA_KO_d10_3 |
| GSM4255958 |
mESCs, smallRNA_KO_d12_1 |
| GSM4255959 |
mESCs, smallRNA_KO_d12_2 |
| GSM4255960 |
mESCs, smallRNA_KO_d12_3 |
| GSM4255961 |
mESCs, BR1_WT_10min_lab |
| GSM4255962 |
mESCs, BR1_WT_15min_lab |
| GSM4255963 |
mESCs, BR1_KO_10min_lab |
| GSM4255964 |
mESCs, BR1_KO_15min_lab |
| GSM4255965 |
mESCs, BR2_WT_10min_lab |
| GSM4255966 |
mESCs, BR2_WT_15min_lab |
| GSM4255967 |
mESCs, BR2_KO_10min_lab |
| GSM4255968 |
mESCs, BR2_KO_15min_lab |
| GSM4255969 |
mESCs, BR1_WT_10min_tot |
| GSM4255970 |
mESCs, BR1_WT_15min_tot |
| GSM4255971 |
mESCs, BR1_KO_10min_tot |
| GSM4255972 |
mESCs, BR1_KO_15min_tot |
| GSM4255973 |
mESCs, BR2_WT_10min_tot |
| GSM4255974 |
mESCs, BR2_WT_15min_tot |
| GSM4255975 |
mESCs, BR2_KO_10min_tot |
| GSM4255976 |
mESCs, BR2_KO_15min_tot |
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| Relations |
| BioProject |
PRJNA599577 |
| SRA |
SRP240275 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE143277_4sU_TPM_table.txt.gz |
6.7 Mb |
(ftp)(http) |
TXT |
| GSE143277_smallRNAseq_counts_table.txt.gz |
21.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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