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| Status |
Public on Nov 20, 2017 |
| Title |
Post-transcriptional 3’UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Here, using genome wide analysis, we demonstrate that canonical mRNA is processed post-transcriptionally through an alternative cleavage and polyadenylation mechanism. As a result of this process, the downstream cleavage fragment of the 3′UTR remains uncapped and stable
This finding indicates that different parts of gene mRNA are separate and independent, by re-annotating the human transcriptome using this model, we provide a new overview of the function and impact of microRNA (miRNA)
Our results shed new light on the mammalian transcriptome and show that what were considered as 3′UTRs are in fact autonomous RNA fragments.
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| Overall design |
Examination of mRNA levels and cleavage across transcripts in U2OS and 293 cell types (3 replicates each)
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| Contributor(s) |
Malka Y, Steiman-Shimony A, Rosenthal E, Argaman L, Cohen-Daniel L, Arbib E, Margalit H, Kaplan T, Berger M |
| Citation(s) |
29229900 |
| Submission date |
Jul 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tommy Kaplan |
| E-mail(s) |
tommy@cs.huji.ac.il
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| Organization name |
Hebrew University
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| Department |
School of Computer Science and Engineering
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| Street address |
Givat Ram Campus
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| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (36)
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| GSM2226716 |
mRNA after TEX U2OS cell rep 1 |
| GSM2226717 |
mRNA after TEX U2OS cell rep 2 |
| GSM2226718 |
mRNA after TEX U2OS cell rep 3 |
| GSM2226719 |
mRNA after 5prime-pulldown U2OS cell rep 1 |
| GSM2226720 |
mRNA after 5prime-pulldown U2OS cell rep 2 |
| GSM2226721 |
mRNA after 5prime-pulldown U2OS cell rep 3 |
| GSM2226722 |
mRNA after 3prime-pulldown U2OS cell rep 1 |
| GSM2226723 |
mRNA after 3prime-pulldown U2OS cell rep 2 |
| GSM2226724 |
mRNA after 3prime-pulldown U2OS cell rep 3 |
| GSM2226725 |
mRNA 293 cell rep 1 |
| GSM2226726 |
mRNA 293 cell rep 2 |
| GSM2226727 |
mRNA 293 cell rep 3 |
| GSM2226728 |
mRNA with let7 MIR after TEX 293 cell rep 1 |
| GSM2226729 |
mRNA with let7 MIR after TEX 293 cell rep 2 |
| GSM2226730 |
mRNA with let7 MIR after TEX 293 cell rep 3 |
| GSM2226731 |
mRNA with mir92a MIR after TEX 293 cell rep 1 |
| GSM2226732 |
mRNA with mir92a MIR after TEX 293 cell rep 2 |
| GSM2226733 |
mRNA with mir92a MIR after TEX 293 cell rep 3 |
| GSM2226734 |
mRNA with TEX in 293 cells, rep 1 |
| GSM2226735 |
mRNA with TEX in 293 cells, rep 2 |
| GSM2226736 |
mRNA with TEX in 293 cells, rep 3 |
| GSM2226737 |
3'-seq, Control, rep 1 |
| GSM2226738 |
3'-seq, Control, rep 2 |
| GSM2226739 |
3'-seq, Control, rep 3 |
| GSM2226740 |
3'-seq, Alpha-amanitin, rep 1 |
| GSM2226741 |
3'-seq, Alpha-amanitin, rep 2 |
| GSM2226742 |
3'-seq, Alpha-amanitin, rep 3 |
| GSM2226743 |
3'-seq, TEX, rep 1 |
| GSM2226744 |
3'-seq, TEX, rep 2 |
| GSM2226745 |
3'-seq, TEX, rep 3 |
| GSM2226746 |
3'-seq, alpha-amanitin +TEX, rep 1 |
| GSM2226747 |
3'-seq, alpha-amanitin +TEX, rep 2 |
| GSM2226748 |
3'-seq, alpha-amanitin +TEX, rep 3 |
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| Relations |
| BioProject |
PRJNA327927 |
| SRA |
SRP077969 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84068_RAW.tar |
3.8 Gb |
(http)(custom) |
TAR (of BIGWIG) |
| GSE84068_Supp_Table1_U2OS_TEX_fit_hmm.tsv.gz |
3.4 Mb |
(ftp)(http) |
TSV |
| GSE84068_Supp_Table2_U2OS_5prime_fit_hmm.tsv.gz |
3.2 Mb |
(ftp)(http) |
TSV |
| GSE84068_Supp_Table3_U2OS_3prime_fit_hmm.tsv.gz |
3.3 Mb |
(ftp)(http) |
TSV |
| GSE84068_Supp_Table4_293_TEX_fit_hmm.tsv.gz |
3.5 Mb |
(ftp)(http) |
TSV |
| GSE84068_Supp_Table5_3end_RNA-seq_peaks_prox+dist.tsv.gz |
126.0 Kb |
(ftp)(http) |
TSV |
| GSE84068_Supp_Table6_293_Mir92_fit_hmm.tsv.gz |
3.2 Mb |
(ftp)(http) |
TSV |
| GSE84068_Supp_Table7_293_Let7_fit_hmm.tsv.gz |
3.0 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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