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GEO help: Mouse over screen elements for information. |
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Status |
Public on Mar 27, 2024 |
Title |
Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops |
Organism |
Mus musculus |
Experiment type |
Other Expression profiling by high throughput sequencing
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Summary |
The RNase III enzyme Drosha has a central role in microRNA (miRNA) biogenesis, where it required to release the stem-loop intermediate from primary (pri)-miRNA transcripts. However, it can also cleave stem-loops embedded within messenger (m)RNAs. This destabilizes the mRNA causing target gene repression and has been found to occur primarily in stem cells. While pri-miRNA stem-loops have been extensively studied, such non-canonical substrates of Drosha has yet to characterized in detail. In this study, we employed high-throughput sequencing to capture all polyA-tailed RNAs that are cleaved by Drosha in mouse embryonic stem cells (ESCs). We then compared the features of non-canonical versus miRNA stem-loop substrates. First, these mRNA substrates are less efficiently processed than miRNA stem-loops. Sequence and structural analyses revealed that these substrates are also less stable and more likely to fold into alternative structures than miRNA stem-loops. Moreover, they lack the sequence and structural motifs found in miRNAs stem-loops that are required for precise cleavage. Notably, we discovered a non-canonical Drosha substrate that is cleaved in an inverse manner, which is a process that is normally inhibited by features in miRNA stem-loops. Our study thus provides valuable insights into the recognition of non-canonical targets by Drosha.
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Overall design |
Investigating noncanonical Drosha cleavage targets and the impact of the cleavage in mouse ESCs.
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Contributor(s) |
Gu K, Mok L, Wakefield MJ, Chong MM |
Citation(s) |
38509178 |
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Submission date |
Mar 27, 2023 |
Last update date |
Mar 27, 2024 |
Contact name |
Mark Chong |
E-mail(s) |
mchong@svi.edu.au
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Phone |
61-3-92313444
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Organization name |
St Vincent's Institute of Medical Research
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Street address |
9 Princes Street
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City |
Fitzroy |
State/province |
Victoria |
ZIP/Postal code |
3065 |
Country |
Australia |
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Platforms (2) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (14)
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GSM7118503 |
Droshafl/fl_CreER_mESC, 4OHT, rep2 |
GSM7118504 |
Dicerfl/fl_mESC, GFP, rep1 |
GSM7118505 |
Dicerfl/fl_mESC, GFP, rep2 |
GSM7118506 |
Dicerfl/fl_mESC, GFP-Cre, rep1 |
GSM7118507 |
Dicerfl/fl_mESC, GFP-Cre, rep2 |
GSM8067226 |
RNAseq, Droshafl/fl_CreER_mESC, notreat, rep1 |
GSM8067227 |
RNAseq, Droshafl/fl_CreER_mESC, notreat, rep2 |
GSM8067228 |
RNAseq, Droshafl/fl_CreER_mESC, notreat, rep3 |
GSM8067229 |
RNAseq, Droshafl/fl_CreER_mESC, 4OHT, rep1 |
GSM8067230 |
RNAseq, Droshafl/fl_CreER_mESC, 4OHT, rep2 |
GSM8067231 |
RNAseq, Droshafl/fl_CreER_mESC, 4OHT, rep3 |
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Relations |
BioProject |
PRJNA949217 |
Supplementary file |
Size |
Download |
File type/resource |
GSE228299_degseq_dicer_pileup_edgeR.txt.gz |
218.6 Kb |
(ftp)(http) |
TXT |
GSE228299_degseq_drosha_pileup_edgeR.txt.gz |
190.6 Kb |
(ftp)(http) |
TXT |
GSE228299_edgeR_drosha_de_withName.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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