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Series GSE228299 Query DataSets for GSE228299
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
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.
Overall design Investigating noncanonical Drosha cleavage targets and the impact of the cleavage in mouse ESCs.
Contributor(s) Gu K, Mok L, Wakefield MJ, Chong MM
Citation(s) 38509178
Submission date Mar 27, 2023
Last update date Mar 27, 2024
Contact name Mark Chong
Phone 61-3-92313444
Organization name St Vincent's Institute of Medical Research
Street address 9 Princes Street
City Fitzroy
State/province Victoria
ZIP/Postal code 3065
Country Australia
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (14)
GSM7118500 Droshafl/fl_CreER_mESC, notreat, rep1
GSM7118501 Droshafl/fl_CreER_mESC, notreat, rep2
GSM7118502 Droshafl/fl_CreER_mESC, 4OHT, rep1
BioProject PRJNA949217

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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
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Raw data are available in SRA
Processed data are available on Series record

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