|
| Status |
Public on Oct 02, 2014 |
| Title |
Global identification of target recognition and cleavage by the Microprocessor in human ESCs. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
The Microprocessor plays an essential role in canonical miRNA biogenesis by facilitating cleavage of stem-loop structures in primary transcripts to yield pre-miRNAs. Although miRNA biogenesis has been extensively studied through biochemical and molecular genetic approaches, it has yet to be addressed to what extent the current miRNA biogenesis models hold true in intact cells. To address the issues of in vivo recognition and cleavage by the Microprocessor, we investigate RNAs that are associated with DGCR8 and Drosha by using immunoprecipitation coupled with next-generation sequencing. Here, we present global protein-RNA interactions with unprecedented sensitivity and specificity. Our data indicate that precursors of canonical miRNAs and miRNA-like hairpins are the major substrates of the Microprocessor. As a result of specific enrichment of nascent cleavage products, we are able to pinpoint the Microprocessor-mediated cleavage sites per se at single-nucleotide resolution. Unexpectedly, a 2-nt 3’ overhang invariably exists at the ends of cleaved bases instead of nascent pre-miRNAs. Besides canonical miRNA precursors, we find that two novel miRNA-like structures embedded in mRNAs are cleaved to yield pre-miRNA-like hairpins, uncoupled from miRNA maturation. Our data provide a framework for in vivo Microprocessor-mediated cleavage and a foundation for experimental and computational studies on miRNA biogenesis in living cells.
|
| |
|
| Overall design |
CLIP-seq for DGCR8 and Drosha, RIP-seq for DGCR8, sequencing of AGO2-assocated miRNA
|
| |
|
| Contributor(s) |
Kwon Y |
| Citation(s) |
25326327 |
| |
| Submission date |
Oct 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Young-Soo Kwon |
| E-mail(s) |
yngskwon@me.com
|
| Phone |
82-2-3408-3841
|
| Organization name |
Sejong University
|
| Department |
Department of Bioscience and Biotechnology
|
| Lab |
Genomics
|
| Street address |
Nungdongro 209, Gwangjingu
|
| City |
Seoul |
| ZIP/Postal code |
05006 |
| Country |
South Korea |
| |
|
| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
|
| Samples (22)
|
| GSM1517843 |
DGCR8-CLIP-seq replicate 1 (High RNase 1 treated) |
| GSM1517844 |
DGCR8-CLIP-seq replicate 2 (Low RNase 1 treated) |
| GSM1517845 |
DGCR8-CLIP-seq replicate 3 (High RNase 1 treated) |
| GSM1517846 |
DGCR8-CLIP-seq replicate 4 (Low RNase 1 treated) |
| GSM1517847 |
DGCR8-CLIP-seq replicate 5 (High RNase 1 treated) |
| GSM1517848 |
DGCR8-CLIP-seq replicate 6 (Low RNase 1 treated) |
| GSM1517849 |
DGCR8-CLIP-seq replicate7 (High RNase 1 treated) |
| GSM1517850 |
DGCR8-CLIP-seq replicate 8 (Low RNase 1 treated) |
| GSM1517851 |
DGCR8-CLIP-seq replicate 9 (Low RNase 1 treated) |
| GSM1517852 |
DGCR8-CLIP-seq replicate 10 (Low RNase 1 treated) |
| GSM1517853 |
DGCR8-CLIP-seq replicate11 (No RNase 1 treated) |
| GSM1517854 |
DGCR8-CLIP-seq replicate 12 (Low RNase 1 treated) |
| GSM1517855 |
DGCR8-CLIP-seq negative control (Low RNase 1 treated) |
| GSM1517856 |
Drosha-CLIP-seq replicate 1 |
| GSM1517857 |
Drosha-CLIP-seq replicate 2 |
| GSM1517858 |
Drosha-CLIP-seq replicate 3 |
| GSM1517859 |
Drosha-CLIP-seq replicate 4 |
| GSM1517860 |
DGCR8-RIP-seq |
| GSM1517861 |
AGO2-associated small RNA seq replicate 1 |
| GSM1517862 |
AGO2-associated small RNA seq replicate 2 |
| GSM1517863 |
AGO2-associated small RNA seq IgG control replicate 1 |
| GSM1517864 |
AGO2-associated small RNA seq IgG control replicate 2 |
|
| Relations |
| BioProject |
PRJNA262853 |
| SRA |
SRP048586 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61979_DGCR8_CLIP_long_cov_neg_IgG_hg19.bedGraph.gz |
20.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_CLIP_long_cov_neg_w_RNase_hg19.bedGraph.gz |
150.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_CLIP_long_cov_neg_wo_RNase_hg19.bedGraph.gz |
223.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_CLIP_long_cov_pos_IgG_hg19.bedGraph.gz |
19.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_CLIP_long_cov_pos_w_RNase_hg19.bedGraph.gz |
149.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_CLIP_long_cov_pos_wo_RNase_hg19.bedGraph.gz |
215.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_RIP_cov_neg_hg19.bedGraph.gz |
1.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_RIP_cov_pos_hg19.bedGraph.gz |
1.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_cov_neg_hg19.bedGraph.gz |
2.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_DGCR8_cov_pos_hg19.bedGraph.gz |
2.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_Drosha_CLIP_cov_neg_hg19.bedGraph.gz |
258.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_Drosha_CLIP_cov_pos_hg19.bedGraph.gz |
288.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE61979_RAW.tar |
50.0 Kb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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