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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 01, 2018 |
| Title |
The abundantly expressed microRNA locus miR-144/451 regulates only about 100 target mRNAs during erythroid development [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
MicroRNAs inhibit gene expression by recruiting the RNA-induced silencing complex (RISC) to mRNAs in a process termed RNA interference (RNAi). While it is generally accepted that RNAi modulates gene expression pervasively, the number of mRNAs bound and repressed by miRNAs in vivo in individual cell types remains unknown, with estimates ranging from a few hundred genes to many thousands. We examined microRNA activities in primary cells by combining genetic loss of function with RNA-sequencing, quantitative proteomics and High-Throughput Sequencing of RNA isolated by Crosslinking Immunoprecipitation (HITS-CLIP), focusing on miR-144/451, the most highly expressed microRNA locus during red blood cell (RBC) formation. We show that Argonaute (Ago) protein binds over one thousand different mRNAs in a miR-144/451-dependent manner, accounting for one third of all Ago-bound mRNAs. However, only about 100 mRNAs are stabilized in RBC precursors after ablation of the miR-144/451 locus. Thus, Ago-miRNA complexes destabilize only a small subset of bound mRNAs, probably no more than a few hundred in erythroblasts under physiological conditions. Our integrated approach identified more than 50 new miR-144/451 target mRNAs, including Cox10, which facilitates assembly of the mitochondrial cytochrome c oxidase (COX) electron transport complex. Loss of miR-144/451 resulted in increased Cox10 expression, accumulation of the COX complex, and increased mitochondrial membrane potential with no change in mitochondrial mass. Thus, miR-144/451 represses mitochondrial respiration during erythropoiesis by inhibiting Cox10.
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| Overall design |
HITS-CLIP analysis of 3 WT mice fetal livers vs 3 miR-144/451 KO mice fetal livers
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| Contributor(s) |
Paralkar VR, Palmer LE, Xu P, Lechauve C, Zhao G, Yao Y, Luan J, Vourekas A, Scheutz JD, Mourelatos Z, Wu G, Weiss MJ |
| Citation(s) |
30971389 |
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| Submission date |
Sep 29, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Lance E Palmer |
| E-mail(s) |
lance.palmer@stjude.org
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| Phone |
9015951007
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Computational Biology
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| Street address |
262 Danny Thomas Place
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38107 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE104455 |
The abundantly expressed microRNA locus miR-144/451 regulates only about 100 target mRNAs during erythroid development |
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| Relations |
| BioProject |
PRJNA412651 |
| SRA |
SRP119158 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104447_ExonIntronCounts.txt.gz |
350.0 Kb |
(ftp)(http) |
TXT |
| GSE104447_RAW.tar |
1009.8 Mb |
(http)(custom) |
TAR (of BW) |
| GSE104447_RNASeqCountsMinusHBMT.NCBIM37.txt.gz |
317.9 Kb |
(ftp)(http) |
TXT |
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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