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| Status |
Public on Jul 31, 2011 |
| Title |
Small RNA profiles from human genic regions suggest biogenic mechanisms and identify new Argonaute-associated species |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Efforts to catalogue eukaryotic transcripts have uncovered a set of species derived from the termini and exon/intron boundaries of protein-coding loci. The biogenesis pathways of these small RNAs (sRNAs) are largely unknown, but a mechanism depending on backtracking of RNA polymerase II (RNAPII) has been suggested. Moreover, the functional relevance, if any, of these sRNAs remains elusive. By sequencing 12-100nt transcripts from cells depleted of major RNA degradation enzymes as well as RNAs associated with the effector-proteins Argonaute (AGO) 1/2, we provide mechanistic models for sRNA production and utilization. We suggest that neither splice site associated (SSa)- nor transcription start site associated (TSSa)-RNAs arise from RNAPII backtracking. Instead SSa-RNAs are largely degradation products of mRNA splicing intermediates, while TSSa-RNAs likely derive from nascent RNA protected by stalled RNAPII against nucleolysis. We also reveal new AGO1/2-associated RNAs, including such derived from 3'ends of introns (5'tailed miRtrons) and from mRNA 3'UTRs. Interestingly, both appear to draw from non-canonical microRNA (miRNA) biogenesis pathways.
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| Overall design |
10 samples all from HeLa in three size ranges: 12-20, 18-30 and 30-100. 1 from 12-20: nuclear; 6 from 18-30: WT, nuclear, RRP40 knockdown, Ago1&2 IP, RRP40 knockdown and Ago1&2 IP, XRN1&2 knockdown; 3 from 30-100: WT, of RRP40 knockdown, XRN1&2 knockdown.
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| Contributor(s) |
Valen E, Jensen TH |
| Citation(s) |
21822281 |
| Submission date |
May 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Eivind Valen |
| E-mail(s) |
eivind.valen@gmail.com
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| Organization name |
University of Copenhagen
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| Department |
Dep. of Biology
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| Lab |
Sandelin
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| Street address |
Ole Maaloes Vej 4
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| City |
Copenhagen E |
| State/province |
Select |
| ZIP/Postal code |
2100 |
| Country |
Denmark |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (10)
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| Relations |
| SRA |
SRP006788 |
| BioProject |
PRJNA140385 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE29116_RAW.tar |
273.6 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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