|
| Status |
Public on May 06, 2020 |
| Title |
Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms |
| Organisms |
Homo sapiens; synthetic construct |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Eukaryotic genes often generate a variety of RNA isoforms that can lead to functionally distinct protein variants. The synthesis and stability of RNA isoforms is however poorly characterized. The reason for this is that current methods to quantify RNA metabolism use short-read sequencing that cannot detect RNA isoforms. Here we present nanopore sequencing-based Isoform Dynamics (nano-ID), a method that detects newly synthesized RNA isoforms and monitors isoform metabolism. nano-ID combines metabolic RNA labeling, long-read nanopore sequencing of native RNA molecules and machine learning. nano-ID derived RNA stability estimates enable a distinctive evaluation of stability determining factors such as sequence, poly(A)-tail length, RNA secondary structure, translation efficiency and RNA binding proteins. Application of nano-ID to the heat shock response in human cells reveals that many RNA isoforms change their stability. nano-ID also shows that the metabolism of individual RNA isoforms differs strongly from that estimated for the combined RNA signal at a specific gene locus. nano-ID enables studies of RNA metabolism on the level of single RNA molecules and isoforms in different cell states and conditions.
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| |
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| Overall design |
Direct RNA nanopore sequencing in human cells
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| |
|
| Contributor(s) |
Maier K, Gressel S, Cramer P, Schwalb B |
| Citation(s) |
32887688 |
| Submission date |
Mar 05, 2019 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Björn Schwalb |
| E-mail(s) |
bschwal@gwdg.de
|
| Organization name |
MPI
|
| Street address |
Fassberg 11
|
| City |
Göttingen |
| ZIP/Postal code |
37077 |
| Country |
Germany |
| |
|
| Platforms (3) |
|
| Samples (22)
|
|
| Relations |
| BioProject |
PRJNA525707 |
| SRA |
SRP187602 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE127890_K562_0_unlabeled_combined.coverage.track.minus.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_0_unlabeled_combined.coverage.track.plus.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_1440_labeled_combined.coverage.track.minus.bw |
1.0 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_1440_labeled_combined.coverage.track.plus.bw |
1.0 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_60_labeled_combined.coverage.track.minus.bw |
2.9 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_60_labeled_combined.coverage.track.plus.bw |
3.0 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_60_labeled_heat_combined.coverage.track.minus.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_60_labeled_heat_combined.coverage.track.plus.bw |
2.2 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_combined.coverage.track.minus.bw |
5.1 Mb |
(ftp)(http) |
BW |
| GSE127890_K562_combined.coverage.track.plus.bw |
5.2 Mb |
(ftp)(http) |
BW |
| GSE127890_RAW.tar |
365.1 Mb |
(http)(custom) |
TAR (of BW) |
| GSE127890_readme.txt |
662 b |
(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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