 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 16, 2020 |
| Title |
SHAPE analysis of RNA structure in living cells with unprecedented accuracy |
| Organisms |
Escherichia coli; Bacillus subtilis; Homo sapiens |
| Experiment type |
Other
|
| Summary |
Due to the mounting evidence that RNA structure plays a critical role in regulating almost any essential physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 performs comparably well to NAI on naked RNA under in vitro conditions and it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.
|
| |
|
| Overall design |
SHAPE-MaP
Definitions:
TGIRT-III/HIV RT/SSII: reverse transcriptase enzymes
I5: Indoline-5-carboxylic acid imidazolide
1M4: 1-Methylimidazole-4-carboxylic acid imidazolide
6A3: 6-Aminopyridine-3-carboxylic acid imidazolide
B5: Benzotriazole-5-carboxylic acid imidazolide
NIC: Nicotinic acid imidazolide
NAI: 2-Methylpyridine-3-carboxylic acid imidazolide
2A3: 2-Aminopyridine-3-carboxylic acid imidazolide
|
| |
|
| Contributor(s) |
Marinus T, Fessler AB, Ogle CA, Incarnato D |
| Citation(s) |
33398343 |
| |
| Submission date |
Jul 16, 2020 |
| Last update date |
Feb 11, 2021 |
| Contact name |
Danny Incarnato |
| E-mail(s) |
d.incarnato@rug.nl
|
| Organization name |
University of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| State/province |
Netherlands |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platforms (3) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
| GPL24109 |
Illumina NextSeq 500 (Bacillus subtilis) |
|
| Samples (36)
|
| GSM4673439 |
NAI, E. coli, ex vivo (HIV RT) |
| GSM4673440 |
DMSO, E. coli, ex vivo (SSII) |
| GSM4673441 |
NAI, E. coli, ex vivo (SSII) |
| GSM4673442 |
I5, E. coli, ex vivo (SSII) |
| GSM4673443 |
1M4, E. coli, ex vivo (SSII) |
| GSM4673444 |
6A3, E. coli, ex vivo (SSII) |
| GSM4673445 |
B5, E. coli, ex vivo (SSII) |
| GSM4673446 |
NIC, E. coli, ex vivo (SSII) |
| GSM4673447 |
2A3, E. coli, ex vivo (SSII) |
| GSM4673448 |
DMSO, E. coli, in vivo (SSII) |
| GSM4673449 |
NAI, E. coli, in vivo (SSII) |
| GSM4673450 |
I5, E. coli, in vivo (SSII) |
| GSM4673451 |
1M4, E. coli, in vivo (SSII) |
| GSM4673452 |
6A3, E. coli, in vivo (SSII) |
| GSM4673453 |
B5, E. coli, in vivo (SSII) |
| GSM4673454 |
NIC, E. coli, in vivo (SSII) |
| GSM4673455 |
2A3, E. coli, in vivo (SSII) |
| GSM4673456 |
DMSO, B. subtilis, in vivo (SSII) |
| GSM4673457 |
NAI, B. subtilis, in vivo (SSII) |
| GSM4673458 |
I5, B. subtilis, in vivo (SSII) |
| GSM4673459 |
1M4, B. subtilis, in vivo (SSII) |
| GSM4673460 |
6A3, B. subtilis, in vivo (SSII) |
| GSM4673461 |
B5, B. subtilis, in vivo (SSII) |
| GSM4673462 |
NIC, B. subtilis, in vivo (SSII) |
| GSM4673463 |
2A3, B. subtilis, in vivo (SSII) |
| GSM4673464 |
DMSO, HEK293, in vivo (SSII) |
| GSM4673465 |
NAI, HEK293, in vivo (SSII) |
| GSM4673466 |
I5, HEK293, in vivo (SSII) |
| GSM4673467 |
1M4, HEK293, in vivo (SSII) |
| GSM4673468 |
6A3, HEK293, in vivo (SSII) |
| GSM4673469 |
B5, HEK293, in vivo (SSII) |
| GSM4673470 |
NIC, HEK293, in vivo (SSII) |
| GSM4673471 |
2A3, HEK293, in vivo (SSII) |
|
| Relations |
| BioProject |
PRJNA646706 |
| SRA |
SRP272240 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE154563_RAW.tar |
2.2 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...