|
| Status |
Public on Oct 30, 2017 |
| Title |
GC-rich coding sequences reduce transposon-like sRNA-mediated transgene silencing in Arabidopsis and maize |
| Organism |
Zea mays |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
The molecular basis of transgene susceptibility to silencing is poorly characterized in plants, thus we evaluated several transgene design parameters as means to reduce heritable sRNA-mediated transgene silencing. Analyses of Arabidopsis plants with transgenes encoding a microalgal polyunsaturated fatty acid (PUFA) synthase revealed that small RNA (sRNA)-mediated silencing, combined with the use of repetitive regulatory elements, led to aggressive transposable element (TE)-like silencing of canola-biased PUFA transgenes. Diversifying regulatory sequences and using native microalgal coding sequences (CDSs) with higher GC content improved transgene expression and resulted in remarkable trans-generational stability via reduced accumulation of sRNAs and DNA methylation. Further experiments in maize with transgenes individually expressing three Bacillus thuringiensis (Bt) crystal proteins tested the impact of CDSs recoding using different codon bias tables. Transgenes with the higher GC content exhibited increased transcript and protein accumulation. These results demonstrate that the sequence composition of transgene CDSs can directly impact silencing providing design strategies for increasing transgene expression levels and reducing risks of heritable loss of transgene expression.
|
| |
|
| Overall design |
Data for Arabidopsis small RNA and DNA methylation studies can be found under a separate GEO submission (GSE76406). Data for maize small RNA studies are in this submission. Maize small RNA data was generated using Illumina TruSeq sample preparation protocol.
|
| |
|
| Contributor(s) |
Sriram S, Sidorenko LV |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Aug 24, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Lyudmila V Sidorenko |
| Organization name |
DOW AgroSciences
|
| Street address |
9330 Zionsville Rd
|
| City |
Indianapolis |
| State/province |
Indiana |
| ZIP/Postal code |
46268 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL15463 |
Illumina HiSeq 2000 (Zea mays) |
| GPL20156 |
Illumina NextSeq 500 (Zea mays) |
|
| Samples (27)
|
|
| This SubSeries is part of SuperSeries: |
| GSE103112 |
GC-rich coding sequences reduce transposon-like sRNA-mediated transgene silencing in Arabidopsis and maize |
|
| Relations |
| BioProject |
PRJNA399853 |
| SRA |
SRP116089 |
Less...
More...