Study : GC-rich coding sequences reduce transposon-like sRNA-mediated transgene silencing in Arabidopsis and maize

Identification

• Name: GC-rich coding sequences reduce transposon-like sRNA-mediated transgene silencing in Arabidopsis and maize
• Identifier: dXJuOkVWQS9zdHVkeS9QUkpOQTMwOTcxMw==
• Data link: Link to this study on EBI European Nucleotide Archive
• Description: 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: For Arabidopsis data in this series, genome-wide small RNA, transcriptome, methylone profilings were done by Illumina TruSeq sample preparation or in-house protocol (methyl C-seq) followed by high-throughput sequencing with Illumina HiSeq 2000 platform. Data for maize small RNA studies are under a separate GEO series GSE103037.
• Data files: SRR3116252; SRR3116253; SRR3116254; SRR3116261; SRR3116262; SRR3116263; SRR3116257; SRR3116232; SRR3116233; SRR3116234; SRR3116235; SRR3116236; SRR3116237; SRR3116238; SRR3116239; SRR3116240; SRR3116241; SRR3116242; SRR3116243; SRR3116244; ERZ1132704; ERZ511784; ERZ1132659; ERZ511770; ERZ1132689; ERZ511779; ERZ1132718; ERZ511787; ERZ1132701; ERZ511783; ERZ1132695; ERZ511781; ERZ1132679; ERZ511777; ERZ1132666; ERZ511772; ERZ1132723; ERZ511788; ERZ1132675; ERZ511776