Transcriptome or Gene expression

PRJNA107023

The processing of Arabidopsis thaliana microRNAs (miRNAs) from longer primary transcripts (pri-miRNAs) requires the activity of several proteins, including DICER-LIKE1 (DCL1), the double stranded RNA binding protein HYPONASTIC LEAVES1 (HYL1), and the zinc finger protein SERRATE (SE). It has been noted before that the morphological appearance of weak se mutants is reminiscent of plants with mutations in ABH1/CBP80 and CBP20, which encode the two subunits of the nuclear cap-binding complex. We report that, like SE, the cap-binding complex is necessary for proper processing of pri-miRNAs. Inactivation of either ABH1/CBP80 or CBP20 results in decreased levels of mature miRNAs accompanied by increased levels of pri-miRNAs. Whole genome tiling array analyses reveal that se, abh1/cbp80 and cbp20 mutants also share similar pre-mRNA splicing defects, leading to the accumulation of many partially spliced transcripts. This is unlikely to be an indirect consequence of improper miRNA processing or other mRNA turnover pathways, since introns retained in se, abh1/cbp80 and cbp20 mutants are not affected by mutations in other genes required for miRNA processing or for non-sense-mediated mRNA decay. Taken together, our results uncover dual roles in splicing and miRNA processing that distinguish SE and the cap-binding complex from specialized miRNA processing factors such as DCL1 and HYL1. Keywords: Tiling array analysis of RNA populations from wild type, se, abh1 and cbp20 mutants Overall design: Wild type, se-1, abh1-285 and cbp20-1 mutant plants were grown under continuous light at 23°C on soil for 14 days. RNA from total plants was isolated using the RNeasy Plant Mini Kit (Qiagen). Targets (hybridization probes) for tiling array hybridization were generated from 1 µg total RNA (three biologigal replicates A, B and C) using the MessageAmp II-Biotin Enhanced Kit (Ambion) using unmodified NTPs instead of biotinylated NTPs, the GeneChip® WT Double-Stranded cDNA Synthesis Kit and the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). Targets were hybridized to Affymetrix Arabidopsis Tiling 1.0R arrays. For washing and scanning, the Affymetrix protocol was used.

download

none

none

pmid:18550839

05-01-2008

Arabidopsis thaliana

ncbitax:3702

NCBI

SCR:006472

National Center for Biotechnology Information

SCR:004801

NCBI BioProject