Kurihara et al. 2018 (PRJNA429734)

General Details

Title Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression during blue light exposure in Arabidopsis
Organism
Number of Samples 4
Release Date 2018/01/12 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP128983
ENA SRP128983
GEO GSE109122
BioProject PRJNA429734

Publication

Title
Authors Kurihara Y, Makita Y, Kawashima M, Fujita T, Iwasaki S, Matsui M
Journal Proceedings of the National Academy of Sciences of the United States of America
Publication Date 2018 Jul 24
Abstract Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced by transcription factors such as HY5. However, few detailed analyses have been carried out on the control of transcription start sites (TSSs). Of the various wavelengths of light, it is blue light (BL) that regulates physiological responses such as hypocotyl elongation and flowering time. To understand how gene expression is controlled not only by transcript abundance but also by TSS selection, we examined genome-wide TSS profiles in Arabidopsis seedlings after exposure to BL irradiation following initial growth in the dark. Thousands of genes use multiple TSSs, and some transcripts have upstream ORFs (uORFs) that take precedence over the main ORF (mORF) encoding proteins. The uORFs often function as translation inhibitors of the mORF or as triggers of nonsense-mediated mRNA decay (NMD). Transcription from TSSs located downstream of the uORFs in 220 genes is enhanced by BL exposure. This type of regulation is found in HY5 and HYH , major regulators of light-dependent gene expression. Translation efficiencies of the genes showing enhanced usage of these TSSs increased upon BL exposure. We also show that transcripts from TSSs upstream of uORFs in 45 of the 220 genes, including HY5 , accumulated in a mutant of NMD. These results suggest that BL controls gene expression not only by enhancing transcriptions but also by choosing the TSS, and transcripts from downstream TSSs evade uORF-mediated inhibition to ensure high expression of light-regulated genes. Copyright © 2018 the Author(s). Published by PNAS.
PMC PMC6064979
PMID 29915080
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR6466829 PRJNA429734 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR6466830 PRJNA429734 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR6466831 PRJNA429734 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
SRR6466832 PRJNA429734 Arabidopsis thaliana 0.0 Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

ⓘ For more Information on the columns shown here see: About