Arabidopsis thaliana strain:Col-0 Transcriptome or Gene expression

All Arabidopsis thaliana lines used in this study had a genetic background of Columbia 0 ecotype. Homozygous upf1-5 mutant line (Arciga-Reyes et al., 2006) was received from Brendan Davies laboratory (Centre for Plant Sciences, University of Leeds, UK). The lba1 (upf1-1) mutant [Yoine et al., 2006] was provided by Masato Yoine, Nagoya University, Japan. Seedlings growth conditions and heat stress treatments: Seeds were sterilized in 50% Bleach, 0.1% Tween 20 for 10 min. followed by washing in sterile water five times. Approximately 200 seeds were plated in one row on MS agar plates (Murashige and Skoog basal medium supplied with vitamins and 1.5% sucrose, Phytotechnologies Laboratories, cat. # M5501; Shawnee Mission, KS, USA). Seeds were vernalized for 4 days at 40C in dark and grown on plates in a Conviron PGR15 (Conviron) growth chamber for ten days under LDHH conditions (12h light : 12 hrs dark, light intensity 300 µmol m-2s-1, at 210C). For heat stress treatments the temperature was increased to 37oC at Zeitgeber time 0 hours. Seedlings were incubated for 12 hours and harvested at subjective dusk (Zeitgeber time 12 hours). Both heat stress treated and non-treated control whole seedlings were collected, flash frozen in liquid nitrogen and stored at -800C prior to RNA isolation. Total and poly(A) RNA were extracted and RNA-seq libraries were prepared for sequencing using Illumina Genome Analyzer GAII as described (Filichkin et al., 2009).