Fig. 1

HL induces miRNA expression changes in Arabidopsis thaliana shoots. a F_v/F_m measured in 4-week-old Arabidopsis plants grown in LL under hydroponic conditions. LLc – control plants; HL—plants exposed to HL for 2 h (n = 18). b TT-qRT PCR for selected miRNA-targeted transcripts of nuclear encoded proteins localized in chloroplasts under LLc and HL. Transcript levels were normalized with respect to small nucleolar85 RNA (sno85) and small nucleolar101 RNA (sno101). c Results of a microtranscriptomic screening for miRNA expression changes in LLc, HL and LLr – plants exposed to HL for 2 h and a subsequent recovery for 4 h in LL. d TT-qRT PCR for miR163 and miR840 and e qRT-PCR for pri-miR163 and pri-miR840 in Col-0 LLc, HL and LLr plants. Transcript levels were normalized with respect to sno85 and sno101 (for miRNAs) or the PP2A and UPL7 genes (for pri-miRNAs), respectively. f Occupancy of PolII on MIR genes. Line charts present ChIP profile of total PolII on examined genes. Grey lines represent results for LLc plants and blue lines represent results for HL plants. Above each chart, gene structure is shown with black boxes representing miR, and grey boxes representing primary transcripts (pri-miRs).Orange lines show amplified regions (primer localization used for qRT-PCR analysis). Above each gene structure 100 bp scale is shown. g RNA stability assay performed on Arabidopsis seedlings in control plants (LLc) and plant exposed to HL (HL). Degradation curves after cordycepin treatment (plot) were used to calculate half-life of pri-miR840, pri-miR163, UBC (control) transcripts and short-lived mRNA transcribed from gene At3G45970 (table h). Presented values are averages from three biological replicates. For better clarity of chart only pri-miRNAs data were presented. Asterisks indicate significant differences according to Tukey’s HSD test (panel: a,b,d,e) or t-test (panel f) at the level of ** ≤ 0.01 and *** ≤ 0.001. Mean values ± SDs (n = 3) were provided