Fig. 2: Light and COP1 control genome-wide alternative splicing in Arabidopsis. | Nature Communications

Fig. 2: Light and COP1 control genome-wide alternative splicing in Arabidopsis.

From: Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis

Fig. 2

a Flowchart for the analysis of light- and COP1-induced changes in AS. For transcriptomic profiling by mRNA-seq, total RNA was extracted from 5-d-old continuous white light- (50.6 μmol m−2 s−1) exposed WT (WT_L) and dark-grown cop1-6 mutant (cop1-6_D) seedlings, while total RNA extracted from 5-d-old WT etiolated seedlings (WT_D) was used as the control. Pie chart illustrating the number of AS events that display light- (b) or COP1-dependent (c) changes. Four major types of AS events, including IR, ES, A3SS, and A5SS, are shown. AS, P < 0.05. Venn diagrams illustrating the number of AS events (d) and IR events (e) that display either light-dependent changes (red), COP1-dependent changes (green), or both light- and COP1-dependent changes (yellow). AS, P < 0.05. f IR isoforms of PIF4, RVE1, ABA3, and HRD1B, identified by mRNA-seq, displaying changes in WT_L, cop1-6_D, and WT_D seedlings. Annotated gene structures are shown, with thick lines representing exons and thin lines representing introns. Wiggle plots showing the normalized read coverage are shown in red for WT_L, in blue for WT_D, and in yellow for cop1-6_D. The black frames indicate the position of the retained introns.

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