Fig. 5.

Suppression of genome-wide transcription under DD conditions. (A) Organization of Synechococcus expression profiles in DD from ZT 12 sorted by induction levels in the dark in the absence or presence of rifampicin. The data were normalized to the value at ZT 12. (B) Double plot of one LD cycle reconstructed by connecting data from hours 4–12 in LL and hours 0–12 in DD. The data were normalized to the average level over one LD cycle. (C) Total mRNA accumulation levels estimated from the sum of mRNA hybridization signals normalized to genomic DNA signals (see SI Methods) under LL (white circles) and DD in the absence (black) or presence (red) of rifampicin. Maximal total signals under LL were normalized to 1,000. (D) Population of nocturnally accumulating or diurnally accumulating transcripts in either subjective dawn (sDawn) or subjective dusk (sDusk) genes or low-amplitude/arrhythmic genes. Transcripts were defined as light-accumulating (yellow) or dark-accumulating (black) if the sum of the expression levels at ZT 4, 8 and 12 was larger or smaller than that at ZT 16, 20 and 24. Because the effect of LD transition is generally higher than the moderate changes in low-amplitude genes under LL, data from 97 higher-amplitude genes were used to identify 87 genes peaking at subjective dusk and 10 peaking at subjective dawn. Data for the 2418 remaining low-amplitude/arrhythmic (LA/AR) genes out of 2515 total genes are also shown.