Figure 5. Analysis of the different classes of rhythmically expressed genes in the mouse liver.
(A): Nascent-Seq/RNA-Seq signal ratio (used as inferred half-life) is similar for the four categories of rhythmically expressed genes: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R) and arrhythmic nascent RNA and mRNA (AR-AR). (B): Similar as (A), using the RNA half-life values from Sharova et al., 2009. (C): Nascent-Seq rhythms of 25 of the 480 R-AR genes can be attributed to the rhythmic transcription of an adjacent gene. This applies to Sphk2 Nascent-Seq rhythm, which likely results from rhythmic Dbp nascent RNA signal that extend the 3ʹend of Dbp gene and read through Sphk2. Genes above the scale bar are transcribed from left to right and those below the scale bar are transcribed from right to left. (D): Gene ontology of three categories of rhythmically expressed genes: rhythmic nascent RNA and mRNA (R-R), rhythmic nascent RNA only (R-AR), rhythmic mRNA only (AR-R).