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In agreement with a role of Xrn1 in translation initiation, activated genes exhibited a general reduction of footprint density while repressed genes exhibited a general increase.
The results of the phylogenetic analysis indicated that only 19 of the 1168 genes exhibited a classification that was different from the HMM search result.
The most prevalent group (group 1; 252 genes) exhibited a canonical IEG dynamic characterized by increased expression at 1 h and a return to baseline by 4 h (e.g., Fosb, Egr1; Fig. 4f).
There were altogether 983 mRNAs revealed ≥1.5-fold increased abundance; conversely, 557 genes exhibited a decline in abundance (≤1.5-fold) owing to the silencing Lsd1 (Fig. 4a and Supplementary Table S2).
Rigorous statistical analysis of the expression profiles indicated that 17 genes exhibited a high probability (P>0.9) of androgen-regulated expression.
Two of the six genes exhibited a consistently decreased expression level in submerged plants for all eight genotypes (Fig. 4).
In our set, the majority of significant genes exhibited a decrease in expression with advancing age.
We found that high-expressing genes exhibited a more pronounced profile of tag density around gene boundaries (Fig. 5), while low-expressing genes exhibited a more subdued contour, closer to genomic background.
A representative part of these genes exhibited a good concordance of expression changes when assessed using tailored Q-PCR.
Fig. 5 shows that E. coli sodA, sodB and katG genes exhibited a rather basal expression in untreated cells.
These genes exhibited a variety of expression patterns, a few of which showed similarity to the patterns of DCL1, TWI1 or PDD1, when inspected visually (data not shown).
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CEO of Professional Science Editing for Scientists @ prosciediting.com