<i>Brahma</i> regulates nucleosome occupancy and transcriptional output at <i>per</i> and <i>tim</i> promoters.

<p>Expression of <i>(A) per</i> and <i>(B) tim</i> was assayed in flies expressing <i>brm</i> RNA<i>i</i> in <i>tim</i>-expressing neurons (<i>brm</i> RNA<i>i</i> v37720 X <i>TUG</i>) compared to control parental line (<i>TUG</i>). Expression of <i>(C) per</i> and <i>(D) tim</i> was assayed in flies expressing the <i>brm</i>^<i>K804R</i> transgene in <i>tim</i>-expressing cells (<i>UAS</i>-<i>brm</i>^<i>K804R</i> X <i>TUG(II)</i>) and compared to control <i>TUG(II</i>) lines. All gene expression analysis was performed with quantitative real-time PCR using SYBR green chemistry. Steady state mRNA levels at six time points (ZT) for <i>(A)</i> and <i>(B)</i> and four time points for <i>(C)</i> and <i>(D)</i> over a circadian cycle were normalized to non-cycling <i>cbp20</i> levels, and expressed as a fraction of the peak expression level (peak = 1). Experiments were performed at least 3 times and representative results are shown. Error bars = SEM for technical triplicates for each biological replicate. <i>(E-H)</i> Corresponding histone H3 ChIP assays for the same genotypes of flies used for gene expression analysis as described in <i>(A-D)</i> illustrating decrease of nucleosome occupancy at the <i>per (E</i> and G) and <i>tim</i> (<i>F</i> and <i>H</i>) promoters in the <i>brm</i> mutants (<i>brm</i> RNA<i>i</i> and <i>brm</i>^<i>K804R</i>). Error bars = SEM (n = 3) for biological replicates. Asterisks denote significant difference between control and <i>brm</i> knockdown at indicated time points (P < 0.05).