Transcription factors primarily regulate gene expression by determining which genes are transcribed at initiation and the extent to which those genes are transcribed during elongation. Brain and muscle Arnt-like protein-1 (BMAL1, ARNTL) is a well-characterized key activator of genes related to circadian rhythm that can specifically bind promoter boxes (E-boxes), cis-acting DNA elements. Previous genetic and biochemical studies have shown that BMAL1 regulates the circadian clock feedback loop, but the role of BMAL1 in transcription is still unclear. BMAL1 is structurally and functionally similar to c-MYC, a canonical regulator of transcription elongation, and both proteins contain beta helix-loop-helix domains and bind to E-boxes. In the current study, we utilized POL2 and H3K4me3 chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) in cells with BMAL1 gene knockout. The results demonstrate that, compared to wild type cells, both POL2 and H3K4me3 enrichment at transcription starting sites of clock-related genes are compromised in BMAL1 gene knockout cell. We also quantified nascent RNA production in wild type and BMAL1 gene knockout of clock-related genes. The results show that, compared to wild type cells, nascent RNA production is also reduced. In conclusion, these results suggest that BMAL1 is a major regulator of transcription initiation and activates circadian clock gene expression. (C) 2016 Elsevier Inc. All rights reserved.