Although Bmal1 is a key component of the mammalian clock system, little is understood about the actual mechanism of circadian Bmal1 gene transcription, particularly at the chromatin level. Here we discovered a unique chromatin structure within the Bmal1 promoter. The RORE region, which is a critical cis element for the circadian regulation of the Bmal1 gene, is comprised of GC-rich open chromatin. The 3-flanking region of the promoter inhibited rhythmic transcription in the reporter gene assay in vitro even in the presence of ROR␣ and REV-ERB␣. We also found that the nuclear matrix protein SAF-A binds to the 3-flanking region with circadian timing, which was correlated with Bmal1 expression by footprinting in vivo. These results suggest that the unique chromatin structure containing SAF-A is required for the circadian transcriptional regulation of the Bmal1 gene in cells.Circadian rhythms in behavior and physiology have an adaptive significance for living organisms from bacteria to humans and reflect the existence of an underlying intrinsic circadian oscillator or biological clock (10). The master clock that generates circadian rhythms in mammals is located in the suprachiasmatic nucleus (SCN) of the hypothalamus. In turn, peripheral clocks directly regulate many local rhythms that probably feed back to the SCN through hypothalamic integration (5). The molecular mechanism of the circadian oscillator consists of autoregulatory transcriptional and translational feedback loops that have both positive and negative elements (10). The key transcription factors, CLOCK and BMAL1, form heterodimers that bind to E-box enhancer sequences and activate the transcription of the three Period genes (Per1, Per2, and Per3) and two Cryptochrome genes (Cry1 and Cry2) (46). The PER and CRY proteins subsequently repress transcription at their own promoters through negative feedback caused by acting on the CLOCK-BMAL1 complex (35). This feedback loop system controls the central clock in the SCN and the peripheral clocks in most peripheral tissues (18).Originally, BMAL1 (also known as MOP3) was characterized by high expression levels in brain and muscle cells (16). As the activity of Bmal1 Ϫ/Ϫ mice immediately becomes completely arrhythmic in constant darkness, BMAL1 is apparently an essential and nonredundant component of the mammalian clock (6). The level of Bmal1 transcripts robustly oscillates in the SCN and in peripheral clock cells (25), and the circadian regulation of Bmal1 transcription contributes to the formation of interconnected feedback loops (35). The Bmal1 promoter contains two recognition motifs for ROR and REV-ERB orphan nuclear receptors (ROREs). Preitner et al. reported that REV-ERB␣, which represses Bmal1 expression, is the major regulator of cyclic Bmal1 transcription (31), and Akashi and Takumi described that ROR␣ acts to promote Bmal1 transcription (1). The opposing activities of the orphan nuclear receptors ROR␣ and REV-ERB␣ are important in the maintenance of circadian clock function (34). It was also suggested...