Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development. Homodimer. Heterodimer with RFX2 and RFX3. Binds DNA (By similarity). Interacts with GPS2 (PubMed:18218630). Isoform 1: Brain-specific. Isoform 2: Testis-specific. Isoform 1: Highly expressed in the suprachiasmatic nucleus, the central pacemaker site of the circadian clock (at protein level). At 8.5 dpc, detected in most of the neural plate but is excluded from the presumptive forebrain region. At 9.5 dpc, its expression is mostly restricted to two large regions, the caudal diencephalon/mesencephalon and the spinal cord. By 10.5 dpc, is present throughout the neural tube, and it is also detected in the cerebral cortex. It is also strongly expressed in the developing subcommissural organ (SCO) from 14.5 dpc to birth. Induced in a subjective night-specific manner. Mice with an insertion of a cardiac-specific epoxygenase transgene into an intron in the Rfx4 locus develop head swelling and rapid neurological decline in young adulthood, and have marked hydrocephalus of the lateral and third ventricles. Interruption of two alleles results in profound failure of dorsal midline brain structure formation and perinatal death. Interruption of a single allele prevents formation of the subcommissural organ, a structure important for cerebrospinal fluid flow through the aqueduct of Sylvius and results in congenital hydrocephalus. Belongs to the RFX family.