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Neuronal PAS domain-containing protein 2 (NPAS2) is a basic helix-loop-helix (bHLH)-PAS protein expressed in the mammalian central nervous system that in humans is encoded by the NPAS2 gene. The gene is on Chromosome 2 in band 2p11.2-2q13 in humans and on Chromosome 1 at 21–22 centimorgans in mice. The 92 kDa protein binds DNA as a heterodimer with BMAL1, implicating it in regulation of the circadian clock. In humans, it is also found in the colon, small intestines, and uterus.

Discovery
NPAS2 was discovered by Yu-Dong Zhou in 1997 along with NPAS1 as having similar primary amino acid sequence to the CLOCK gene, a known regulator of circadian rhythms. First the gene was isolated and sequenced, using the GenBank database for expressed sequence tags (EST) that had a similar sequence to PAS domains. After sequencing they used in situ hybridization to determine the expression patterns of NPAS1 and NPAS2, localizing it to the forebrain.

Later, NPAS2 was shown to take over the job of CLOCK as the regulatory oscillator in the mammalian forebrain (see below).

Function
NPAS2 is a member of the basic helix-loop-helix (bHLH)-PAS family of transcription factors. NPAS2 is found in both the cytosol and the nucleus, but is only active in the nucleus of most mammalian cells. In the nucleus it binds to the E-box, a DNA promoter element upstream of the period genes (PER1, PER2 and PER3) and cryptochrome genes (CRY1 and CRY2). Along with the period and cryptochrome proteins, NPAS2 is involved in the negative feedback loop that maintains each cell's circadian clock. When NPAS2 binds to the E-box, transcription of the period and cryptochrome genes is increased. The period and cryptochrome proteins then go on to inhibit the activity of NPAS2, returning expression of period and cryptochrome back to baseline, allowing NPAS2 to become active again and increase period and cryptochrome transcription.

Circadian Clock
NPAS2 is a redundant paralog of the CLOCK protein. NPAS2 has been shown to be analogous to the function of CLOCK in CLOCK deficient mice. In mice heterozygous for the CLOCK∆19 mutation, which renders the protein unable to induce gene transcription, there is still some normal CLOCK expression, and NPAS2 substitutes for the deficient CLOCK proteins by forming a heterodimer with BMAL1 and inducing transcription of the period and cryptochrome genes. The homozygous CLOCK∆19 mutants have a drastically shortened period. Meanwhile, NPAS2 mutants demonstrate a less severe phenotype than CLOCK mutants with only a moderately shortened period. This suggests that CLOCK's role in circadian rhythms takes precedence over that of NPAS2. Mice who lack both NPAS2 and CLOCK are unable to entrain to their environmental light-dark cycle.

Memory
Outside of the role that NPAS2 plays in maintaining circadian rhythms, a mouse model has demonstrated that it is also important for specific types of memory. Mice lacking NPAS2 performed worse than controls in cued and contextual memory tasks, but whether this is due to a distinct role for NPAS2 in memory or is a consequence of losing rhythmicity in gene expression is unknown.

Regulation
Experimental evidence suggests both PAS domains of NPAS2 bind heme as a prosthetic group and that the heme status controls DNA binding in vitro. Heme-bound, or holo-NPAS2 will not heterodimerize with BMAL1 when exposed to low concentrations of carbon monoxide. These results indicate that the heterodimerization of NPAS2, and presumably the expression of its target genes, are regulated by a gas through the heme-based sensor.

Clinical significance
NPAS2 has been implicated in a variety of clinical disorders. Single-nucleotide polymorphisms within the NPAS2 gene have been associated with major depressive disorder, seasonal affective disorder, and breast cancer. Whether these effects are due to disruptions in circadian rhythms or other functions of the gene are unknown.

Interactions
NPAS2 has been shown to interact with:
 * ARNTL,
 * EP300, and
 * Retinoic acid receptor alpha.