Evaluation of Per4 Sequence Length As the Only Pseudogene in the Molecular Clock

Background and aim: almost all living organisms from single cells to sophisticated organisms are affected by circadian cycle, in fact, they are equipped with a time measuring system which is known as the circadian clock. in mammals the center of circadian clock is located at the scn. dysregulation of circadian rhythms is closely related to development of various human metabolic diseases and different cancers. at the molecular level, central oscillators are composed of at least three interconnected feedback loops. in the first feedback loop the core clock genes (ccg) such as bmal1 and clock form a heterodimer transcription factor; then this complex binds to e-box element existing in the promoter of per and cry genes and activates the expression of them. per and cry genes create the complex and negatively regulates the transcription of bmal1 and clock. the fourth member of per genes family is called per4 (per3p1) and it is the only pseudogene in the molecular clock genes family. recently, there is a disagreement about the number of per4 exons in ensembl and ncbi database. the purpose of this study is to investigate the per4 sequence.methods: mcf-7 cell line was cultured in standard conditions. then dna and rna were extracted from mcf-7 cells and pcr reaction was performed on dna and cdna samples. the pcr and rt-pcr product was evaluated on 1% agarose gel.results: the length of the pcr and rt-pcr products are about 1.5 kb and 750 bp, respectively.conclusion: according to data from ncbi database, per4 pseudogene has only one exon with 1548 bp length. whereas ensembl showed that the cdna sequence of this pseudogene contains 2 exons. the first and second exons are 516 and 313 bp, respectively, which separated by an intron with 605 bp length. the results showed that this pseudogene has 2 exons. because the length of the rt-pcr product was shorter than the pcr product, which indicates an intron has been deleted in the per4 sequence.