Circadian Oscillation of Natural Antisense Transcripts Related to Human Core Clock Genes

Therapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention

Antisense transcription, a prevalent occurrence in mammalian genomes, gives rise to natural antisense transcripts (NATs) as RNA molecules. These NATs serve as agents of diverse transcriptional and post-transcriptional regulatory mechanisms, playing crucial roles in various biological processes vital for cell function and immune response. However, when their normal functions are disrupted, they can contribute to human diseases. This comprehensive review aims to establish the molecular foundation linking NATs to the development of disorders like cancer, neurodegenerative conditions, and cardiovascular ailments. Additionally, we evaluate the potential of oligonucleotide-based therapies targeting NATs, presenting both their advantages and limitations, while also highlighting the latest advancements in this promising realm of clinical investigation.Abbreviations: NATs- Natural antisense transcripts, PRC1- Polycomb Repressive Complex 1, PRC2- Polycomb Repressive Complex 2, ADARs- Adenosine deaminases acting on RNA, BDNF-AS- Brain-derived neurotrophic factor antisense transcript, ASOs- Antisense oligonucleotides, SINEUPs- Inverted SINEB2 sequence-mediated upregulating molecules, PTBP1- Polypyrimidine tract binding protein-1, HNRNPK- heterogeneous nuclear ribonucleoprotein K, MAPT-AS1- microtubule-associated protein tau antisense 1, KCNQ1OT- (KCNQ1 opposite strand/antisense transcript 1, ERK- extracellular signal-regulated kinase 1, USP14- ubiquitin-specific protease 14, EGF- Epidermal growth factor, LSD1- Lysine Specific Demethylase 1, ANRIL- Antisense Noncoding RNA in the INK4 Locus, BWS- Beckwith-Wiedemann syndrome, VEGFA- Vascular Endothelial Growth component A.

Natural antisense transcripts as drug targets

The recent discovery of vast non-coding RNA-based regulatory networks that can be easily modulated by nucleic acid-based drugs has opened numerous new therapeutic possibilities. Long non-coding RNA, and natural antisense transcripts (NATs) in particular, play a significant role in networks that involve a wide variety of disease-relevant biological mechanisms such as transcription, splicing, translation, mRNA degradation and others. Currently, significant efforts are dedicated to harnessing these newly emerging NAT-mediated biological mechanisms for therapeutic purposes. This review will highlight the recent clinical and pre-clinical developments in this field and survey the advances in nucleic acid-based drug technologies that make these developments possible.

Dysregulation of PER3 clock gene and its only pseudogene in colorectal cancer and type 2 diabetes

The period (PER) family genes (PER1, PER2, and PER3) play a fundamental role in regulating the day/night cycle. PER3 has a pseudogene variant, PER3P1 or PER4, whose role and expression pattern is unclear in human health and diseases. This study was performed to evaluate the expression levels of normal PER family members and the PER3P1 pseudogene in colorectal cancer (CRC) and type 2 diabetes (T2D). Blood samples were taken from 50 diabetic patients and analyzed using real-time PCR for quantification of PER3 and PER3P1 expression. Colorectal tumor tissues of 50 individuals were also used to evaluate the expression of PER members. All PER members, including PER3P1, were found to be downregulated in colorectal tumor samples. Blood samples collected from diabetic subjects revealed an opposite expression pattern; both PER3 and its pseudogene were found to be upregulated when compared to the control group. Our results reveal coordination between the expression pattern of PER3P1 and normal PER family genes. Based on our findings and the pathological importance of this pseudogene, it can be suggested that PER3P1 may be one of the key regulators of the molecular clock network and PER family expression. This hypothesis needs to be confirmed by further studies.