Hidden Treasure in “Junk DNA”

3 Reasons Why You Should Take “Pseudogenes” Seriously in Your Research

Protein-coding DNA, or “functional” genes, only accounts for up to 2% in the human genome. Until recently, the remaining 98% have been referred to as “junk DNA” for their putative noncoding feature. The name itself implies that junk DNA is useless and can be ignored. Further research, however, has shown that junk DNA may actually be crucial in the functionality of our genome. For instance, have you ever wondered why human astrocytes and hepatocytes originated from the same fertilized egg, and carry exactly the same genetic information, yet they differ greatly in their development, morphology and functions? While part of the reason lies in epigenetics, where gene expression is regulated by epigenetic modification such as DNA methylation, some researchers have also been searching for clues in the so-called junk DNA. As a result, “pseudogenes” were identified, and their diverse roles in maintaining normal cell biology were revealed.

Pseudogene Timeline

By definition, pseudogenes are segments of DNA bearing high sequence similarity to their corresponding functional genes, but have lost some or all of their functionality. Compared to the scope of functional gene research, the research on pseudogenes is in its infancy. Nevertheless, there are reasons why you should take pseudogenes seriously in your research.

  1. Pseudogene occurrence is more common and important than you might think. It is now well-accepted that in the human genome, the number of pseudogenes is quite comparable to that of protein-coding “functional” genes, if not more. Numerous genes, maybe even your genes-of-interest, have one or more corresponding pseudogenes. Although still considered junk DNA, a lot of pseudogenes do get transcribed and some even are translated. Evidence suggests that the transcription level of some pseudogenes is critical, and the dysregulation of pseudogenes may contribute to the pathogenesis of various diseases and disorders.
  1. Pseudogenes may affect functional gene expression. As you know, gene transcription levels play decisive roles in many aspects of normal cell metabolism, and are tightly regulated through a complicated network. Pseudogenes can play a role in this regulation too. Many pseudogenes originate by gene duplication events, and therefore, share high sequence similarity with the corresponding functional genes. Consequently, when pseudogenes are transcribed, their mRNAs, similar to that of the functional genes, can serve as competing endogenous RNAs (ceRNAs) to regulate the expression level of the corresponding functional genes.
  1. Failure to distinguish the transcription level of pseudogenes from their corresponding functional genes may skew your research data. Although highly similar to each other in sequence, pseudogenes and corresponding functional genes apparently play different roles in cell biology, and are regulated through distinct mechanisms. Separate analysis of each is a prerequisite for drawing trustworthy conclusions. With their high sequence similarity, telling them apart by qPCR is no easy task. Primers must be designed deliberately to ensure not only high PCR efficiency, but also specificity for the pseudogene or functional gene only. Many times the difference is merely a few nucleotides, requiring expertise for successful qPCR analysis. Nondiscriminating or less-discriminating qPCR primers will certainly lead to unreliable and even faulty conclusions.

ScienCell has developed the world’s first pseudogene transcription analysis qPCR kits to better assist you in analyzing pseudogene transcription and its influence on functional gene expression. Our kits guarantee that each primer set only amplifies the designated gene or pseudogene without cross-amplification. Whether you already have pseudogenes in mind or are just learning about pseudogenes today, we are here to help. Simply email us at info@sciencellonline.com and our scientists will help identify the pseudogenes relevant to your research and the best way to assess them. For more information on pseudogene categories and roles, please go to our pseudogene webpage: https://www.sciencellonline.com/products-services/gene-expression-profiling/pseudogene-transcription-analysis.html.

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