Frontiers in Molecular Neuroscience | |
Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities | |
Molecular Neuroscience | |
Rekha Khandia1  Magdi E. A. Zaki2  Sami A. Al-Hussain2  Igor Baklanov3  Pankaj Gurjar4  Megha Katare Pandey5  | |
[1] Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, India;Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia;Department of Philosophy, North Caucasus Federal University, Stavropol, Russia;Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia;Translational Medicine Center, All India Institute of Medical Sciences, Bhopal, India; | |
关键词: codon usage; codon pattern; synonymous codons; neurodegeneration; cancer; CRISPR/Cas; | |
DOI : 10.3389/fnmol.2023.1200523 | |
received in 2023-04-05, accepted in 2023-05-23, 发布年份 2023 | |
来源: Frontiers | |
【 摘 要 】
IntroductionNeurodegeneration and cancer present in comorbidities with inverse effects due to the expression of genes and pathways acting in opposition. Identifying and studying the genes simultaneously up or downregulated during morbidities helps curb both ailments together.MethodsThis study examines four genes. Three of these (Amyloid Beta Precursor Protein (APP), Cyclin D1 (CCND1), and Cyclin E2 (CCNE2) are upregulated, and one protein phosphatase 2 phosphatase activator (PTPA) is simultaneously downregulated in both disorders. We investigated molecular patterns, codon usage, codon usage bias, nucleotide bias in the third codon position, preferred codons, preferred codon pairs, rare codons, and codon context.ResultsParity analysis revealed that T is preferred over A, and G is preferred over C in the third codon position, suggesting composition plays no role in nucleotide bias in both the upregulated and downregulated gene sets and that mutational forces are stronger in upregulated gene sets than in downregulated ones. Transcript length influenced the overall %A composition and codon bias, and the codon AGG exerted the strongest influence on codon usage in both the upregulated and downregulated gene sets. Codons ending in G/C were preferred for 16 amino acids, and glutamic acid-, aspartic acid-, leucine-, valine-, and phenylalanine-initiated codon pairs were preferred in all genes. Codons CTA (Leu), GTA (Val), CAA (Gln), and CGT (Arg) were underrepresented in all examined genes.DiscussionUsing advanced gene editing tools such as CRISPR/Cas or any other gene augmentation technique, these recoded genes may be introduced into the human body to optimize gene expression levels to augment neurodegeneration and cancer therapeutic regimens simultaneously.
【 授权许可】
Unknown
Copyright © 2023 Khandia, Pandey, Zaki, Al-Hussain, Baklanov and Gurjar.
【 预 览 】
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RO202310102005797ZK.pdf | 5972KB | download |