A Crosstalk on Codon Usage in Genes Associated with Leukemia

Chakraborty, Supriyo; Nath, Durbba; Paul, Subrata; Choudhury, Yashmin; Ahn, Yeongseon; Cho, Yoon Shin; Uddin, Arif

doi:10.1007/s10528-020-10000-3

Cited by 4 publications

(3 citation statements)

References 61 publications

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“…The CUB and codon context bias are important parameters to be considered during heterologous protein expression 80 . In our study, it was evident that few of the codons remain minimally used, and this is in accord with the studies of Chakraborty et al, 81 on codon context in leukemia-associated genes. Identical codon pairs, GTG-GTG and CTG-CTG codon pairs were the most favored codon pairs in the depression-associated gene set.…”

Section: Discussionsupporting

confidence: 93%

Relative synonymous codon usage and codon pair analysis of depression associated genes

Khandia,

Gurjar,

Kamal

et al. 2024

Sci Rep

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Depression negatively impacts mood, behavior, and mental and physical health. It is the third leading cause of suicides worldwide and leads to decreased quality of life. We examined 18 genes available at the genetic testing registry (GTR) from the National Center for Biotechnological Information to investigate molecular patterns present in depression-associated genes. Different genotypes and differential expression of the genes are responsible for ensuing depression. The present study, investigated codon pattern analysis, which might play imperative roles in modulating gene expression of depression-associated genes. Of the 18 genes, seven and two genes tended to up- and down-regulate, respectively, and, for the remaining genes, different genotypes, an outcome of SNPs were responsible alone or in combination with differential expression for different conditions associated with depression. Codon context analysis revealed the abundance of identical GTG-GTG and CTG-CTG pairs, and the rarity of methionine-initiated codon pairs. Information based on codon usage, preferred codons, rare, and codon context might be used in constructing a deliverable synthetic construct to correct the gene expression level of the human body, which is altered in the depressive state. Other molecular signatures also revealed the role of evolutionary forces in shaping codon usage.

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Section: Discussionsupporting

confidence: 93%

Relative synonymous codon usage and codon pair analysis of depression associated genes

Khandia,

Gurjar,

Kamal

et al. 2024

Sci Rep

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show abstract

“…The CUB and codon context bias are important parameters to be considered during heterologous protein expression (47) . In our study, it was advent that few of the codons remained almost unused and corroborated with the studies of Chakraborty et al, 2020 on codon context in leukemia-associated genes (48). GTG-GTG and CTG-CTG codon pairs were the most favored codon pairs in the depression-associated gene set.…”

Section: Discussionsupporting

confidence: 92%

The G nucleotide guides codon usage bias in genes associated with depression

Khandia

Puranik

Pandey

et al. 2022

Preprint

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Depression or major depressive disorder is a psychiatric disorder affecting mood, behavior, and mental and physical health. Depression runs in families, suggestive of the genetic basis of the disease. Much research is going to understand the molecular basis of depression. In the present work, we tried to envisage the codon usage pattern analysis of genes involved in depression. The investigation revealed that all the genes were highly expressed, and codon usage bias (CUB) is influenced by the length of the gene, nucleotide disproportion, nucleotide compositional constraints, and CAI. The detailed investigation related to the effect of codon composition of CUB revealed that out of 20 compositional constraints, only G nucleotide showed a relationship at overall %G, %G2, %G3 and %GC2 positions. E of composition is further evidenced by the relationship between CUB and nucleotide skew. Neutrality, parity, P2 analysis, suppression of CpG, and TpA dinucleotide and over-representation of TpG dinucleotide followed by under abundance of TpA and CpG encompassing codons and over-representation of CTG and GTG codons all indicated towards the selectional force in shaping codon usage in genes linked to depression. The genes showed a significant positive correlation with each other based on RSCU value indicative of similar codon usage. Based on protein properties, all genes correlated with each other except for the CYP3A4 gene. The association is suggestive of identical protein properties also of genes involved. The analysis helps unveil the compositional features and various forces affecting codon usage of the gene.

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“…The CTG codon was overexpressed (overrepresentation, RSCU > 1.6) in 80.95% of genes, underexpressed (underrepresentation, RSCU = 0) in 2.38% of genes, and randomly used (RSCU >0.6 and <1.6) in 16.66% of genes. The CTG codon has been found overexpressed in obesity, housekeeping [45], and central nervous system genes [46]. In Y-linked genes, the RSCU values indicated overrepresentation of both AGA and CTG codons [47].…”

Section: Discussionmentioning

confidence: 99%

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage

Khandia

Alqahtani

2021

Biomedicines

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Primary immunodeficiencies (PIDs) are disorders of the immune system that involve faulty cellular, humoral, or both cellular and humoral functions. PIDs are present at the crossroad between infections, immune dysregulation, and cancers. A panel encompassing 42 genes involved in both PIDs and cancer has been investigated for the genes’ compositional properties, codon usage patterns, various forces affecting codon choice, protein properties, and gene expression profiles. In the present study, the codon choice of genes was found to be dependent upon the richness of the nucleotide; the viz AT nucleotide rich genome preferred AT ending codons. The dinucleotide TpA adversely affected protein expression, while CpG did not. The CTG codon was the most overrepresented codon in 80.95% of genes. Analysis of various protein properties, including GRAVY, AROMA, isoelectric point, aliphatic index, hydrophobicity, instability index, and numbers of acidic, basic, and neutral amino acid residues revealed that the hydrophobicity index, instability index, and numbers of acidic and basic amino acid residues are the factors affecting gene expression. Based on neutrality analysis, parity analysis, ENc-GC3 analysis, and regression analysis of nucleotides present at the first and third positions of the codon, it was determined that selection pressure, mutation pressure, and compositional constraints all participated in shaping codon usage. The study will help determine the various evolutionary forces acting on genes common to both PIDs and cancer. Codon usage analysis might be helpful in the future to augment both diseases simultaneously. The research also indicates a peculiar pattern adapted by a set of genes involved in any disease.

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A Crosstalk on Codon Usage in Genes Associated with Leukemia

Cited by 4 publications

References 61 publications

Relative synonymous codon usage and codon pair analysis of depression associated genes

Relative synonymous codon usage and codon pair analysis of depression associated genes

The G nucleotide guides codon usage bias in genes associated with depression

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage

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