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

Abstract

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.