Estimating RNA Secondary Structure by Maximizing Stacking Regions

Sen, Piyali; Tula, Debapriya; Ray, Suvendra Kumar; Satapathy, Siddhartha Sankar

doi:10.1007/978-981-15-6198-6_15

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“…The distribution of polymorphisms among the strains in reference to rpoB and rpoC genes (Supplementary Figure 3) shows that, in general, polymorphism observed in this study is not because of any specific strain but mutations accumulated among all the strains (Supplementary Table 4). A known set of previously published high expression genes (Sharp et al 2005;Sen et al 2020) were considered in this work for the analysis of nucleotide composition and polymorphism at FFS in high expression genes (HEGs) (Supplementary Table 5 and 6).…”

Section: Polymorphism Analysis At Irs and At Ffs In Cds Of The Bacterial Chromosomesmentioning

confidence: 99%

Polymorphism at four-fold degenerate site, but not at the intergenic regions, explains nucleotide compositional strand asymmetry in bacteria

Sen

Aziz

Das

et al. 2021

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We investigated single nucleotide polymorphism in intergenic regions (IRs) and four-fold degenerate sites (FFS) in genomes of three γ-Proteobacteria and two Firmicutes to understand the mechanism of nucleotide compositional asymmetry between the leading and the lagging strands. Pattern of the polymorphism spectra were alike regarding transitions but variable regarding transversions in the IRs of these bacteria. Contrasting trends of complementary polymorphisms such as C->T vs G->A as well as A->G vs T->C in the IRs vindicated similar replication-associated strand asymmetry regarding cytosine and adenine deamination, respectively, across these bacteria. Surprisingly, the polymorphism pattern at FFS was different from that of the IRs and its frequency was always more than the IRs in these bacteria. Further, the polymorphism patterns within a bacterium were inconsistent across the five amino acids, which neither the replication nor the transcription-associated mutations could explain. However, the polymorphism at FFS coincided with amino acid specific codon usage bias in the five bacteria. Further, strand asymmetry in nucleotide composition could be explained by the polymorphism at FFS, not at the IRs. Therefore, polymorphisms at FFS might not be treated as nearly neutral unlike that in IRs in these bacteria.

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Section: Polymorphism Analysis At Irs and At Ffs In Cds Of The Bacterial Chromosomesmentioning

confidence: 99%