Nucleotide composition determines the role of translational efficiency in human genes

Halder, Binata; Malakar, Arup Kumar; Chakraborty, Supriyo

doi:10.6026/97320630013046

Cited by 17 publications

(17 citation statements)

References 28 publications

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“…C > T substitutions were 1.9 times more frequent in the CpG dinucleotide context than in the non-CpG dinucleotide context after correcting for the base composition. This result suggests hypermutability of CpG dinucleotides in which methylated cytosine undergoes deamination, leading to more frequent C > T changes [25,26].…”

Section: Resultsmentioning

confidence: 99%

Functional annotation of de novo variants from healthy individuals

Lee

Hong

2019

Genomics Inform

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The implications of germline de novo variants (DNVs) in diseases are well documented. Despite extensive research, inconsistencies between studies remain a challenge, and the distribution and genetic characteristics of DNVs need to be precisely evaluated. To address this issue at the whole-genome scale, a large number of DNVs identified from the whole-genome sequencing of 1,902 healthy trios (i.e., parents and progeny) from the Simons Foundation for Autism Research Initiative study and 20 healthy Korean trios were analyzed. These apparently nonpathogenic DNVs were enriched in functional elements of the genome but relatively depleted in regions of common copy number variants, implying their potential function as triggers of evolution even in healthy groups. No strong mutational hotspots were identified. The pathogenicity of the DNVs was not strongly elevated, reflecting the health status of the cohort. The mutational signatures were consistent with previous studies. This study will serve as a reference for future DNV studies.

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Section: Resultsmentioning

confidence: 99%

Functional annotation of de novo variants from healthy individuals

Lee

Hong

2019

Genomics Inform

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“…It may be possible that genes of higher transcriptional importance could have higher (GC) content [16,31]. Similar researches concerning different species have been done by Halder [30]. Every single deviation in codon usage is based on the codon preference by using the exact codon during the translation process.…”

Section: Adenovirus Diversitymentioning

confidence: 87%

“…Principal component analysis also supported that most codons showed biased effect on (G) and (C) at the third codon position and at the preferred codons that end with either (G) or (C). Halder [30] also indicated that positive significant correlation in gene expression parameters with a few amino acids such as Val (V), Arg (A), Ser (S), and Ile (I) might influence the gene expression.…”

Section: Adenovirus Diversitymentioning

confidence: 99%

“…The relative synonymous codon usage (RSCU) is a simple measure of the heterogeneity in the usage pattern of synonymous codons. The value was calculated and performed by [11,21,26,30,31,63]. RSCU value >1 means that the codon is more frequently used than expected and over-represented, while the RSCU value <1 means that the codon is less frequently used than expected [11].…”

Section: Molecular Study On Hvrs1-4 and Rscu Diversitymentioning

confidence: 99%

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Adenoviruses and Their Diversity in Poultry

Niczyporuk¹

2018

Application of Genetics and Genomics in Poultry Science

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An investigation into the aetiology of fowl adenovirus strains and their distribution worldwide in populations of poultry flocks industry has been conducted. Pathogenic role of the viruses is not always clear. They can cause latent infection or several diseases and are the reason of economic losses in poultry flock industry. Ubiquity of adenovirus strains was commonly described, and stand-alone pathogenicity for a long time has been disputed. A globally emerging trend of adenoviruses and adenovirus-associated diseases has been increasing from year to year in all over the world. Mainly, type FAdV-4 is responsible for hydropericardium hepatitis syndrome (HP), type FAdV-1 for gizzard erosion and ulceration (GEU), and types FAdV-2, 8a, 8b, and 11 seem to be responsible for inclusion body hepatitis (IBH). Defining the spreading of the avian adenovirus strains in different types of fowl profile production, recognising their property and determining their types and molecular characterisation are very important from the epidemiological point of view and are considered as excellent basis for vaccine development and gene therapy implementation. This chapter provides a comprehensive review of FAdVs, including their epidemiology, pathogenesis, diagnostic, detection, and molecular characterisation. This comprehensive review is needed to better understand the latest progress in study of the viruses and prospects regarding disease control and implementation of gene therapy.

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“…Since there are 61 possible codons (and three stop codons) which encode only 20 amino acids, there is redundancy in the genetic code. Although synonymous codons encode the same amino acid, recent research has shown that translational efficiency differs between synonymous codons [6][7][8]. These differences cause a change in translational speed, which affects gene expression [9], [10].…”

Section: Introductionmentioning

confidence: 99%

A Comprehensive Analysis of the Phylogenetic Signal in Ramp Sequences in 211 Vertebrates

McKinnon

Miller

Whiting

et al. 2020

Preprint

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Background: Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented.Methods: Ramp sequences were compared from 211 vertebrates (110 Mammalian and 101 non-mammalian). The presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life taxonomy to determine the number of parallelisms and reversals that occurred, and these results were compared to what would be expected due to random chance. Lastly, aligned nucleotides in ramp sequences were compared to the rest of the sequence in order to examine possible differences in phylogenetic signal between these regions of the gene.Results: Parsimony and maximum likelihood analyses of the presence/absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, the retention index of ramp sequences is significantly higher than would be expected due to random chance (p-value = 0). A chi-square analysis of completely orthologous ramp sequences resulted in a pvalue of approximately zero as compared to random chance.Discussion: Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches.

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Nucleotide composition determines the role of translational efficiency in human genes

Cited by 17 publications

References 28 publications

Functional annotation of de novo variants from healthy individuals

Functional annotation of de novo variants from healthy individuals

Adenoviruses and Their Diversity in Poultry

A Comprehensive Analysis of the Phylogenetic Signal in Ramp Sequences in 211 Vertebrates

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