ライフサイエンスコーパス: codon bias

1 lationships with other known determinants of codon bias.

2 d by peculiar rates of mutation or levels of codon bias.

3 respectively, of human and mouse TNRs showed codon bias.

4 with theoretical predictions of the level of codon bias.

5 on efficiency in vitro through alteration of codon bias.

6 more compatible with the observed levels of codon bias.

7 ein in Chlamydomonas reinhardtii chloroplast codon bias.

8 natural selection as a mechanism leading to codon bias.

9 relative mutational load of genes caused by codon bias.

10 e association between recombination rate and codon bias.

11 atistically significant N1 context-dependent codon bias.

12 DNA divergence is inversely correlated with codon bias.

13 d approximate estimation methods that ignore codon bias.

14 tual correlation between synonymous rate and codon bias.

15 , in that synonymous rates were unrelated to codon bias.

16 at their low diversity is not due to extreme codon bias.

17 g region and the recombination rate modulate codon bias.

18 t, can have a moderately strong influence on codon bias.

19 tween protein abundance, mRNA abundance, and codon bias.

20 s to have allowed a genome-wide reduction in codon bias.

21 with high codon bias than in genes with low codon bias.

22 did not alter the amino acid sequence or the codon bias.

23 a model from a strictly mutational model of codon bias.

24 rgone a reduction in selection intensity for codon bias.

25 conserved N-terminal region with synonymous codon bias.

26 during osteoblast differentiation displayed codon bias.

27 ertebrates have been analyzed for synonymous codon bias.

28 with abundant Orb2 binding sites have a rare-codon bias.

29 timal for a cell generates the phenomenon of codon bias.

30 as is the major driving force for generating codon bias.

31 an evolutionary theory on the origin of this codon bias.

32 inement than other commonly used measures of codon bias.

33 ticipates in the creation and maintenance of codon bias.

34 different frequencies, a phenomenon known as codon bias.

35 ound no changes in nucleotide composition or codon bias.

36 RNA structural elements and use of different codon biases.

37 to translation activities) show less extreme codon biases.

38 network (RNN) to define cell type-dependent codon biases.

39 selection weak independently of the level of codon bias?

40 iv) What is the exact nature of selection on codon bias?

41 ematically characterize the contributions of codon bias, AA bias and protein structural motifs to the

42 olutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial geno

43 en GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whol

44 le metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial

45 However, past metrics that compare codon bias across species are confounded by among-specie

46 and may explain the unexpected constancy of codon bias across species of very different census popul

47 tly linked genes, can change very greatly in codon bias across species.

48 determine many of a gene's features, such as codon bias, amino acid composition, and size.

49 This insensitivity indicates a consistent codon bias amongst highly expressed genes.

50 Codon bias analysis revealed strong purifying selection,

51 detecting genomic rearrangement events; (v) codon bias analysis; (vi) annotation of orthogroups with

52 This phenomenon is known as codon bias and appears to be a universal feature of geno

53 by synthesizing the lsc gene in chloroplast codon bias and by driving expression of the chimeric gen

54 lihood-based method for estimating levels of codon bias and determining major codon preference that r

55 Intragenic variation in codon bias and elongation rate is significant, with a st

56 nificant, with a strong trend for increasing codon bias and elongation rate towards the 3' end of the

57 In some species, patterns of codon bias and empirical findings on the biology of tran

58 and SSD are similarly biased with respect to codon bias and evolutionary rate, although differing sig

59 gly, there is a negative correlation between codon bias and expression levels for group 3 genes, i.e.

60 ions are neutral, which we test by analyzing codon bias and G+C content in a set of 92 gene loci.

61 Codon bias and GC content differs among MyHC genes with

62 Levels of codon bias and gene expression are highest for those gen

63 Long coding regions have both a lower codon bias and higher synonymous substitution rates, sug

64 Here we review currently known types of codon bias and how they may influence translation.

65 somal protein genes was associated with high codon bias and increased nucleotide skew.

66 also predicts a negative correlation between codon bias and Ks, which is also not found.

67 nes, Adh and Adhr, which differ in degree of codon bias and level of gene expression.

68 This may result in atypical codon bias and particular evolutionary constraints.

69 me with a GC content that relates synonymous codon bias and protein folding.

70 Here we show that codon bias and recombination rate are correlated strongl

71 Humanin and SHLP6 show strong synonymous codon bias and sequence conservation.

72 e controversies over the roles of N-terminal codon bias and suggest a straightforward method for opti

73 discuss how understanding the principles of codon bias and translation can contribute to improved pr

74 ategories: preferred mutations that increase codon bias and unpreferred changes in the opposite direc

75 imulations were performed to maintain/remove codon bias and/or to maintain or alter third-codon posit

76 he translation machinery, known to be highly codon biased and using preferentially fast codons, are h

77 rough small variations in codon frequencies, codon biases and context-dependent codon biases between

78 ression levels are correlated with proteins' codon biases and mRNA expression levels, as measured by

79 est that elongation rate is affected by both codon biases and specific amino acid composition.

80 investigations into the connections between codon biases and translation rates.

81 gher repeat density, larger gene size, lower codon bias, and a higher rate of gene rearrangement comp

82 pecies-specific GC content, GC and AT skews, codon bias, and mutation bias.

83 tionship among the coding region length, the codon bias, and the synonymous divergence and polymorphi

84 ce can considerably reduce adaptation, e.g., codon bias, and, to a lesser extent, levels of polymorph

85 enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact.

86 divergences (dinucleotide bias); extremes of codon bias; and anomalies of amino acid usage.

87 In this lineage, codon bias appears to be maintained under roughly equal

88 ction for preferred codons is weak only when codon bias approaches equilibrium and may be quite stron

89 We find that while context-dependent codon biases are widespread in bacteria, few are conserv

90 Therefore, we propose this codon bias as a regulatory layer to control cell context

91 rience stronger natural selection for higher codon bias as a result of maladaptive reduction of their

92 s variants that cause large changes in local codon bias as independent data sets, we found strong, ph

93 f 69 in human, and 18 of 42 in mouse) showed codon bias at p<0.05.

94 ies also provide a molecular explanation for codon bias at the 5' end of this essential determinant o

95 ot-specific catalases are their extreme high codon bias at the third position and low degree of seque

96 consistent with translational selection for codon bias being stronger in the larval stage and sugges

97 quencies, codon biases and context-dependent codon biases between the samples.

98 We detected a stronger codon bias but a lower frequency of GC at synonymous sit

99 This was not attributable to codon bias but to the change in prohormone sequence.

100 of genes and even the particular pattern of codon bias can remain phylogenetically invariant for ver

101 ed; quantify the effects of genomic context, codon bias, chromatin accessibility, and number of prote

102 hat X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophil

103 fus1 gene in the mt+ locus, mid displays low codon bias compared with other nuclear genes.

104 ein synthesis, it is generally accepted that codon bias contributes to translation efficiency by tuni

105 In this formulation, codon bias correlations for Escherichia coli genes are e

106 bout half of all cases the context-dependent codon bias could not be explained by the sequence compos

107 In addition, a few data repositories of codon bias data are available, differing in the metrics

108 e have created a new web resource called the Codon Bias Database (CBDB) which provides information re

109 The Codon Bias Database provides a centralized repository of

110 nge" which was also regarded as a measure of codon bias (defined as preferential use either in TNR or

111 Codon bias deoptimization has been previously used to su

112 als a function of snoRNAs in controlling the codon-biased dichotomous cellular states of proliferatio

113 and bacterial growth rates also varied, but codon bias did not correlate with gene expression.

114 This study addresses the cause of codon bias differences between the sibling species, Dros

115 Unusual codon bias differences between the two families may resu

116 synthesis in HIV-infected cells by means of codon-bias discrimination.

117 integrate the effect of purifying selection, codon bias, DNA repair and GC content on s/v ratio of pr

118 dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR express

119 uences to determine the pattern of change in codon bias during angiosperm divergence.

120 Codon bias engendered by an A + T rich genome may influe

121 nonymous codons, including one gene with low codon bias, esterase-6.

122 Codon bias even varies by isoform within a species.

123 Here we investigate patterns of codon bias evolution on the X chromosome and autosomes i

124 limit plausible explanations for patterns of codon bias evolution to selection- or drift-based proces

125 A favorable codon bias for the mutated codon with consequently incre

126 cs were applied to compare context-dependent codon biases for codons from different synonymous groups

127 The fus1 gene is remarkable in lacking the codon bias found in all other nuclear genes of C. reinha

128 es are conventional in length, with the same codon bias found in other minicircle genes.

129 s highly deviant in its genome signature and codon bias from the rest of the genome.

130 ual validation, ranged from 5 to 39 kDa, had codon biases from 0.93 to 0.083, and were primarily asso

131 We used sequence-based analysis to examine codon bias, gene duplications, and levels of divergence

132 rrelated with up-regulation of proteins from codon-biased genes involved in energy metabolism.

133 translation of stress response proteins from codon-biased genes.

134 anisms with nucleotide-biased, and therefore codon-biased, genomes or isochores.

135 re, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years.

136 Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significa

137 There is limited evidence that selection on codon bias has an effect on differentiation (as measured

138 s that codon arrangement, rather than simply codon bias, has a key role in determining translational

139 , and not simply relaxation of constraint on codon bias, has contributed to the higher levels of unpr

140 pendent on local nucleotide context, and not codon bias, has occurred in these species.

141 crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain

142 The NNNNT codon set enables low codon bias, high fidelity, and high efficiency for the p

143 d nucleotide/amino acid composition bias and codon bias higher, in more-overlapped than in less-overl

144 ter regimes in which fast initiation or high codon bias in a transgene increases protein yield and in

145 us studies have investigated codon usage and codon bias in an effort to better understand how species

146 ide a resource for researchers investigating codon bias in bacteria, facilitating comparisons between

147 Thus, our results show intragenic codon bias in both mouse and human genes expressed in di

148 te of nonsynonymous substitutions (d(N)) and codon bias in D. melanogaster.

149 sence is positively correlated with a gene's codon bias in D. melanogaster.

150 Evolutionary analysis of codon bias in Drosophila indicates that synonymous mutat

151 The total codon bias in each taxon, when regressed against the tot

152 Therefore, genome-wide codon bias in eubacteria and archaea may be predicted fr

153 s, natural selection leads to high levels of codon bias in genes that are highly expressed.

154 This difference is ascribed to common codon bias in HRAS, which leads to much higher protein e

155 Yet, the importance of this codon bias in regulating cell state-specific expression

156 riation over different function classes, for codon bias in relation to possible lateral transfer and

157 We found that codon bias in ribosomal protein genes was the strongest

158 ithout introns showing significantly reduced codon bias in the center of coding regions.

159 entrally located introns do not show reduced codon bias in the center of the coding region.

160 onstrated that the experimental reduction of codon bias in the Drosophila alcohol dehydrogenase (Adh)

161 ontradict each other and cloud the origin of codon bias in the taxon.

162 th the nucleotide bias 3' of the stop codon, codon bias in the two codon positions 5' of the terminat

163 The pattern of codon bias in these genes is suggestive of selection for

164 undance played a role in creating intragenic codon bias in these genes.

165 elect tissues, revealing a critical role for codon bias in tissue biology.

166 hly expressed, tandem-repeated genes display codon bias in Trypanosoma cruzi, Trypanosoma brucei and

167 generating both global and local synonymous codon biases in many unicellular organisms, this explana

168 e two strands, on differences in residue and codon biases in relation to gene function, expression le

169 leotides, evaluations and interpretations of codon biases in several large prokaryotic genomes, and c

170 Independent of gene size, the codon biases in the 5' third of genes deviate by more th

171 Factors with proposed roles in causing codon bias include degree and timing of gene expression,

172 Known causes of codon bias include differences in mutation rates as well

173 pression levels of individual genes, whereas codon bias influences global translation efficiency and

174 Thus codon bias is an indicator of the intensity of one kind

175 In addition, relative codon bias is broadly conserved among syntenic genes fro

176 It is shown that average relative codon bias is correlated with expression level and that,

177 Synonymous codon bias is correlated with tRNA gene copy number and

178 We find that cell state-specific codon bias is determined by the guanine-cytosine (GC) co

179 esults suggest that, in general, genome-wide codon bias is determined primarily by mutational process

180 ral lines of evidence that this elevation in codon bias is due exclusively to their chromosomal locat

181 mous sites are under weak selection and that codon bias is maintained by a balance between selection,

182 Another interesting observation is that codon bias is not a predictor of either protein or mRNA

183 However, unlike other organisms, Plasmodium codon bias is not correlated to tRNA gene copy number.

184 f dietary nitrogen on genome composition and codon bias is poorly understood.

185 Whereas the degree of codon bias is positively correlated with level of gene e

186 honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of partic

187 However, codon bias is significantly negatively correlated with f

188 , the role of selective pressures in shaping codon bias is still controversial in vertebrates, partic

189 Codon bias is strongly related to gene expression levels

190 ppears that the major cause for selection on codon bias is that certain preferred codons are translat

191 Codon bias is very low, as seen for other genes in regio

192 However, codon bias, itself, does not indicate that selection is

193 uestions are addressed: (1) How variable are codon bias levels across the phylogeny? (2) How variable

194 ibrium and may be quite strong on genes with codon bias levels that are much lower and/or above equil

195 Here we report that differences in codon bias limit TLR7 expression relative to TLR9.

196 As judged by calculation of codon bias, low-abundance proteins were identified from

197 m again have similar values, and genome-wide codon bias may also be predicted from intergenic sequenc

198 ces cerevisiae, and Drosophila melanogaster, codon bias may be maintained by a balance among mutation

199 techniques nor predictable by mRNA levels or codon bias measurements.

200 for each strain in addition to the strain's codon bias measurements.

201 odon bias, the relationship between d(N) and codon bias might be a by-product of gene expression.

202 conversion (BGC) models and selection-driven codon bias models.

203 mechanism involving selective translation of codon-biased mRNA for crucial proteins.

204 ment of m(3)C32 tRNA modification for serine codon-biased mRNA translation of cell cycle, and DNA rep

205 gain insights into the relationship between codon bias, mRNA secondary structure, third-codon positi

206 of the epitranscriptome, specific tRNAs, and codon-biased mRNAs are used by oncogenic programs to pro

207 The potential use of this kind of codon bias mutant as a master donor strain to generate o

208 The viral proteins generated from the codon bias mutants are identical to the wild-type viral

209 (iii) How do shifts in codon bias occur?

210 rs effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms.

211 plays a significant role in determining the codon bias of chloroplast genes but that it acts with di

212 ion among the algae genomes in the degree of codon bias of homologous genes.

213 er, our data indicate that the inherent rare codon bias of KRAS plays an integral role in tumorigenes

214 A new measure for assessing codon bias of one group of genes with respect to a secon

215 The codon bias of the actual gene is then compared to a dist

216 Here, to determine the effect of the rare codon bias of the KRAS gene on de novo tumorigenesis, we

217 a zero order Markov chain determined by the codon bias of the same set of sequences.

218 based on the two lines of evidence, that the codon bias of this gene currently is not being maintaine

219 Among the function classes, codon biases of ribosomal proteins are the most deviant

220 It is shown that the codon biases of the ancestral genes are much stronger th

221 pe 1 (HIV-1) infection and the expression of codon-biased open reading frames.

222 nd (3) Are there phylogenetic constraints on codon bias or preference?

223 als related, for instance, to reading frame, codon bias, pairwise codon bias, splice sites and transc

224 as without changing N3 content indicate that codon bias per se has only a weak effect on the formatio

225 ective translation of mRNAs from families of codon-biased persistence genes.

226 These findings demonstrate that codon bias plays a critical role in KRAS-driven resistan

227 Moreover, codon bias plays an important role in controlling a mult

228 known correlations with mRNA abundances and codon bias, providing absolute protein concentrations ac

229 verage gene exceeds a high threshold and the codon bias relative to ribosomal proteins is also approp

230 n (possibly horizontally transferred) if its codon bias relative to the average gene exceeds a high t

231 biases and natural selection in maintaining codon bias remain a contentious issue.

232 The mechanisms that induce codon biases remain an open question; studies have attri

233 lation between mRNA half-lives and ORF size, codon bias, ribosome density, or abundance.

234 he C. reinhardtii chloroplast was due to the codon bias seen in the C. reinhardtii chloroplast genome

235 he efficiency of selection, and thus average codon bias, should decline with gene density.

236 Analysis of genome-wide codon bias shows that only two parameters effectively di

237 Rather, the atypical codon bias simply may be a remnant of an ancestral codon

238 ance, to reading frame, codon bias, pairwise codon bias, splice sites and transcription regulation, n

239 is explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC cont

240 w that differences in transcript leaders and codon bias substantially contribute to divergent transla

241 to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this

242 so that the selective constraints imposed by codon bias sustain this reduced optimization in IDRs.

243 d the impact of CDS recoding using different codon bias tables.

244 selection on codon usage in genes with high codon bias than in genes with low codon bias.

245 he codons that overlap have lower synonymous codon bias than those which do not.

246 bias simply may be a remnant of an ancestral codon bias that now is being degraded by the mutation bi

247 t gene expression is a strong determinant of codon bias, the relationship between d(N) and codon bias

248 The evolution of codon bias, the unequal usage of synonymous codons, is t

249 permutation of an ultralong DH with a severe codon bias toward mutation to cysteine.

250 RsxA displays a codon bias toward tyrosine TAT and overabundance of RsxA

251 tem of tRNA modifications and translation of codon-biased transcripts that enhance expression of stre

252 Transfer RNA modification reprogramming and codon bias translation is a conserved epitranscriptomic

253 RNA synthetase (VARS) is a key player in the codon-biased translation reprogramming induced by resist

254 Termed 'codon-biased translation' and originally identified in s

255 TRM112 illustrate the principal mechanism of codon-biased translation, with gene amplifications, incr

256 ned by a mechanism of tRNA reprogramming and codon-biased translation.

257 nd evidence for stress-induced, tRNA-driven, codon-biased translation.

258 nd tRNA molecules as drivers of pathological codon-biased translation.

259 , including PfK13, that are regulated by Lys codon-biased translation.

260 bosome and its associated RNA substrates for codon-bias translational repression.

261 ownstream cognate tRNAs-elicits a downstream codon-biased translational gene network response that en

262 There is high variation in the level of codon bias values among the 88 taxa, but few readily app

263 horetic separation, proteins from genes with codon bias values of <0.1 (lower abundance proteins) wer

264 Proteins from genes with codon bias values of <0.1 were found, however, if protei

265 Other codon bias variants include biased codon pairs and codon

266 hus the contribution that selection makes to codon bias variation among genes, can be adequately expl

267 A synthetic gene containing an E. coli codon bias was cloned into a modified pET32 plasmid, and

268 ide survey, similar gene pairs with opposing codon bias were identified that not only manifest dichot

269 tRNA with a specific codon bias were not targeted-rather increased transcript

270 le to detect position dependent selection on codon bias which correlates with gene expression levels

271 We propose that suboptimal codon bias, which correlates with low guanine-cytosine (

272 structure of the genetic code and conserved codon biases, which ensure that similar multivalent RNA

273 ribosome density, tRNA adaptation index and codon bias while achieving a feature reduction from 37 t

274 e found regularities in N1 context-dependent codon bias with respect to the codon nucleotide composit

275 DB) which provides information regarding the codon bias within the set of highly expressed genes for

276 On the other hand, simulations that reduce codon bias without changing N3 content indicate that cod