(Q34485607)

2 August 2017

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title

Hearing silence: non-neutral evolution at synonymous sites in mammals (English)

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2 August 2017

3

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2 August 2017

2

Joanna L Parmley

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2 August 2017

1

J V Chamary

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2 August 2017

1 February 2006

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2 August 2017

Nature Reviews Genetics

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2 August 2017

7

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2 August 2017

98-108

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2 August 2017

2

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https://scigraph.springernature.com/pub.10.1038/nrg1770

2 August 2017

0 references

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The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution

21 January 2018

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Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation

21 January 2018

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The neutral theory is dead. Long live the neutral theory

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31 March 2020

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Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution

31 March 2020

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Translational selection and molecular evolution

31 March 2020

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Evolution of synonymous codon usage in metazoans

31 March 2020

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31 March 2020

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Evidence for widespread degradation of gene control regions in hominid genomes

31 March 2020

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31 March 2020

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DNA sequence evolution: the sounds of silence

31 March 2020

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An analysis of codon usage in mammals: selection or mutation bias?

31 March 2020

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The mosaic genome of warm-blooded vertebrates

31 March 2020

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The evolution of isochores

31 March 2020

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31 March 2020

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Recombination drives the evolution of GC-content in the human genome.

31 March 2020

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Gene conversion drives GC content evolution in mammalian histones

31 March 2020

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A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes.

31 March 2020

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Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

31 March 2020

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Site-to-site variation of synonymous substitution rates

31 March 2020

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What drives codon choices in human genes?

31 March 2020

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The signature of selection mediated by expression on human genes

31 March 2020

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Comparative evolutionary rates of introns and exons in murine rodents

31 March 2020

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Within-intron correlation with base composition of adjacent exons in different genomes.

31 March 2020

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Extraordinarily high evolutionary rate of pseudogenes: evidence for the presence of selective pressure against changes between synonymous codons

31 March 2020

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Transcription-associated mutational asymmetry in mammalian evolution

31 March 2020

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Dependence of mutational asymmetry on gene-expression levels in the human genome

31 March 2020

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Chromosomal location effects on gene sequence evolution in mammals

31 March 2020

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Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile

31 March 2020

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Mutation pattern variation among regions of the primate genome

31 March 2020

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Distribution and characterization of regulatory elements in the human genome

31 March 2020

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Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents

31 March 2020

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31 March 2020

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Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA

31 March 2020

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Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes

31 March 2020

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Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees

31 March 2020

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Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences.

31 March 2020

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Sensitivity of patterns of molecular evolution to alterations in methodology: a critique of Hughes and Yeager

31 March 2020

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Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee

31 March 2020

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Codon bias as a factor in regulating expression via translation rate in the human genome.

31 March 2020

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Coevolution of codon usage and transfer RNA abundance

31 March 2020

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Variation in the strength of selected codon usage bias among bacteria

31 March 2020

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Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence

31 March 2020

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In NF1, CFTR, PER3, CARS and SYT7, alternatively included exons show higher conservation of surrounding intron sequences than constitutive exons

31 March 2020

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Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis.

31 March 2020

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Initial sequencing and analysis of the human genome

31 March 2020

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Solving the riddle of codon usage preferences: a test for translational selection

31 March 2020

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Retroviral transfer and expression of a humanized, red-shifted green fluorescent protein gene into human tumor cells

31 March 2020

1 reference

Codon optimization for high-level expression of human erythropoietin (EPO) in mammalian cells

31 March 2020

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A unification of mosaic structures in the human genome

31 March 2020

1 reference

Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance

31 March 2020

1 reference

Dualism of gene GC content and CpG pattern in regard to expression in the human genome: magnitude versus breadth

31 March 2020

1 reference

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

31 March 2020

1 reference

Influence of RNA secondary structure on the pre-mRNA splicing process

31 March 2020

1 reference

Single-nucleotide polymorphisms can cause different structural folds of mRNA.

31 March 2020

1 reference

Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor

31 March 2020

1 reference

A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups

31 March 2020

1 reference

mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences

31 March 2020

1 reference

Natural selection and algorithmic design of mRNA.

31 March 2020

1 reference

Strategies for RNA folding and assembly

31 March 2020

1 reference

Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure

31 March 2020

1 reference

Mammalian mutation pressure, synonymous codon choice, and mRNA degradation

31 March 2020

1 reference

Listening to silence and understanding nonsense: exonic mutations that affect splicing

31 March 2020

1 reference

Genomic variants in exons and introns: identifying the splicing spoilers

31 March 2020

1 reference

Natural selection affects frequencies of AG and GT dinucleotides at the 5' and 3' ends of exons

31 March 2020

1 reference

Predictive identification of exonic splicing enhancers in human genes

31 March 2020

1 reference

Systematic identification and analysis of exonic splicing silencers.

31 March 2020

1 reference

Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases

31 March 2020

1 reference

Evidence for codon bias selection at the pre-mRNA level in eukaryotes.

31 March 2020

1 reference

Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else?

31 March 2020

1 reference

Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers

31 March 2020

1 reference

Evidence for purifying selection acting on silent sites in BRCA1

31 March 2020

1 reference

Purifying selection on silent sites -- a constraint from splicing regulation?

31 March 2020

1 reference

Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution.

31 March 2020

1 reference

Single nucleotide polymorphism-based validation of exonic splicing enhancers

31 March 2020

1 reference

Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers

31 March 2020

1 reference

Changes in Alternative Splicing of Human and Mouse Genes Are Accompanied by Faster Evolution of Constitutive Exons

31 March 2020

1 reference

The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis

31 March 2020

1 reference

Silent mutations affect in vivo protein folding in Escherichia coli

31 March 2020

1 reference

Ribosome-mediated translational pause and protein domain organization

31 March 2020

1 reference

Specific correlations between relative synonymous codon usage and protein secondary structure.

31 March 2020

1 reference

Recombination of protein domains facilitated by co-translational folding in eukaryotes.

31 March 2020

1 reference

Tissue-specific codon usage and the expression of human genes

31 March 2020

1 reference

The Ka/Ks ratio: diagnosing the form of sequence evolution

31 March 2020

1 reference

Context-dependent codon bias and messenger RNA longevity in the yeast transcriptome.

31 March 2020

1 reference

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

31 March 2020

1 reference

Small fitness effect of mutations in highly conserved non-coding regions

31 March 2020

1 reference

Expected relationship between the silent substitution rate and the GC content: implications for the evolution of isochores.

31 March 2020

1 reference

An activated 5' cryptic splice site in the human ALG3 gene generates a premature termination codon insensitive to nonsense-mediated mRNA decay in a new case of congenital disorder of glycosylation type Id (CDG-Id)

31 March 2020

1 reference

Familial adenomatous polyposis: aberrant splicing due to missense or silent mutations in the APC gene.

31 March 2020

1 reference

A splicing mutation affecting expression of ataxia-telangiectasia and Rad3-related protein (ATR) results in Seckel syndrome

31 March 2020

1 reference

Improved superoxide-generating ability by interferon gamma due to splicing pattern change of transcripts in neutrophils from patients with a splice site mutation in CYBB gene.

31 March 2020

1 reference

An alpha-thalassemia phenotype in a Dutch Hindustani, caused by a new point mutation that creates an alternative splice donor site in the first exon of the alpha2-globin gene

31 March 2020

1 reference

Severe subacute GM2 gangliosidosis caused by an apparently silent HEXA mutation (V324V) that results in aberrant splicing and reduced HEXA mRNA.

31 March 2020

1 reference

Type I Glanzmann thrombasthenia caused by an apparently silent beta3 mutation that results in aberrant splicing and reduced beta3 mRNA.

31 March 2020

1 reference

Analysis of the LAMB3 gene in a junctional epidermolysis bullosa patient reveals exonic splicing and allele-specific nonsense-mediated mRNA decay

31 March 2020

1 reference

A silent mutation, C924T (G308G), in the L1CAM gene results in X linked hydrocephalus (HSAS).

31 March 2020

1 reference

Splicing mosaic of the myophosphorylase gene due to a silent mutation in McArdle disease

31 March 2020

1 reference

Heterozygous TGFBR2 mutations in Marfan syndrome

31 March 2020

1 reference

Nervous system targets of RNA editing identified by comparative genomics

31 March 2020

1 reference

No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

31 March 2020

1 reference

A "humanized" green fluorescent protein cDNA adapted for high-level expression in mammalian cells

31 March 2020

1 reference

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NRG1770

1 reference

PubMed ID

16418745

Dimensions Publication ID

2 August 2017

0 references

1 reference

PubMed ID

16418745