(Q33383232)

26 July 2017

The impact of the nucleosome code on protein-coding sequence evolution in yeast (English)

1 reference

26 July 2017

0 references

3

1 reference

26 July 2017

Nizar N Batada

2

0 references

Tobias Warnecke

object named as

Tobias Warnecke

series ordinal

1

0 references

publication date

7 November 2008

1 reference

26 July 2017

1 reference

26 July 2017

4

1 reference

26 July 2017

e1000250

1 reference

26 July 2017

11

1 reference

Creative Commons Attribution 4.0 International

26 July 2017

start time

7 November 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

A high-resolution map of nucleosome positioning on a fission yeast centromere

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

RNA landscape of evolution for optimal exon and intron discrimination

21 June 2018

1 reference

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Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Genomic sequence is highly predictive of local nucleosome depletion

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

A high-resolution atlas of nucleosome occupancy in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Positive selection for unpreferred codon usage in eukaryotic genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Nucleosome positioning signals in genomic DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

A "silent" polymorphism in the MDR1 gene changes substrate specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Synonymous codon usage in Escherichia coli: selection for translational accuracy.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

A genomic code for nucleosome positioning

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Antagonistic forces that position nucleosomes in vivo.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

A periodic pattern of mRNA secondary structure created by the genetic code

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Genome-scale identification of nucleosome positions in S. cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Single nucleotide polymorphism-based validation of exonic splicing enhancers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Evolution of prokaryotic DNA: intragenic and extragenic divergences observed with orthologs from three related species

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Widespread selection for local RNA secondary structure in coding regions of bacterial genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Translational selection and yeast proteome evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Suppression of homologous recombination by the Saccharomyces cerevisiae linker histone

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Non-homologous end joining as an important mutagenic process in cell cycle-arrested cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Pushing the limits of the scanning mechanism for initiation of translation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Evolution of synonymous codon usage in metazoans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Role of DNA sequence in nucleosome stability and dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

A downstream regulatory element located within the coding sequence mediates autoregulated expression of the yeast fatty acid synthase gene FAS2 by the FAS1 gene product

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

RNA secondary structure and compensatory evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

A role for REV3 in mutagenesis during double-strand break repair in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Unbiased estimation of the rates of synonymous and nonsynonymous substitution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Reduced synonymous substitution rate at the start of enterobacterial genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

DNA synthesis errors associated with double-strand-break repair

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Periodicity of strong nucleosome positioning sites around the chicken adult beta-globin gene may encode regularly spaced chromatin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Codon usage and tRNA content in unicellular and multicellular organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Structural features in eukaryotic mRNAs that modulate the initiation of translation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

TGGA repeats impair nucleosome formation.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

Periodicities of 10-11bp as indicators of the supercoiled state of genomic DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

Evidence for nucleosome depletion at active regulatory regions genome-wide

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

A single determinant dominates the rate of yeast protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

Identification and distinct regulation of yeast TATA box-containing genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

[Statistical analysis of nucleosome formation sites]

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Highly expressed genes in yeast evolve slowly.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Evolutionary footprints of nucleosome positions in yeast

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570795

Exonic Splicing Regulatory Elements Skew Synonymous Codon Usage near Intron-exon Boundaries in Mammals

31 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1000250

Distribution of rare triplets along mRNA and their relation to protein folding

21 January 2018

1 reference

12 December 2020

Selection conflicts, gene expression, and codon usage trends in yeast

1 reference

12 December 2020

Nucleosome positions predicted through comparative genomics

1 reference

12 December 2020

Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation

1 reference

12 December 2020

Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast

1 reference

12 December 2020

10.1371/JOURNAL.PGEN.1000250

Identifiers

DOI

1 reference

26 July 2017

1 reference

26 July 2017

1 reference

PubMed ID

18989456