Exonic transcription factor binding directs codon choice and affects protein evolution (Q37668081)

21 August 2017

Exonic transcription factor binding directs codon choice and affects protein evolution (English)

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21 August 2017

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21 August 2017

John Stamatoyannopoulos

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object named as

John A Stamatoyannopoulos

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21 August 2017

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Benjamin Vernot

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21 August 2017

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Joshua M Akey

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21 August 2017

Andrew B Stergachis

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21 August 2017

Anthony Shafer

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21 August 2017

Wenqing Fu

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21 August 2017

Alex Reynolds

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21 August 2017

Anthony Raubitschek

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21 August 2017

Steven Ziegler

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21 August 2017

Emily M LeProust

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21 August 2017

language of work or name

English

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publication date

1 December 2013

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21 August 2017

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21 August 2017

342

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6164

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21 August 2017

1367-1372

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Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

21 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Discovery and characterization of human exonic transcriptional regulatory elements

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

An expansive human regulatory lexicon encoded in transcription factor footprints

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Transcriptional enhancers in protein-coding exons of vertebrate developmental genes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Coding exons function as tissue-specific enhancers of nearby genes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Overlapping codes within protein-coding sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Virus attenuation by genome-scale changes in codon pair bias

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

The genetic code is nearly optimal for allowing additional information within protein-coding sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Increased expression and immunogenicity of sequence-modified human immunodeficiency virus type 1 gag gene

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Codon catalog usage and the genome hypothesis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Codon usage in bacteria: correlation with gene expressivity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

The selection-mutation-drift theory of synonymous codon usage

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Molecular basis of base substitution hotspots in Escherichia coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

A transcriptional regulatory element in the coding sequence of the human Bcl-2 gene.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Transcriptional selectivity of viral genes in mammalian cells

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Gene body-specific methylation on the active X chromosome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Reduced synonymous substitution rate at the start of enterobacterial genes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Codon catalog usage is a genome strategy modulated for gene expressivity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Coevolution of codon usage and transfer RNA abundance

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

The protooncogene c-jun contains an unusual estrogen-inducible enhancer within the coding sequence

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967546

The accessible chromatin landscape of the human genome

1 September 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

BEDOPS: high-performance genomic feature operations

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

A method and server for predicting damaging missense mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Integrating common and rare genetic variation in diverse human populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Systematic localization of common disease-associated variation in regulatory DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Genome-wide association analysis identifies three psoriasis susceptibility loci

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

A map of human genome variation from population-scale sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

MEME SUITE: tools for motif discovery and searching

21 January 2018

1 reference

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WebLogo: A Sequence Logo Generator

21 January 2018

1 reference

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SignalP 4.0: discriminating signal peptides from transmembrane regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Analysis and prediction of leucine-rich nuclear export signals

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Detection of nonneutral substitution rates on mammalian phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Evolution and functional impact of rare coding variation from deep sequencing of human exomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1243490

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24337295

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1126/SCIENCE.1243490

1 reference

21 August 2017

1 reference

21 August 2017

PubMed publication ID

24337295

1 reference