(Q33840711)

English

Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate

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scholarly article

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Europe PubMed Central

PubMed publication ID

29 July 2017

Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate (English)

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

DNA methylation

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1 reference

based on heuristic

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author name string

Trees-Juen Chuang

1

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Tai-Wei Chiang

2

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

publication date

12 June 2014

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Europe PubMed Central

PubMed publication ID

29 July 2017

Genome Biology and Evolution

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Europe PubMed Central

PubMed publication ID

29 July 2017

6

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

6

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

1530-1541

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

MicroRNA-mediated regulation of target genes in several brain regions is correlated to both microRNA-targeting-specific promoter methylation and differential microRNA expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

The impact of trans-regulation on the evolutionary rates of metazoan proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

An integrated encyclopedia of DNA elements in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Functions of DNA methylation: islands, start sites, gene bodies and beyond

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

What are the determinants of gene expression levels and breadths in the human genome?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Regulatory mechanisms and networks couple the different phases of gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

A comparative analysis of DNA methylation across human embryonic stem cell lines

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Biological functions of methyl-CpG-binding proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

The honey bee epigenomes: differential methylation of brain DNA in queens and workers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Combinatorial regulation of transcription factors and microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Functional conservation of DNA methylation in the pea aphid and the honeybee

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Expression breadth and expression abundance behave differently in correlations with evolutionary rates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Conserved role of intragenic DNA methylation in regulating alternative promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Protein evolution in yeast transcription factor subnetworks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Conservation and divergence of methylation patterning in plants and animals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Genome-wide evolutionary analysis of eukaryotic DNA methylation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Gene family size conservation is a good indicator of evolutionary rates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Dynamic changes in the human methylome during differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Comparing models of evolution for ordered and disordered proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Human DNA methylomes at base resolution show widespread epigenomic differences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

The relationship between the evolution of microRNA targets and the length of their UTRs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Integrated assessment of genomic correlates of protein evolutionary rate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

DNA methylation and methyl-CpG binding proteins: developmental requirements and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Developmental programming of CpG island methylation profiles in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

A census of human transcription factors: function, expression and evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

MicroRNAs: target recognition and regulatory functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Most mammalian mRNAs are conserved targets of microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Analysis of regulatory network topology reveals functionally distinct classes of microRNAs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Genome-scale DNA methylation maps of pluripotent and differentiated cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Contact density affects protein evolutionary rate from bacteria to animals.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

A macaque's-eye view of human insertions and deletions: differences in mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Global and local architecture of the mammalian microRNA-transcription factor regulatory network.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Gene body-specific methylation on the active X chromosome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Proportion of solvent-exposed amino acids in a protein and rate of protein evolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

MicroRNAs preferentially target the genes with high transcriptional regulation complexity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Structural determinants of the rate of protein evolution in yeast.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Canalization of development by microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

SCRATCH: a protein structure and structural feature prediction server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Intron size and exon evolution in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Alternative splicing of Bcl-2-related genes: functional consequences and potential therapeutic applications.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Epigenetics in human disease and prospects for epigenetic therapy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

MicroRNAs: genomics, biogenesis, mechanism, and function

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

The history of cancer epigenetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

An evolutionary approach reveals a high protein-coding capacity of the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Epigenetic reprogramming in mammalian development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

The role of DNA methylation in mammalian epigenetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Transcription of IAP endogenous retroviruses is constrained by cytosine methylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

X-chromosome inactivation in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Role for DNA methylation in genomic imprinting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

5-Methylcytosine in eukaryotic DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

Variable patterns of total DNA and rDNA methylation in animals.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4080426

5 July 2018

The role of disorder in interaction networks: a structural analysis

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

Evolution of protein-coding genes in Drosophila.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

Impact of extracellularity on the evolutionary rate of mammalian proteins

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

The evolution of invertebrate gene body methylation

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

DNA methylation represses transcription in vivo.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

Factors that contribute to variation in evolutionary rate among Arabidopsis genes

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU124

21 January 2018

Understanding relationship between sequence and functional evolution in yeast proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/24923326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural determinants of protein evolution are context-sensitive at the residue level

1 reference

https://pubmed.ncbi.nlm.nih.gov/24923326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/24923326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Assessing the determinants of evolutionary rates in the presence of noise

1 reference

https://pubmed.ncbi.nlm.nih.gov/24923326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/GBE/EVU124

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

ResearchGate publication ID

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