(Q34583957)

3 August 2017

Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements (English)

1 reference

3 August 2017

1 reference

1 reference

Andrew Bagshaw

2

0 references

Mik Black

object named as

Michael A Black

6

0 references

Neil Gemmell

object named as

Neil Gemmell

7

0 references

Emmanuel Buschiazzo

3

object named as

Emmanuel Buschiazzo

1 reference

3 August 2017

1

Sterling Sawaya

1 reference

3 August 2017

Pankaj Kumar

4

0 references

author name string

Shantanu Chowdhury

5

1 reference

PubMed ID

23405090

3 August 2017

language of work or name

English

0 references

publication date

6 February 2013

1 reference

3 August 2017

1 reference

3 August 2017

8

1 reference

3 August 2017

2

1 reference

3 August 2017

e54710

1 reference

Creative Commons Attribution 4.0 International

3 August 2017

start time

6 February 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Association of Sp1 tandem repeat polymorphism of ALOX5 with coronary artery disease in Indian subjects

1 reference

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A direct characterization of human mutation based on microsatellites

7 July 2018

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Hybrid error correction and de novo assembly of single-molecule sequencing reads

7 July 2018

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Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model

7 July 2018

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Tandem repeat sequence variation as causative cis-eQTLs for protein-coding gene expression variation: the case of CSTB.

7 July 2018

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A regulatory role for repeated decoy transcription factor binding sites in target gene expression

7 July 2018

1 reference

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Whole-genome sequencing reveals a coding non-pathogenic variant tagging a non-coding pathogenic hexanucleotide repeat expansion in C9orf72 as cause of amyotrophic lateral sclerosis

7 July 2018

1 reference

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Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals.

7 July 2018

1 reference

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Repetitive DNA and next-generation sequencing: computational challenges and solutions

7 July 2018

1 reference

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A matter of life or death: how microsatellites emerge in and vanish from the human genome

7 July 2018

1 reference

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BioMart Central Portal: an open database network for the biological community

7 July 2018

1 reference

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CpG islands and the regulation of transcription

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

G4 motifs correlate with promoter-proximal transcriptional pausing in human genes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

The UCSC Genome Browser database: update 2011

7 July 2018

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Variable tandem repeats accelerate evolution of coding and regulatory sequences.

7 July 2018

1 reference

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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

A genomic portrait of human microsatellite variation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

How long is too long? Effects of loop size on G-quadruplex stability

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

GREAT improves functional interpretation of cis-regulatory regions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Conservation of human microsatellites across 450 million years of evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Galaxy: a web-based genome analysis tool for experimentalists

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Tandem repeat polymorphisms: modulators of disease susceptibility and candidates for 'missing heritability'.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

AC and AG dinucleotide repeats in the PAX6 P1 promoter are associated with high myopia.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Genome-wide colonization of gene regulatory elements by G4 DNA motifs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Unstable tandem repeats in promoters confer transcriptional evolvability

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Selection for the G4 DNA motif at the 5' end of human genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

BioMart--biological queries made easy

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

UTR dinucleotide simple sequence repeat evolution exhibits recurring patterns including regulatory sequence motif replacements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Embryonic nervous system genes predominate in searches for dinucleotide simple sequence repeats flanked by conserved sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

A unified approach to false discovery rate estimation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Genome analysis of the platypus reveals unique signatures of evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

The genome-wide determinants of human and chimpanzee microsatellite evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Naturally extended CT . AG repeats increase H-DNA structures and promoter activity in the smooth muscle myosin light chain kinase gene

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

A novel variable number of tandem repeats (VNTR) polymorphism containing Sp1 binding elements in the promoter of XRCC5 is a risk factor for human bladder cancer

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Individual differences in allocation of funds in the dictator game associated with length of the arginine vasopressin 1a receptor RS3 promoter region and correlation between RS3 length and hippocampal mRNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Dynamic mutations as digital genetic modulators of brain development, function and dysfunction.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Z-DNA, an active element in the genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Supercoil-driven DNA structures regulate genetic transactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

An RNA G-quadruplex in the 5' UTR of the NRAS proto-oncogene modulates translation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Timescales of genetic and epigenetic inheritance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

G-quadruplexes in promoters throughout the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

The influence of recombination on human genetic diversity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

The rise, fall and renaissance of microsatellites in eukaryotic genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Galaxy: a platform for interactive large-scale genome analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Dinucleotide repeats negatively modulate the promoter activity of Cyr61 and is unstable in hepatocellular carcinoma patients.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Microsatellites: simple sequences with complex evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Arachidonate 5-lipoxygenase promoter genotype, dietary arachidonic acid, and atherosclerosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Regulation of the major isoform of human endothelin-converting enzyme-1 by a strong housekeeping promoter modulated by polymorphic microsatellites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

A microsatellite repeat in the promoter of the N-methyl-D-aspartate receptor 2A subunit (GRIN2A) gene suppresses transcriptional activity and correlates with chronic outcome in schizophrenia

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Abundant raw material for cis-regulatory evolution in humans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

The human reduced folate carrier gene is regulated by the AP2 and sp1 transcription factor families and a functional 61-base pair polymorphism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

DNA methylation and Z-DNA formation as mediators of quantitative differences in the expression of alleles

7 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

7 July 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

A polypyrimidine/polypurine tract within the Hmga2 minimal promoter: a common feature of many growth-related genes

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Short tandem repeat-based identification of individuals and parents

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Microsatellite polymorphism in the heme oxygenase-1 gene promoter is associated with susceptibility to emphysema

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Evidence for a functional repeat polymorphism in the promoter of the human NRAMP1 gene that correlates with autoimmune versus infectious disease susceptibility

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Modulation of epidermal growth factor receptor gene transcription by a polymorphic dinucleotide repeat in intron 1.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Secondary structures in d(CGG) and d(CCG) repeat tracts

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Triplex-forming oligonucleotides with unexpected affinity for a nontargeted GA repeat sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

Simple repetitive sequences in the genome: structure and functional significance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566118

The effect of a promoter polymorphism on the transcription of nitric oxide synthase 1 and its relevance to Parkinson's disease.

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

Influence of functional variant of neuronal nitric oxide synthase on impulsive behaviors in humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

NOS1 ex1f-VNTR polymorphism influences prefrontal brain oxygenation during a working memory task.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

A promoter-associated polymorphic repeat modulates PAX-6 expression in human brain.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

Microsatellite polymorphism in promoter of heme oxygenase-1 gene is associated with susceptibility to coronary artery disease in type 2 diabetic patients

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

Variation in dinucleotide (GT) repeat sequence in the first exon of the STAT6 gene is associated with atopic asthma and differentially regulates the promoter activity in vitro

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5'-UTR region

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

Trinucleotide repeat variants in the promoter of the thiopurine S-methyltransferase gene of patients exhibiting ultra-high enzyme activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

Guanine quadruplex DNA structure restricts methylation of CpG dinucleotides genome-wide.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

Recombinant Human DNA (Cytosine-5) Methyltransferase

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

SciRoKo: a new tool for whole genome microsatellite search and investigation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

The Relationship Between Microsatellite Polymorphism and Recombination Hot Spots in the Human Genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0054710

RNA quadruplex-based modulation of gene expression

21 January 2018

1 reference

12 December 2020

Transcriptional regulation of the human type I collagen alpha2 (COL1A2) gene by the combination of two dinucleotide repeats

1 reference

12 December 2020

Influence of a GT repeat element on shear stress responsiveness of the VWF gene promoter

1 reference

12 December 2020

CA-Repeat Polymorphism in Intron 1 of HSD11B2

1 reference

12 December 2020

A CT repeat in the promoter of the chicken malic enzyme gene is essential for function at an alternative transcription start site

1 reference

12 December 2020

Association between a polymorphism in the promoter of a glutamate receptor subunit gene (GRIN2A) and alcoholism

1 reference

12 December 2020

Shortened microsatellite d(CA)21 sequence down-regulates promoter activity of matrix metalloproteinase 9 gene

1 reference

12 December 2020

Indirect selection for mutability

1 reference

12 December 2020

Purification and preliminary characterization of a cardiac Kv1.5 repressor element binding factor

1 reference

12 December 2020

Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0054710

Identifiers

DOI

1 reference

3 August 2017

0 references

1 reference

3 August 2017

1 reference

PubMed ID

23405090