(Q24674136)

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Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters

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Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters (English)

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author name string

Chuhu Yang

1

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Eugene Bolotin

2

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Tao Jiang

3

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Frances M Sladek

4

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Ernest Martinez

5

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language of work or name

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publication date

1 March 2007

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389

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1

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52-65

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A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Comprehensive analysis of the base composition around the transcription start site in Metazoa

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Identifying biological themes within lists of genes with EASE

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Identification and characterization of the potential promoter regions of 1031 kinds of human genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

CpG islands in vertebrate genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Functional characterization of core promoter elements: DPE-specific transcription requires the protein kinase CK2 and the PC4 coactivator

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

Molecular genetics of the RNA polymerase II general transcriptional machinery

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

7 April 2017

A high-resolution map of transcription in the yeast genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

10 May 2017

Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Rate of promoter class turn-over in yeast evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

A core promoter element downstream of the TATA box that is recognized by TFIIB.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Genome-scale identification of nucleosome positions in S. cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Synergy of human Pol II core promoter elements revealed by statistical sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Clustering of DNA sequences in human promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

The MTE, a new core promoter element for transcription by RNA polymerase II.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Structure and mechanism of the RNA polymerase II transcription machinery

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

The RNA polymerase II core promoter

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Identification and functional analysis of human transcriptional promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Distribution and characterization of regulatory 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=1955227

28 September 2017

Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA) small middle dotpoly(dT) tracts in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Role of general and gene-specific cofactors in the regulation of eukaryotic transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Accurate positioning of RNA polymerase II on a natural TATA-less promoter is independent of TATA-binding-protein-associated factors and initiator-binding proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

The yeast genome project: what did we learn?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Experimentally determined weight matrix definitions of the initiator and TBP binding site elements of promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Core promoter-specific function of a mutant transcription factor TFIID defective in TATA-box binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

DNA sequence requirements for transcriptional initiator activity in mammalian cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

TATA-binding protein-associated factor(s) in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Yeast mRNA initiation sites are determined primarily by specific sequences, not by the distance from the TATA element

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Each of three "TATA elements" specifies a subset of the transcription initiation sites at the CYC-1 promoter of Saccharomyces cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Functional binding of the "TATA" box binding component of transcription factor TFIID to the -30 region of TATA-less promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 September 2017

Functional characterization of core promoter elements: the downstream core element is recognized by TAF1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

30 May 2018

Mechanism of initiator-mediated transcription: evidence for a functional interaction between the TATA-binding protein and DNA in the absence of a specific recognition sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

30 May 2018

Two alternative pathways of transcription initiation in the yeast negative regulatory gene GAL80.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

30 May 2018

CpG islands as gene markers 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=1955227

30 May 2018

Roles of TATA and initiator elements in determining the start site location and direction of RNA polymerase II transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

19 June 2018

Evidence for nucleosome depletion at active regulatory regions genome-wide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 November 2018

Content analysis of the core promoter region of human genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 November 2018

Identification and distinct regulation of yeast TATA box-containing genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 November 2018

Composition-sensitive analysis of the human genome for regulatory signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 November 2018

A basal transcription factor that activates or represses transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1955227

28 November 2018

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/17123746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Role of core promoter structure in assembly of the RNA polymerase II preinitiation complex. A common pathway for formation of preinitiation intermediates at many TATA and TATA-less promoters

1 reference

https://pubmed.ncbi.nlm.nih.gov/17123746

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural basis of core promoter recognition in a primitive eukaryote

1 reference

https://api.crossref.org/works/10.1016%2FJ.GENE.2006.09.029

7 January 2021

based on heuristic

inferred from DOI database lookup

Quantitative analysis of in vivo initiator selection by yeast RNA polymerase II supports a scanning model

1 reference

https://api.crossref.org/works/10.1016%2FJ.GENE.2006.09.029

7 January 2021

based on heuristic

inferred from DOI database lookup

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.GENE.2006.09.029

7 January 2021

based on heuristic

inferred from DOI database lookup

Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes

1 reference

https://api.crossref.org/works/10.1016%2FJ.GENE.2006.09.029

7 January 2021

based on heuristic

inferred from DOI database lookup

The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters

1 reference

https://api.crossref.org/works/10.1016%2FJ.GENE.2006.09.029

7 January 2021

based on heuristic

inferred from DOI database lookup

Computational analysis of core promoters in the Drosophila genome

1 reference

https://api.crossref.org/works/10.1016%2FJ.GENE.2006.09.029

7 January 2021

based on heuristic

inferred from DOI database lookup

1 reference

https://api.crossref.org/works/10.1016%2FJ.GENE.2006.09.029

7 January 2021

based on heuristic

inferred from DOI database lookup

Identifiers

10.1016/J.GENE.2006.09.029

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

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