Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription (Q33984507)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25085421%20AND%20SRC:MED&resulttype=core&format=json

11 March 2020

title

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription (English)

1 reference

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11 March 2020

10

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11 March 2020

Sebastian Maerkl

11

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11 March 2020

David Shore

13

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11 March 2020

author name string

Britta Knight

1

1 reference

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11 March 2020

Slawomir Kubik

2

1 reference

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11 March 2020

Bhaswar Ghosh

3

1 reference

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11 March 2020

Maria Jessica Bruzzone

4

1 reference

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11 March 2020

Marcel Geertz

5

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11 March 2020

Victoria Martin

6

1 reference

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11 March 2020

Nicolas Dénervaud

7

1 reference

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11 March 2020

Philippe Jacquet

8

1 reference

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11 March 2020

Burak Ozkan

9

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11 March 2020

Félix Naef

12

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11 March 2020

publication date

1 August 2014

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11 March 2020

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11 March 2020

volume

28

1 reference

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11 March 2020

issue

15

1 reference

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11 March 2020

page(s)

1695-1709

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Integration of multiple nutrient cues and regulation of lifespan by ribosomal transcription factor Ifh1

11 March 2020

cites work

1 reference

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A chemostat array enables the spatio-temporal analysis of the yeast proteome

5 July 2018

1 reference

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Gcn5 and sirtuins regulate acetylation of the ribosomal protein transcription factor Ifh1

5 July 2018

1 reference

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Mapping the fine structure of a eukaryotic promoter input-output function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The evolutionary rewiring of the ribosomal protein transcription pathway modifies the interaction of transcription factor heteromer Ifh1-Fhl1 (interacts with forkhead 1-forkhead-like 1) with the DNA-binding specificity element

5 July 2018

1 reference

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Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

5 July 2018

1 reference

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Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function

5 July 2018

1 reference

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Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

5 July 2018

1 reference

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A high-throughput microfluidic method for generating and characterizing transcription factor mutant libraries

5 July 2018

1 reference

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Epigenome characterization at single base-pair resolution.

5 July 2018

1 reference

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Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

DNA-end capping by the budding yeast transcription factor and subtelomeric binding protein Tbf1

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Transcription of functionally related constitutive genes is not coordinated.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Sequential Recruitment of SAGA and TFIID in a Genomic Response to DNA Damage in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The role of nucleosome positioning in the evolution of gene regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Evolutionary tinkering with conserved components of a transcriptional regulatory network

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

An auxin-based degron system for the rapid depletion of proteins in nonplant cells.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Distinguishing direct versus indirect transcription factor-DNA interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

From DNA sequence to transcriptional behaviour: a quantitative approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Precise regulation of gene expression dynamics favors complex promoter architectures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

High-resolution DNA-binding specificity analysis of yeast transcription factors

5 July 2018

1 reference

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A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The DNA-encoded nucleosome organization of a eukaryotic genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Stress-activated genomic expression changes serve a preparative role for impending stress in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Design of compact, universal DNA microarrays for protein binding microarray experiments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Two strategies for gene regulation by promoter nucleosomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Transcription factor substitution during the evolution of fungal ribosome regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Potential interface between ribosomal protein production and pre-rRNA processing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

MEME: discovering and analyzing DNA and protein sequence motifs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Fine-structure analysis of ribosomal protein gene transcription

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The TOR signalling network from yeast to man.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains.

5 July 2018

1 reference

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Global position and recruitment of HATs and HDACs in the yeast genome.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Transcriptional regulatory code of a eukaryotic genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Control of stochasticity in eukaryotic gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The tor pathway regulates gene expression by linking nutrient sensing to histone acetylation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Transcriptional regulatory networks in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

In vivo topography of Rap1p-DNA complex at Saccharomyces cerevisiae TEF2 UAS(RPG) during transcriptional regulation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

A comprehensive two-hybrid analysis to explore the yeast protein interactome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The economics of ribosome biosynthesis in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Transcription activation of yeast ribosomal protein genes requires additional elements apart from binding sites for Abf1p or Rap1p

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

Chromatin structure snap-shots: rapid nuclease digestion of chromatin in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4117944

MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor–DNA Interaction

5 July 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25085421

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

How the multifunctional yeast Rap1p discriminates between DNA target sites: a crystallographic analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25085421

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GAD.244434.114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25085421%20AND%20SRC:MED&resulttype=core&format=json

11 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25085421%20AND%20SRC:MED&resulttype=core&format=json

11 March 2020

PubMed publication ID

25085421

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25085421%20AND%20SRC:MED&resulttype=core&format=json