Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. (Q33911793)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16081534%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

title

Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting (English)

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5 January 2020

1 reference

1

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5 January 2020

author name string

Kouji Hayashi

series ordinal

2

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5 January 2020

Takashi Horiuchi

series ordinal

3

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5 January 2020

Takehiko Kobayashi

series ordinal

4

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5 January 2020

language of work or name

English

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publication date

4 August 2005

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16081534%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

5 January 2020

published in

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5 January 2020

volume

102

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5 January 2020

issue

33

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5 January 2020

page(s)

11787-11792

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16081534%20AND%20SRC:MED&resulttype=core&format=json

rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication.

5 January 2020

cites work

1 reference

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The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae

5 July 2018

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Eukaryotic regulatory element conservation analysis and identification using comparative genomics

5 July 2018

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The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork

5 July 2018

1 reference

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Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs).

5 July 2018

1 reference

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Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

5 July 2018

1 reference

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Sequencing and comparison of yeast species to identify genes and regulatory elements

5 July 2018

1 reference

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Yeast RNA polymerase I enhancer is dispensable for transcription of the chromosomal rRNA gene and cell growth, and its apparent transcription enhancement from ectopic promoters requires Fob1 protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Identification of DNA cis elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiae

5 July 2018

1 reference

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Chromosomal addresses of the cohesin component Mcd1p

5 July 2018

1 reference

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Conserved noncoding sequences are reliable guides to regulatory elements.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Ribosomal DNA replication fork barrier and HOT1 recombination hot spot: shared sequences but independent activities

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Extraordinary ribosomal spacer length heterogeneity in a neotyphodium endophyte hybrid: implications for concerted evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Transcriptional silencing of Ty1 elements in the RDN1 locus of 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=1182552

An unusual form of transcriptional silencing in yeast ribosomal 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=1182552

A possible role for the yeast TATA-element-binding protein in DNA replication

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

cis-acting components in the replication origin from ribosomal DNA of 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=1182552

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Transcription termination of RNA polymerase I due to a T-rich element interacting with Reb1p

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Structure and function of the nontranscribed spacer regions of yeast rDNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Regular distribution of length heterogeneities within non-transcribed spacer regions of cloned and genomic rDNA of 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=1182552

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Connections between transcriptional activators, silencers, and telomeres as revealed by functional analysis of a yeast DNA-binding protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Properties of promoters cloned randomly from 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=1182552

Linker scanning of the yeast RNA polymerase I promoter

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Proteins that bind to the yeast rDNA enhancer

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Mapping replication origins in yeast chromosomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Topography of transcription factor complexes on the Saccharomyces cerevisiae 5 S RNA gene

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

The arrest of replication forks in the rDNA of yeast occurs independently of 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=1182552

Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Nucleotide sequence of an RNA polymerase binding site from the DNA of bacteriophage fd

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1182552

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504905102

The major promoter element of rRNA transcription in yeast lies 2 kb upstream

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504905102

Transcription-mediated hyper-recombination in HOT1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504905102

SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504905102

Apparent recombination or gene conversion in the ribosomal ITS region of a Flammulina (Fungi, Agaricales) hybrid.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504905102

Site-specific in vivo cleavages by DNA topoisomerase I in the regulatory regions of the 35 S rRNA in Saccharomyces cerevisiae are transcription independent

21 January 2018

1 reference

12 December 2020

1 reference

12 December 2020

Phylogenetic relationships among yeasts of the ? complex? determined from multigene sequence analyses

1 reference

12 December 2020

Enhancers and ribosomal gene spacers

1 reference

12 December 2020

Recombination-stimulating sequences in yeast ribosomal DNA correspond to sequences regulating transcription by RNA polymerase I

1 reference

12 December 2020

Transcription of the 5 S rRNA gene of Saccharomyces cerevisiae requires a promoter element at +1 and a 14-base pair internal control region

1 reference

12 December 2020

A yeast ribosomal DNA-binding protein that binds to the rDNA enhancer and also close to the site of Pol I transcription initiation is not important for enhancer functioning

1 reference

12 December 2020

Identification of a site required for DNA replication fork blocking activity in the rRNA gene cluster in Saccharomyces cerevisiae

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0504905102

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16081534%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16081534%20AND%20SRC:MED&resulttype=core&format=json

5 January 2020

1 reference