(Q30413341)

19 August 2017

Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins (English)

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19 August 2017

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6

Stefan Bekiranov

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author name string

Larry D Mesner

1

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19 August 2017

Veena Valsakumar

2

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19 August 2017

Marcin Cieslik

3

1 reference

19 August 2017

Rebecca Pickin

4

1 reference

19 August 2017

Joyce L Hamlin

5

1 reference

19 August 2017

Stefan Bekiranov

6

1 reference

19 August 2017

16 July 2013

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19 August 2017

1 reference

19 August 2017

23

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19 August 2017

11

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19 August 2017

1774-1788

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describes a project that uses

19 August 2017

GM06990

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cites work

DNA secondary structures: stability and function of G-quadruplex structures

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

20 June 2018

1 reference

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The accessible chromatin landscape of the human genome

20 June 2018

1 reference

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An integrated encyclopedia of DNA elements in the human genome

20 June 2018

1 reference

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Rif1 choreographs DNA replication timing

20 June 2018

1 reference

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Genome-scale identification of active DNA replication origins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs.

20 June 2018

1 reference

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New insights into replication origin characteristics in metazoans

20 June 2018

1 reference

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Genome-wide depletion of replication initiation events in highly transcribed regions

20 June 2018

1 reference

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Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Eukaryotic lagging strand DNA replication employs a multi-pathway mechanism that protects genome integrity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Evaluating genome-scale approaches to eukaryotic DNA replication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Human origin recognition complex is essential for HP1 binding to chromatin and heterochromatin organization.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Fast and accurate short read alignment with Burrows-Wheeler transform

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

An integrated software system for analyzing ChIP-chip and ChIP-seq data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Genome-wide studies highlight indirect links between human replication origins and gene regulation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

A revisionist replicon model for higher eukaryotic genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Replication in context: dynamic regulation of DNA replication patterns in metazoans

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Isolating apparently pure libraries of replication origins from complex genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Prevalence of quadruplexes in the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Promiscuous initiation on mammalian chromosomal DNA templates and its possible suppression by transcription

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Temporal profile of replication of human chromosomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

The mammalian beta globin origin of DNA replication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

The replicon revisited: an old model learns new tricks in metazoan chromosomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Plasticity of DNA replication initiation in Epstein-Barr virus episomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Initiation sites are distributed at frequent intervals in the Chinese hamster dihydrofolate reductase origin of replication but are used with very different efficiencies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Drosophila heterochromatin protein 1 (HP1)/origin recognition complex (ORC) protein is associated with HP1 and ORC and functions in heterochromatin-induced silencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Discrete start sites for DNA synthesis in the yeast ARS1 origin.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Association of the origin recognition complex with heterochromatin and HP1 in higher eukaryotes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Characterizing replication intermediates in the amplified CHO dihydrofolate reductase domain by two novel gel electrophoretic techniques

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Composite patterns in neutral/neutral two-dimensional gels demonstrate inefficient replication origin usage

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

On the mechanism of DNA replication in mammalian chromosomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

The localization of replication origins on ARS plasmids in S. cerevisiae

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Mapping initiation sites of DNA replication in vivo using polymerase chain reaction amplification of nascent strand segments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Isolation of human sequences that replicate autonomously in human cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Single-Step Method of RNA Isolation by Acid Guanidinium Thiocyanate–Phenol–Chloroform Extraction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Multiple origins of replication in the dihydrofolate reductase amplicons of a methotrexate-resistant chinese hamster cell line

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: stabilization and enrichment of replication intermediates by isolation on the nuclear matrix

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Transcription factors and the control of DNA replication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814878

Isolation of restriction fragments containing origins of replication from complex genomes

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1101%2FGR.155218.113

Purification of restriction fragments containing replication intermediates from complex genomes for 2-D gel analysis

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1101%2FGR.155218.113

21 January 2018

Identifiers

DOI

10.1101/GR.155218.113

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

23861383

1 reference