(Q40174771)

English

Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

scientific article published on 18 February 2015

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins (English)

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

1 reference

based on heuristic

inferred from title

author name string

Michael S Foulk

1

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

John M Urban

2

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Cinzia Casella

3

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Susan A Gerbi

4

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

publication date

18 February 2015

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

Genome Research

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

25

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

5

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

725-735

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

The hunt for origins of DNA replication in multicellular eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

G4 motifs affect origin positioning and efficiency in two vertebrate replicators

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Human origin recognition complex binds preferentially to G-quadruplex-preferable RNA and single-stranded DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

DNA replication origins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Genome-wide identification and characterization of replication origins by deep sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Human telomeres replicate using chromosome-specific, rather than universal, replication programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Fast gapped-read alignment with Bowtie 2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Targeting MYC Expression through G-Quadruplexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Eukaryotic DNA replication origins: many choices for appropriate answers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Evaluating genome-scale approaches to eukaryotic DNA replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Structure, location and interactions of G‐quadruplexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Conserved nucleosome positioning defines replication origins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

BEDTools: a flexible suite of utilities for comparing genomic features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Lambda exonuclease digestion of CGG trinucleotide repeats.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Transcription initiation activity sets replication origin efficiency in mammalian cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Model-based analysis of ChIP-Seq (MACS)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Prevalence of quadruplexes 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=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

The UCSC Table Browser data retrieval tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Sequence-dependent pausing of single lambda exonuclease molecules.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): stability, heat, and hydration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Activity of the c-myc replicator at an ectopic chromosomal location

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

An exonuclease induced by bacteriophage lambda. II. Nature of the enzymatic reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

22 September 2017

Nucleosome positioning can affect the function of a cis-acting DNA element in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

25 September 2017

Intrinsic coupling of lagging-strand synthesis to chromatin assembly.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

15 June 2018

New insights into replication origin characteristics in metazoans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

15 June 2018

An exonuclease I hydrolysis assay for evaluating G-quadruplex stabilization by small molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

15 June 2018

QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

15 June 2018

Replication initiation point mapping

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

15 June 2018

Stable G-quadruplexes are found outside nucleosome-bound regions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

20 August 2018

Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

20 August 2018

Nucleosomes positioned by ORC facilitate the initiation of DNA replication.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

20 August 2018

Initiation of DNA replication at CpG islands in mammalian chromosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417120

20 August 2018

Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals

1 reference

https://pubmed.ncbi.nlm.nih.gov/25695952

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Regulation of lambda exonuclease. I. Properties of lambda exonuclease purified from lysogens of lambda T11 and wild type

1 reference

https://pubmed.ncbi.nlm.nih.gov/25695952

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Next-generation sequencing of Okazaki fragments extracted from Saccharomyces cerevisiae

1 reference

https://pubmed.ncbi.nlm.nih.gov/25695952

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1101/GR.183848.114

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 September 2017

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