Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline (Q33657704)

28 July 2017

title

Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline (English)

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28 July 2017

8

Tina Graves

0 references

Evan E. Eichler

7

object named as

Evan E Eichler

1 reference

28 July 2017

Nicholas Stong

1

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28 July 2017

Zhong Deng

2

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28 July 2017

Ravi Gupta

3

1 reference

28 July 2017

Sufen Hu

4

1 reference

28 July 2017

Shiela Paul

5

1 reference

28 July 2017

Amber K Weiner

6

1 reference

28 July 2017

Catrina C Fronick

9

1 reference

28 July 2017

Laura Courtney

10

1 reference

28 July 2017

Richard K Wilson

11

1 reference

28 July 2017

Paul M Lieberman

12

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28 July 2017

Ramana V Davuluri

13

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28 July 2017

Harold Riethman

14

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28 July 2017

publication date

27 March 2014

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28 July 2017

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28 July 2017

volume

24

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28 July 2017

issue

6

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28 July 2017

page(s)

1039-1050

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describes a project that uses

28 July 2017

ImageQuant

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11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4032850/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

cites work

SA1 binds directly to DNA through its unique AT-hook to promote sister chromatid cohesion at telomeres

1 reference

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CTCF and cohesin: linking gene regulatory elements with their targets

14 July 2018

1 reference

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A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection.

14 July 2018

1 reference

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

14 July 2018

1 reference

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Widespread plasticity in CTCF occupancy linked to DNA methylation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Telomere length regulates TERRA levels through increased trimethylation of telomeric H3K9 and HP1α.

14 July 2018

1 reference

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Identification of host-chromosome binding sites and candidate gene targets for Kaposi's sarcoma-associated herpesvirus LANA

14 July 2018

1 reference

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Cohesin-SA1 deficiency drives aneuploidy and tumourigenesis in mice due to impaired replication of telomeres

14 July 2018

1 reference

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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

14 July 2018

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14 July 2018

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Cohesin: a critical chromatin organizer in mammalian gene regulation

14 July 2018

1 reference

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Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data

14 July 2018

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A user's guide to the encyclopedia of DNA elements (ENCODE)

14 July 2018

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Human telomeric proteins occupy selective interstitial sites

14 July 2018

1 reference

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The human TTAGGG repeat factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats

14 July 2018

1 reference

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D4Z4 as a prototype of CTCF and lamins-dependent insulator in human cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Cohesin: genomic insights into controlling gene transcription and development

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

A human genome structural variation sequencing resource reveals insights into mutational mechanisms

14 July 2018

1 reference

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A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Mediator and cohesin connect gene expression and chromatin architecture

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Molecular dissection of telomeric repeat-containing RNA biogenesis unveils the presence of distinct and multiple regulatory pathways.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Senescent cells as a source of inflammatory factors for tumor progression

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Linking functional decline of telomeres, mitochondria and stem cells during ageing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

BEDTools: a flexible suite of utilities for comparing genomic features

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

The senescence-associated secretory phenotype: the dark side of tumor suppression

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Does CTCF mediate between nuclear organization and gene expression?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

CpG-island promoters drive transcription of human telomeres

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Identification of a perinuclear positioning element in human subtelomeres that requires A-type lamins and CTCF.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

CTCF: master weaver of the genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

MLL associates with telomeres and regulates telomeric repeat-containing RNA transcription

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

SHRiMP: accurate mapping of short color-space reads

14 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Fast and accurate short read alignment with Burrows-Wheeler transform

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

The D4Z4 macrosatellite repeat acts as a CTCF and A-type lamins-dependent insulator in facio-scapulo-humeral dystrophy.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Design and analysis of ChIP-seq experiments for DNA-binding proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Chromatin insulators: regulatory mechanisms and epigenetic inheritance

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Model-based analysis of ChIP-Seq (MACS)

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

How shelterin protects mammalian telomeres

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

CTCF physically links cohesin to chromatin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Human telomere structure and biology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Mapping and sequencing of structural variation from eight human genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Cohesins functionally associate with CTCF on mammalian chromosome arms

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Cohesin mediates transcriptional insulation by CCCTC-binding factor

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Cohesins localize with CTCF at the KSHV latency control region and at cellular c-myc and H19/Igf2 insulators

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Human subtelomeric WASH genes encode a new subclass of the WASP family

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Specific sequence variations within the 4q35 region are associated with facioscapulohumeral muscular dystrophy

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Human subtelomeric duplicon structure and organization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Spreading of mammalian DNA-damage response factors studied by ChIP-chip at damaged telomeres

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Elevated rates of sister chromatid exchange at chromosome ends

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

At the heart of the chromosome: SMC proteins in action

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Structural stability and chromosome-specific telomere length is governed by cis-acting determinants in humans.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

The structure and function of SMC and kleisin complexes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Cell cycle regulation of chromatin at an origin of DNA replication

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Finishing the euchromatic sequence of the human genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Does a sentinel or a subset of short telomeres determine replicative senescence?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Mapping and initial analysis of human subtelomeric sequence assemblies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Telomere Repeat Binding Factors TRF1, TRF2, and hRAP1 Modulate Replication of Epstein-Barr Virus OriP

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

The pattern of chromosome-specific variations in telomere length in humans is determined by inherited, telomere-near factors and is maintained throughout life

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Segmental polymorphisms in the proterminal regions of a subset of human chromosomes

14 July 2018

1 reference

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The human genome browser at UCSC

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

THE COMPLEX STRUCTURE AND DYNAMIC EVOLUTION OF HUMAN SUBTELOMERES

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Spidey: a tool for mRNA-to-genomic alignments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Transcriptional activity of multiple copies of a subtelomerically located olfactory receptor gene that is polymorphic in number and location

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Tandem repeats finder: a program to analyze DNA sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Mechanisms underlying telomere repeat turnover, revealed by hypervariable variant repeat distribution patterns in the human Xp/Yp telomere

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

The telomeric 60 kb of chromosome arm 4p is homologous to telomeric regions on 13p, 15p, 21p, and 22p.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Differential regulation of telomere and centromere cohesion by the Scc3 homologues SA1 and SA2, respectively, in human cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Human subtelomeric copy number variations

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Sequence comparison of human and yeast telomeres identifies structurally distinct subtelomeric domains

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4032850

Hypomethylation of subtelomeric regions in ICF syndrome is associated with abnormally short telomeres and enhanced transcription from telomeric regions

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24676094

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Allele-specific relative telomere lengths are inherited

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24676094

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.166983.113

1 reference

28 July 2017

1 reference

28 July 2017

1 reference