Bipartite structure of the inactive mouse X chromosome (Q35964734)

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21 February 2020

title

Bipartite structure of the inactive mouse X chromosome (English)

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2

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Ferhat Ay

6

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21 February 2020

9

Jay Shendure

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12

Christine M Disteche

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21 February 2020

author name string

Xinxian Deng

1

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21 February 2020

Vijay Ramani

3

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21 February 2020

Andrew Hill

4

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21 February 2020

Fan Yang

5

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21 February 2020

Joel B Berletch

7

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21 February 2020

Carl Anthony Blau

8

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21 February 2020

Zhijun Duan

10

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21 February 2020

William S Noble

11

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21 February 2020

publication date

7 August 2015

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21 February 2020

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21 February 2020

volume

16

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page(s)

152

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Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

21 February 2020

cites work

1 reference

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The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse

2 October 2017

1 reference

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Systematic discovery of Xist RNA binding proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Escape from X inactivation varies in mouse tissues

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF.

2 October 2017

1 reference

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A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

2 October 2017

1 reference

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Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes

2 October 2017

1 reference

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RNA Function. RNA and dynamic nuclear organization

2 October 2017

1 reference

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Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation.

2 October 2017

1 reference

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A statistical approach for inferring the 3D structure of the genome

2 October 2017

1 reference

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Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

X chromosome regulation: diverse patterns in development, tissues and disease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Nucleolus and nuclear periphery: velcro for heterochromatin.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

RefSeq: an update on mammalian reference sequences

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The spatial organization of the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The hierarchy of the 3D genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Spatial partitioning of the regulatory landscape of the X-inactivation centre

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Topological domains in mammalian genomes identified by analysis of chromatin interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Mammalian genomic imprinting.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Characterization of DXZ4 conservation in primates implies important functional roles for CTCF binding, array expression and tandem repeat organization on the X chromosome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

FIMO: scanning for occurrences of a given motif

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

A three-dimensional model of the yeast genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Global survey of escape from X inactivation by RNA-sequencing in mouse

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Initial genomics of the human nucleolus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Fast and accurate long-read alignment with Burrows-Wheeler transform

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar satellite during accelerated nucleoprotein synthesis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The ins and outs of gene regulation and chromosome territory organisation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Dosage compensation in mammals: fine-tuning the expression of the X chromosome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Gene action in the X-chromosome of the mouse (Mus musculus L.)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The human genome browser at UCSC

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Human acrocentric chromosomes with transcriptionally silent nucleolar organizer regions associate with nucleoli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

New data on the in-situ position of the inactive X chromosome in the interphase nucleus of human fibroblasts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

The Barr body is a looped X chromosome formed by telomere association

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Interaction between transcription regulatory regions of prolactin chromatin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Role of the Xist Gene in X Chromosome Choosing

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

Escape from X inactivation of Smcx is preceded by silencing during mouse development

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4539712

On the implementation of an interior-point filter line-search algorithm for large-scale nonlinear programming

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/S13059-015-0728-8

High-resolution organization of mouse centromeric and pericentromeric DNA

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26248554

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The distinguishing sequence characteristics of mouse imprinted genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26248554

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-015-0728-8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26248554 AND SRC:MED&resulttype=core&format=json

Dimensions Publication ID

21 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26248554 AND SRC:MED&resulttype=core&format=json

21 February 2020

PubMed publication ID

26248554

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26248554 AND SRC:MED&resulttype=core&format=json