(Q36879698)

16 August 2017

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming (English)

1 reference

16 August 2017

11

Konrad Hochedlinger

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author name string

Jonathan A Beagan

1

1 reference

16 August 2017

Thomas G Gilgenast

2

1 reference

16 August 2017

Jesi Kim

3

1 reference

16 August 2017

Zachary Plona

4

1 reference

16 August 2017

Heidi K Norton

5

1 reference

16 August 2017

Gui Hu

6

1 reference

16 August 2017

Sarah C Hsu

7

1 reference

16 August 2017

Emily J Shields

8

1 reference

16 August 2017

Xiaowen Lyu

9

1 reference

16 August 2017

Effie Apostolou

10

1 reference

16 August 2017

Victor G Corces

12

1 reference

16 August 2017

Job Dekker

13

1 reference

16 August 2017

Jennifer E Phillips-Cremins

14

1 reference

16 August 2017

language of work or name

English

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publication date

1 May 2016

1 reference

16 August 2017

1 reference

16 August 2017

18

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16 August 2017

5

1 reference

16 August 2017

611-624

1 reference

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Early reprogramming regulators identified by prospective isolation and mass cytometry

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Chromatin architecture reorganization during stem cell differentiation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Topologically associating domains are stable units of replication-timing regulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

CellNet: network biology applied to stem cell engineering

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

A high-resolution map of the three-dimensional chromatin interactome in human cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Deterministic direct reprogramming of somatic cells to pluripotency

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

The pluripotent genome in three dimensions is shaped around pluripotency factors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Maturation, not initiation, is the major roadblock during reprogramming toward pluripotency from human fibroblasts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Intrachromosomal looping is required for activation of endogenous pluripotency genes during reprogramming.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Architectural protein subclasses shape 3D organization of genomes during lineage commitment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

A molecular roadmap of reprogramming somatic cells into iPS cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

The long-range interaction landscape of gene promoters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

The transcriptional and epigenomic foundations of ground state pluripotency.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Topological domains in mammalian genomes identified by analysis of chromatin interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

CTCF-mediated functional chromatin interactome in pluripotent cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Reprogramming factor expression initiates widespread targeted chromatin remodeling

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Aligning short sequencing reads with Bowtie

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Mediator and cohesin connect gene expression and chromatin architecture

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Epigenetic memory in induced pluripotent stem cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Direct cell reprogramming is a stochastic process amenable to acceleration

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Determining spatial chromatin organization of large genomic regions using 5C technology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

TopHat: discovering splice junctions with RNA-Seq

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Reprogramming of neural progenitor cells into induced pluripotent stem cells in the absence of exogenous Sox2 expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

The ground state of embryonic stem cell self-renewal

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

Klf4 organizes long-range chromosomal interactions with the oct4 locus in reprogramming and pluripotency.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4859942

10.1016/J.STEM.2016.04.004

4 September 2018

Identifiers

DOI

1 reference

16 August 2017

1 reference

16 August 2017

PubMed publication ID

27152443

1 reference