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Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells

https://doi.org/10.1016/j.immuni.2018.01.013

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The 69 checked references that resolve

resolves10.1371/journal.pone.0087646

Homeodomain Transcription Factor Meis1 Is a Critical Regulator of Adult Bone Marrow Hematopoiesis

resolves10.1101/gr.160374.113

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

resolves10.1016/j.cell.2007.05.009

High-Resolution Profiling of Histone Methylations in the Human Genome

resolves10.1038/nri1778

From stem cell to T cell: one route or many?

resolves10.1016/j.immuni.2016.08.012

Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region

resolves10.1038/ni.1887

Decision checkpoints in the thymus

resolves10.1016/j.celrep.2014.12.055

Global Reorganization of the Nuclear Landscape in Senescent Cells

resolves10.1038/cr.2012.15

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

resolves10.1007/978-1-59745-406-3_15

Multicolor 3D Fluorescence In Situ Hybridization for Imaging Interphase Chromosomes

resolves10.1016/j.febslet.2015.08.044

Structural and functional diversity of Topologically Associating Domains

resolves10.1101/gad.281964.116

The second decade of 3C technologies: detailed insights into nuclear organization

resolves10.1038/nature11082

Topological domains in mammalian genomes identified by analysis of chromatin interactions

resolves10.1038/nature14222

Chromatin architecture reorganization during stem cell differentiation

resolves10.1016/j.molcel.2016.05.018

Chromatin Domains: The Unit of Chromosome Organization

resolves10.1038/nature21711

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

resolves10.1093/bioinformatics/btr064

FIMO: scanning for occurrences of a given motif

resolves10.1038/msb.2011.28

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

resolves10.1016/j.molcel.2010.05.004

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

resolves10.1016/j.cell.2017.02.007

A Phase Separation Model for Transcriptional Control

resolves10.1016/j.immuni.2016.08.020

Looping around Bcl6 in Germinal Center to Sharpen B Cell Immunity

resolves10.1038/nprot.2008.211

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

resolves10.1126/science.1188995

An Essential Developmental Checkpoint for Production of the T Cell Lineage

resolves10.1038/nmeth.2148

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

resolves10.1101/gr.184986.114

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

resolves10.1016/j.cell.2017.09.001

Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate

resolves10.1016/j.cell.2016.09.037

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

resolves10.1038/nature15740

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

resolves10.1038/ng.2628

Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

resolves10.1016/j.cell.2013.11.039

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

resolves10.1016/j.stem.2016.01.007

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

resolves10.1128/MCB.01915-06

A Two-Step, PU.1-Dependent Mechanism for Developmentally Regulated Chromatin Remodeling and Transcription of the c-fms Gene

resolves10.1038/ni.3514

Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment

resolves10.1038/nmeth.1923

Fast gapped-read alignment with Bowtie 2

resolves10.1126/science.1188989

An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor Bcl11b

resolves10.1126/science.1188063

Reprogramming of T Cells to Natural Killer–Like Cells upon Bcl11b Deletion

resolves10.1182/blood-2012-08-447839

A far downstream enhancer for murine Bcl11b controls its T-cell specific expression

resolves10.1093/bioinformatics/btu747

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data

resolves10.1126/science.1181369

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

resolves10.1038/ni.2432

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

resolves10.1073/pnas.1610617114

Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network

resolves10.1016/j.molimm.2003.08.007

PU.1 as a chromatin accessibility factor for immunoglobulin genes

resolves10.1038/ncomms10069

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

resolves10.1038/nbt.1630

GREAT improves functional interpretation of cis-regulatory regions

resolves10.1016/j.smim.2011.08.004

Factors and networks that underpin early hematopoiesis

resolves10.1038/nmeth.1226

Mapping and quantifying mammalian transcriptomes by RNA-Seq

resolves10.1038/ng.3963

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

resolves10.1093/intimm/dxr078

Transcriptional control of T-cell development

resolves10.1038/nature11049

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

resolves10.1038/ncomms9823

Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2

resolves10.1016/j.cell.2009.06.001

CTCF: Master Weaver of the Genome

resolves10.1038/nprot.2014.006

Full-length RNA-seq from single cells using Smart-seq2

resolves10.1038/ni.3812

MLL4 prepares the enhancer landscape for Foxp3 induction via chromatin looping

resolves10.1016/j.cell.2014.11.021

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

resolves10.1016/j.molcel.2017.08.026

CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression

resolves10.1093/bioinformatics/btp616

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

resolves10.2144/03342mt01

TM4: A Free, Open-Source System for Microarray Data Management and Analysis

resolves10.1016/j.cell.2012.01.010

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

resolves10.1093/nar/gkv1505

TopDom: an efficient and deterministic method for identifying topological domains in genomes

resolves10.1038/ni1115

Long-range intrachromosomal interactions in the T helper type 2 cytokine locus

resolves10.1016/j.immuni.2011.08.007

Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types

resolves10.1038/ni.3456

Tcf1 and Lef1 transcription factors establish CD8+ T cell identity through intrinsic HDAC activity

resolves10.1038/nature01084

SATB1 targets chromatin remodelling to regulate genes over long distances

resolves10.1038/17812

Development of peripheral lymphoid organs and natural killer cells depends on the helix–loop–helix inhibitor Id2

resolves10.1038/nri3702

Developmental gene networks: a triathlon on the course to T cell identity

resolves10.4049/jimmunol.1000679

Fine-Scale Staging of T Cell Lineage Commitment in Adult Mouse Thymus

resolves10.1093/bioinformatics/btp340

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

resolves10.1016/j.cell.2012.01.056

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

resolves10.1016/j.celrep.2015.10.004

Low-Cell-Number Epigenome Profiling Aids the Study of Lens Aging and Hematopoiesis

resolves10.1038/nmeth.2440

Exploring long-range genome interactions using the WashU Epigenome Browser

The 1 reference without a DOI — listed, not checked

no DOI — not checkedTranscription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

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