A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus

[1]  Anton J. Enright,et al.  Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci , 2018, Genome Biology.

[2]  John L Rinn,et al.  Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging: SNP-CLING , 2017, Nature Structural & Molecular Biology.

[3]  Daniel S. Day,et al.  YY1 Is a Structural Regulator of Enhancer-Promoter Loops , 2017, Cell.

[4]  Leonardo Beccari,et al.  The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes , 2017, bioRxiv.

[5]  Erez Lieberman Aiden,et al.  A Cell type-specific Class of Chromatin Loops Anchored at Large DNA Methylation Nadirs , 2017, bioRxiv.

[6]  Jennifer E. Phillips-Cremins,et al.  Crossed wires: 3D genome misfolding in human disease , 2017, The Journal of cell biology.

[7]  Chris Berdik.  Bladder cancer: 4 big questions , 2017, Nature.

[8]  Bing Ren,et al.  The Three-Dimensional Organization of Mammalian Genomes. , 2017, Annual review of cell and developmental biology.

[9]  Erez Lieberman Aiden,et al.  Cohesin Loss Eliminates All Loop Domains , 2017, Cell.

[10]  Nuno A. Fonseca,et al.  Two independent modes of chromatin organization revealed by cohesin removal , 2017, Nature.

[11]  Yijun Ruan,et al.  Evolutionarily Conserved Principles Predict 3D Chromatin Organization. , 2017, Molecular cell.

[12]  F. Pauler,et al.  Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression , 2017, eLife.

[13]  Sébastien Phan,et al.  ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells , 2017, Science.

[14]  William Stafford Noble,et al.  Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome , 2017, Nature Communications.

[15]  Job Dekker,et al.  Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. , 2017, Methods.

[16]  Jennifer E. Phillips-Cremins,et al.  YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment , 2017, Genome research.

[17]  L. Mirny,et al.  Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization , 2017, Cell.

[18]  Jeannie T. Lee,et al.  The X chromosome in space , 2017, Nature Reviews Genetics.

[19]  Edith Heard,et al.  Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation , 2017, Nature Structural &Molecular Biology.

[20]  Z. Kutalik,et al.  cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture. , 2017, Cell reports.

[21]  James Taylor,et al.  Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes. , 2017, Cell reports.

[22]  G. Stein,et al.  The connection between BRG1, CTCF and topoisomerases at TAD boundaries , 2017, Nucleus.

[23]  Jesse M. Engreitz,et al.  Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression , 2016, Nature Reviews Molecular Cell Biology.

[24]  S. Mundlos,et al.  Formation of new chromatin domains determines pathogenicity of genomic duplications , 2016, Nature.

[25]  Michael D. Wilson,et al.  Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders , 2016, Genome Biology.

[26]  Job Dekker,et al.  SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells , 2016, Genome research.

[27]  Howard Y. Chang,et al.  Structural organization of the inactive X chromosome in the mouse , 2016, Nature.

[28]  Neva C. Durand,et al.  Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture , 2016, Proceedings of the National Academy of Sciences.

[29]  James T. Robinson,et al.  Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. , 2016, Cell systems.

[30]  Neva C. Durand,et al.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.

[31]  J. Rinn,et al.  "Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription. , 2016, Molecular cell.

[32]  Jesse R. Dixon,et al.  Chromatin Domains: The Unit of Chromosome Organization. , 2016, Molecular cell.

[33]  L. Mirny,et al.  Formation of Chromosomal Domains in Interphase by Loop Extrusion , 2015, bioRxiv.

[34]  Chinmay J. Shukla,et al.  Function and evolution of local repeats in the Firre locus , 2016, Nature Communications.

[35]  Anton Goloborodko,et al.  Compaction and segregation of sister chromatids via active loop extrusion , 2016, bioRxiv.

[36]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[37]  Peter H. L. Krijger,et al.  CTCF Binding Polarity Determines Chromatin Looping. , 2015, Molecular cell.

[38]  S. Hadjur,et al.  Genetic Tailors: CTCF and Cohesin Shape the Genome During Evolution. , 2015, Trends in genetics : TIG.

[39]  Neva C. Durand,et al.  Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes , 2015, Proceedings of the National Academy of Sciences.

[40]  Judith B. Zaugg,et al.  Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions , 2015, Cell.

[41]  Michael Q. Zhang,et al.  CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function , 2015, Cell.

[42]  William Stafford Noble,et al.  Bipartite structure of the inactive mouse X chromosome , 2015, Genome Biology.

[43]  J. Rinn,et al.  Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display , 2015, Nature Methods.

[44]  A. Visel,et al.  Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.

[45]  J. Dekker,et al.  Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation , 2015, Nature.

[46]  Pedro P. Rocha,et al.  CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation , 2015, Science.

[47]  D. Odom,et al.  Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture , 2015, Cell reports.

[48]  Jennifer A. Erwin,et al.  Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. , 2015, Molecular cell.

[49]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[50]  Yanli Wang,et al.  Topologically associating domains are stable units of replication-timing regulation , 2014, Nature.

[51]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[52]  Mitchell Guttman,et al.  RNA and dynamic nuclear organization , 2014, Science.

[53]  Meagan E. Sullender,et al.  Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation , 2014, Nature Biotechnology.

[54]  V. Corces,et al.  CTCF: an architectural protein bridging genome topology and function , 2014, Nature Reviews Genetics.

[55]  David R. Kelley,et al.  Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre , 2014, Nature Structural &Molecular Biology.

[56]  Jennifer E. Phillips-Cremins,et al.  Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment , 2013, Cell.

[57]  K. Niakan,et al.  Derivation of extraembryonic endoderm stem (XEN) cells from mouse embryos and embryonic stem cells , 2013, Nature Protocols.

[58]  Job Dekker,et al.  Analysis of long-range chromatin interactions using Chromosome Conformation Capture. , 2012, Methods.

[59]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[60]  Matthew T. Maurano,et al.  Widespread plasticity in CTCF occupancy linked to DNA methylation , 2012, Genome research.

[61]  J. Sedat,et al.  Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.

[62]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[63]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[64]  Martin Renqiang Min,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[65]  Thomas M. Keane,et al.  Mouse genomic variation and its effect on phenotypes and gene regulation , 2011, Nature.

[66]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[67]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[68]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[69]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[70]  V. Corces,et al.  CTCF: Master Weaver of the Genome , 2009, Cell.

[71]  Richard A Young,et al.  Chromatin immunoprecipitation and microarray-based analysis of protein location , 2006, Nature Protocols.

[72]  Wyeth W. Wasserman,et al.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..