CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

[1]  K. Abromeit.  Music Received , 2023, Notes.

[2]  J. Banerji,et al.  Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. , 1981, Cell.

[3]  J. Banerji,et al.  Expression of a β-globin gene is enhanced by remote SV40 DNA sequences , 1981, Cell.

[4]  Victor V Lobanenkov,et al.  A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene. , 1990, Oncogene.

[5]  T. Maniatis,et al.  A Striking Organization of a Large Family of Human Neural Cadherin-like Cell Adhesion Genes , 1999, Cell.

[6]  M Dickson,et al.  Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. , 2001, Genome research.

[7]  T. Cremer,et al.  Chromosome territories, nuclear architecture and gene regulation in mammalian cells , 2001, Nature Reviews Genetics.

[8]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[9]  Tom Maniatis,et al.  Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing. , 2002, Molecular cell.

[10]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[11]  Tom Maniatis,et al.  Promoter Choice Determines Splice Site Selection in Protocadherin α and γ Pre-mRNA Splicing , 2002 .

[12]  T. Miikue-Yobe.  Comparative , 2004 .

[13]  Qiang Wu,et al.  Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. , 2003, Genome research.

[14]  Clifford S. Deutschman,et al.  Transcription , 2003, The Quran: Word List (Volume 3).

[15]  Tom Maniatis,et al.  Identification of long-range regulatory elements in the protocadherin-α gene cluster , 2006, Proceedings of the National Academy of Sciences.

[16]  Bosiljka Tasic,et al.  Identification of long-range regulatory elements in the protocadherin-alpha gene cluster. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Michael Q. Zhang,et al.  Statistical significance of cis-regulatory modules. , 2007, BMC bioinformatics.

[18]  N. Galjart,et al.  CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. , 2007, Genes & development.

[19]  Wouter de Laat,et al.  CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. , 2006, Genes & development.

[20]  B. Steensel,et al.  Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) , 2006, Nature Genetics.

[21]  T. Mikkelsen,et al.  Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites , 2007, Proceedings of the National Academy of Sciences.

[22]  G. Felsenfeld,et al.  Critical DNA Binding Interactions of the Insulator Protein CTCF , 2007, Journal of Biological Chemistry.

[23]  Michael Q. Zhang,et al.  Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome , 2007, Cell.

[24]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[25]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[26]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[27]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[28]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[29]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[30]  D. Schreiner,et al.  Combinatorial homophilic interaction between γ-protocadherin multimers greatly expands the molecular diversity of cell adhesion , 2010, Proceedings of the National Academy of Sciences.

[31]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[32]  Xuegong Zhang,et al.  DEGseq: an R package for identifying differentially expressed genes from RNA-seq data , 2010, Bioinform..

[33]  Ryan Dale,et al.  Cell type specificity of chromatin organization mediated by CTCF and cohesin , 2010, Proceedings of the National Academy of Sciences.

[34]  Chee Seng Chan,et al.  CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells , 2011, Nature Genetics.

[35]  T. Maniatis,et al.  Regulatory elements required for the activation and repression of the protocadherin-α gene cluster , 2011, Proceedings of the National Academy of Sciences.

[36]  G. Felsenfeld,et al.  Specific Sites in the C Terminus of CTCF Interact with the SA2 Subunit of the Cohesin Complex and Are Required for Cohesin-Dependent Insulation Activity , 2011, Molecular and Cellular Biology.

[37]  B. Pugh,et al.  Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution , 2011, Cell.

[38]  M. Groudine,et al.  Functional and Mechanistic Diversity of Distal Transcription Enhancers , 2011, Cell.

[39]  R. Kaneko,et al.  Identification of the Cluster Control Region for the Protocadherin-β Genes Located beyond the Protocadherin-γ Cluster* , 2011, The Journal of Biological Chemistry.

[40]  Elzo de Wit,et al.  Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. , 2012, Methods.

[41]  R. Myers,et al.  CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice , 2012, Proceedings of the National Academy of Sciences.

[42]  Tom Maniatis,et al.  PROTOCADHERINS MEDIATE DENDRITIC SELF-AVOIDANCE IN THE MAMMALIAN NERVOUS SYSTEM , 2012, Nature.

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

[44]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[45]  Raymond K. Auerbach,et al.  Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.

[46]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[47]  Michael D. Wilson,et al.  Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages , 2012, Cell.

[48]  K. Monahan,et al.  Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of Protocadherin-α gene expression , 2012, Proceedings of the National Academy of Sciences.

[49]  Lee E. Edsall,et al.  A map of the cis-regulatory sequences in the mouse genome , 2012, Nature.

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

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

[52]  D. Schreiner,et al.  γ-Protocadherins Control Cortical Dendrite Arborization by Regulating the Activity of a FAK/PKC/MARCKS Signaling Pathway , 2012, Neuron.

[53]  Ming Hu,et al.  HiCNorm: removing biases in Hi-C data via Poisson regression , 2012, Bioinform..

[54]  Y. Yoshimura,et al.  CTCF is required for neural development and stochastic expression of clustered Pcdh genes in neurons. , 2012, Cell reports.

[55]  Bosiljka Tasic,et al.  Functional Significance of Isoform Diversification in the Protocadherin Gamma Gene Cluster , 2012, Neuron.

[56]  M. Capecchi,et al.  Protocadherin clusters and cell adhesion kinase regulate dendrite complexity through Rho GTPase. , 2012, Journal of molecular cell biology.

[57]  Jesse R. Dixon,et al.  Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells , 2013, Proceedings of the National Academy of Sciences.

[58]  Yu Zhang,et al.  Mechanisms of Programmed DNA Lesions and Genomic Instability in the Immune System , 2013, Cell.

[59]  T. Maniatis,et al.  Clustered protocadherins , 2013, Development.

[60]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[61]  Xiaojun Zhu,et al.  Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos , 2013, Cell Research.

[62]  D. Duboule,et al.  Topology of mammalian developmental enhancers and their regulatory landscapes , 2013, Nature.

[63]  Victor V Lobanenkov,et al.  A genome-wide map of CTCF multivalency redefines the CTCF code. , 2013, Cell reports.

[64]  J. Dekker,et al.  The hierarchy of the 3D genome. , 2013, Molecular cell.

[65]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[66]  Qiang Wu,et al.  Regulation of the Protocadherin Celsr3 Gene and Its Role in Globus Pallidus Development and Connectivity , 2014, Molecular and Cellular Biology.

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

[68]  Robert Tjian,et al.  Looping Back to Leap Forward: Transcription Enters a New Era , 2014, Cell.

[69]  Leonid A. Mirny,et al.  Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions , 2014, bioRxiv.

[70]  Jill M Dowen,et al.  Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes , 2014, Cell.

[71]  J. Tapia,et al.  Single-Cell Identity Generated by Combinatorial Homophilic Interactions between α, β, and γ Protocadherins , 2014, Cell.

[72]  V. Iyer,et al.  Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects , 2014, Nature Methods.

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

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

[75]  Jing Liang,et al.  Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.

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

[77]  Ya Guo,et al.  Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9 , 2015, Journal of molecular cell biology.