Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders
暂无分享,去创建一个
Michael D. Wilson | Petra C. Schwalie | A. Gingras | J. Reimand | A. Medina-Rivera | Dominic Schmidt | S. Hadjur | H. Mohammed | Liis Uusküla-Reimand | Minggao Liang | Huayun Hou | P. Samavarchi-Tehrani | Edwin J. Young | M. V. Rudan | M. Wilson | Payman Samavarchi-Tehrani | Matteo Vietri Rudan | Hisham Mohammed | Suzana Hadjur
[1] S. Cockell,et al. Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells , 2015, Biology Open.
[2] Brian T. Lee,et al. The UCSC Genome Browser database: 2015 update , 2014, Nucleic Acids Res..
[3] Jonathan K. Pritchard,et al. WASP: allele-specific software for robust molecular quantitative trait locus discovery , 2015, Nature Methods.
[4] Michael Q. Zhang,et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function , 2015, Cell.
[5] Niko Välimäki,et al. CTCF/cohesin-binding sites are frequently mutated in cancer , 2015, Nature Genetics.
[6] Paola Bovolenta,et al. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders , 2015, Proceedings of the National Academy of Sciences.
[7] Andreas R. Pfenning,et al. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes , 2015, Cell.
[8] Denis Thieffry,et al. RSAT 2015: Regulatory Sequence Analysis Tools , 2015, Nucleic Acids Res..
[9] Anne-Claude Gingras,et al. Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. , 2015, Journal of proteomics.
[10] Reham Atteya,et al. Topoisomerase-mediated chromosomal break repair: an emerging player in many games , 2015, Nature Reviews Cancer.
[11] Pedro P. Rocha,et al. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation , 2015, Science.
[12] Céline Hernandez,et al. ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors , 2015, Genome research.
[13] D. Odom,et al. Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture , 2015, Cell reports.
[14] Paz Polak,et al. Cell-of-origin chromatin organization shapes the mutational landscape of cancer , 2015, Nature.
[15] Neva C. Durand,et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.
[16] C. Creppe,et al. A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation , 2014, PLoS genetics.
[17] Shane J. Neph,et al. A comparative encyclopedia of DNA elements in the mouse genome , 2014, Nature.
[18] J. Carroll,et al. Genomic interaction between ER and HMGB2 identifies DDX18 as a novel driver of endocrine resistance in breast cancer cells , 2014, Oncogene.
[19] Michael T. Zimmermann,et al. MACE: model based analysis of ChIP-exo , 2014, Nucleic acids research.
[20] W. H. Kim,et al. PHF2 histone demethylase acts as a tumor suppressor in association with p53 in cancer , 2014, Oncogene.
[21] H. Kimura,et al. Nuclear dynamics of topoisomerase IIβ reflects its catalytic activity that is regulated by binding of RNA to the C-terminal domain , 2014, Nucleic acids research.
[22] Michael P. Snyder,et al. Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures , 2014, Bioinform..
[23] J. Schuurs-Hoeijmakers,et al. TDP2 protects transcription from abortive topoisomerase activity and is required for normal neural function , 2014, Nature Genetics.
[24] Eric Nestler,et al. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases , 2014, BMC Genomics.
[25] Steven J. M. Jones,et al. ALEA: a toolbox for allele-specific epigenomics analysis , 2014, Bioinform..
[26] Guomin Liu,et al. SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. , 2014, Journal of proteomics.
[27] M. Pende,et al. Ribosomal protein S6 kinase activity controls the ribosome biogenesis transcriptional program , 2014, Oncogene.
[28] E. Tzatzalos,et al. Topoisomerase IIbeta is required for proper retinal development and survival of postmitotic cells , 2014, Biology Open.
[29] Petra C. Schwalie,et al. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes , 2013, Genome Biology.
[30] P. Scacheri,et al. Genomic Characterization of the Mouse Ribosomal DNA Locus , 2013, G3: Genes, Genomes, Genetics.
[31] 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.
[32] Xin-Hua Feng,et al. Zinc Finger Protein 451 Is a Novel Smad Corepressor in Transforming Growth Factor-β Signaling* , 2013, The Journal of Biological Chemistry.
[33] Boris Lenhard,et al. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments , 2013, Genome research.
[34] G. Schroth,et al. Cohesin-mediated interactions organize chromosomal domain architecture , 2013, The EMBO journal.
[35] Angela Garding,et al. Gene regulation and priming by topoisomerase IIα in embryonic stem cells , 2013, Nature Communications.
[36] Dawang Zhou,et al. TOP2β is essential for ovarian follicles that are hypersensitive to chemotherapeutic drugs. , 2013, Molecular endocrinology.
[37] Stormy J. Chamberlain,et al. Topoisomerases facilitate transcription of long genes linked to autism , 2013, Nature.
[38] Amber L. Couzens,et al. The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data , 2013, Nature Methods.
[39] Caleb Webber,et al. GAT: a simulation framework for testing the association of genomic intervals , 2013, Bioinform..
[40] T. Hsieh,et al. New mechanistic and functional insights into DNA topoisomerases. , 2013, Annual review of biochemistry.
[41] Jennifer E. Phillips-Cremins,et al. Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment , 2013, Cell.
[42] Victor V Lobanenkov,et al. A genome-wide map of CTCF multivalency redefines the CTCF code. , 2013, Cell reports.
[43] A. Volkov,et al. Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation , 2013, Nature Communications.
[44] Carlos Caldas,et al. Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor. , 2013, Cell reports.
[45] S. Cockroft,et al. Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures , 2013, Nature Structural &Molecular Biology.
[46] J. Eng,et al. Comet: An open‐source MS/MS sequence database search tool , 2013, Proteomics.
[47] Jie Wang,et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium , 2012, Nucleic Acids Res..
[48] L. Aravind,et al. MORC2 signaling integrates phosphorylation-dependent, ATPase-coupled chromatin remodeling during the DNA damage response. , 2012, Cell reports.
[49] Michael D. Wilson,et al. The Evolutionary Landscape of Alternative Splicing in Vertebrate Species , 2012, Science.
[50] E. Yeh,et al. Identification of the molecular basis of doxorubicin-induced cardiotoxicity , 2012, Nature Medicine.
[51] Matthew T. Maurano,et al. Widespread plasticity in CTCF occupancy linked to DNA methylation , 2012, Genome research.
[52] Marc D. Perry,et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia , 2012, Genome research.
[53] Philip Cayting,et al. An encyclopedia of mouse DNA elements (Mouse ENCODE) , 2012, Genome Biology.
[54] Michael D. Wilson,et al. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules , 2012, Genome research.
[55] Christopher J. Hale,et al. MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing , 2012, Science.
[56] Catriona Manville,et al. Model for MLL translocations in therapy-related leukemia involving topoisomerase IIβ-mediated DNA strand breaks and gene proximity , 2012, Proceedings of the National Academy of Sciences.
[57] J. Sedat,et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.
[58] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[59] Lukas Burger,et al. Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state , 2012, Proceedings of the National Academy of Sciences.
[60] Brian Burke,et al. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells , 2012, The Journal of cell biology.
[61] Yuval Kluger,et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. , 2012, Molecular cell.
[62] Michael D. Wilson,et al. Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages , 2012, Cell.
[63] J. van Helden,et al. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets , 2011, Nucleic acids research.
[64] I. Ellis,et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer , 2011, Nature.
[65] 布川 朋也. DDX31 regulates the p53-HDM2 pathway and rRNA gene transcription through its interaction with NPM1 in renal cell carcinomas , 2012 .
[66] B. Pugh,et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution , 2011, Cell.
[67] Thomas M. Keane,et al. Mouse genomic variation and its effect on phenotypes and gene regulation , 2011, Nature.
[68] Natalie I. Tasman,et al. iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates* , 2011, Molecular & Cellular Proteomics.
[69] A. Look,et al. Ddx18 is essential for cell-cycle progression in zebrafish hematopoietic cells and is mutated in human AML. , 2011, Blood.
[70] M. Grunstein,et al. Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast , 2011, Proceedings of the National Academy of Sciences.
[71] A. D. De Marzo,et al. Transcription-Induced DNA Double Strand Breaks: Both Oncogenic Force and Potential Therapeutic Target? , 2011, Clinical Cancer Research.
[72] Jaak Vilo,et al. g:Profiler—a web server for functional interpretation of gene lists (2011 update) , 2011, Nucleic Acids Res..
[73] M. Meistrich,et al. Poly(ADP-Ribose) Polymerases PARP1 and PARP2 Modulate Topoisomerase II Beta (TOP2B) Function During Chromatin Condensation in Mouse Spermiogenesis1 , 2011, Biology of reproduction.
[74] Jonathan Schug,et al. The Nucleosome Map of the Mammalian Liver , 2011, Nature Structural &Molecular Biology.
[75] E. Birney,et al. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. , 2011, Genome research.
[76] Gary D Bader,et al. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.
[77] N. Galjart,et al. CTCF regulates the local epigenetic state of ribosomal DNA repeats , 2010, Epigenetics & Chromatin.
[78] Tony Pawson,et al. ProHits: an integrated software platform for mass spectrometry-based interaction proteomics , 2010, Nature Biotechnology.
[79] Martin J. Aryee,et al. Androgen-induced TOP2B mediated double strand breaks and prostate cancer gene rearrangements , 2010, Nature Genetics.
[80] R. Durbin,et al. Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins , 2010, Science.
[81] Natalie I. Tasman,et al. A guided tour of the Trans‐Proteomic Pipeline , 2010, Proteomics.
[82] Aaron R. Quinlan,et al. Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .
[83] I. Grummt,et al. Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans , 2010, EMBO reports.
[84] Tao Liu,et al. CEAS: cis-regulatory element annotation system , 2009, Bioinform..
[85] Michael D. Wilson,et al. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. , 2009, Methods.
[86] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[87] B. Emerson,et al. Epigenetic silencing of the p16(INK4a) tumor suppressor is associated with loss of CTCF binding and a chromatin boundary. , 2009, Molecular cell.
[88] J. Nitiss. DNA topoisomerase II and its growing repertoire of biological functions , 2009, Nature Reviews Cancer.
[89] J. Nitiss. Targeting DNA topoisomerase II in cancer chemotherapy , 2009, Nature Reviews Cancer.
[90] L. Zon,et al. Topoisomerase IIα Is Required for Embryonic Development and Liver Regeneration in Zebrafish , 2009, Molecular and Cellular Biology.
[91] William Stafford Noble,et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting , 2009, Nature Methods.
[92] R. Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[93] E. Liu,et al. Evolution of the mammalian transcription factor binding repertoire via transposable elements. , 2008, Genome research.
[94] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[95] Robert Burke,et al. ProteoWizard: open source software for rapid proteomics tools development , 2008, Bioinform..
[96] Z. Weng,et al. The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome , 2008, PLoS genetics.
[97] G. Boissonneault,et al. DNA Damage Response During Chromatin Remodeling in Elongating Spermatids of Mice1 , 2008, Biology of reproduction.
[98] E. Avvedimento,et al. DNA Oxidation as Triggered by H3K9me2 Demethylation Drives Estrogen-Induced Gene Expression , 2008, Science.
[99] Chao-Po Lin,et al. Roles of DNA topoisomerase II isozymes in chemotherapy and secondary malignancies , 2007, Proceedings of the National Academy of Sciences.
[100] J. Shaman,et al. Topoisomerase II-Mediated Breaks in Spermatozoa Cause the Specific Degradation of Paternal DNA in Fertilized Oocytes1 , 2007, Biology of reproduction.
[101] Jeannie T. Lee,et al. Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. , 2007, Molecular cell.
[102] Chao-Po Lin,et al. Role of Topoisomerase IIβ in the Expression of Developmentally RegulatedGenes , 2006, Molecular and Cellular Biology.
[103] C. Glass,et al. A Topoisomerase IIß-Mediated dsDNA Break Required for Regulated Transcription , 2006, Science.
[104] S. Batzoglou,et al. Distribution and intensity of constraint in mammalian genomic sequence. , 2005, Genome research.
[105] A. Porter,et al. Construction, characterization, and complementation of a conditional-lethal DNA topoisomerase IIalpha mutant human cell line. , 2004, Molecular biology of the cell.
[106] S. Sakoda,et al. Hepatoma-derived Growth Factor Is a Neurotrophic Factor Harbored in the Nucleus* , 2004, Journal of Biological Chemistry.
[107] M. Farinacci,et al. Expression and Localization Studies of hSDA, the Human Ortholog of the Yeast SDA1 Gene , 2004, Cell cycle.
[108] R. Weksberg,et al. Insulator and silencer sequences in the imprinted region of human chromosome 11p15.5. , 2003, Human molecular genetics.
[109] Jacques van Helden,et al. Regulatory Sequence Analysis Tools , 2003, Nucleic Acids Res..
[110] N. Akimitsu,et al. Enforced cytokinesis without complete nuclear division in embryonic cells depleting the activity of DNA topoisomerase IIα , 2003, Genes to cells : devoted to molecular & cellular mechanisms.
[111] J. Champoux. DNA topoisomerases: structure, function, and mechanism. , 2001, Annual review of biochemistry.
[112] Wei Li,et al. DNA topoisomerase IIβ and neural development , 2000 .
[113] J. Wang,et al. DNA topoisomerase IIbeta and neural development. , 2000, Science.
[114] J. D. Engel,et al. Effects of altered gene order or orientation of the locus control region on human β-globin gene expression in mice , 1999, Nature.
[115] J. Sng,et al. Molecular cloning and characterization of the human topoisomerase IIalpha and IIbeta genes: evidence for isoform evolution through gene duplication. , 1999, Biochimica et biophysica acta.
[116] M. Sehested,et al. Essential Mitotic Functions of DNA Topoisomerase IIα Are Not Adopted by Topoisomerase IIβ in Human H69 Cells* , 1998, The Journal of Biological Chemistry.
[117] S. Mirski,et al. Structural organization of the human TOP2A and TOP2B genes. , 1998, Gene.
[118] A. Andersen,et al. Active heterodimers are formed from human DNA topoisomerase II alpha and II beta isoforms. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[119] W. Yue,et al. The human breast cell DNA synthesome: its purification from tumor tissue and cell culture. , 1996, Oncology research.
[120] M. Paalman,et al. Stimulation of the mouse rRNA gene promoter by a distal spacer promoter , 1995, Molecular and cellular biology.
[121] V. Meller,et al. Nuclear distribution of Drosophila DNA topoisomerase II is sensitive to both RNase and DNase. , 1995, Journal of cell science.
[122] P. Walker,et al. Role of topoisomerase II in the structural and functional evolution of mitogen-stimulated lymphocyte nuclei. , 1994, Experimental cell research.
[123] F. Zunino,et al. Different patterns of gene expression of topoisomerase II isoforms in differentiated tissues during murine development. , 1992, Biochimica et biophysica acta.
[124] M. Muller,et al. DNase I hypersensitivity is independent of endogenous topoisomerase II activity during chicken erythrocyte differentiation , 1988, Molecular and cellular biology.
[125] M. Muller,et al. A consensus sequence for cleavage by vertebrate DNA topoisomerase II. , 1988, Nucleic acids research.