Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization
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Marc A Marti-Renom | Gonzalo Gómez-López | M. Martí-Renom | G. Gómez-López | A. Cuadrado | François le Dily | A. Losada | M. Rodríguez-Corsino | Ana Cuadrado | François Le Dily | Aleksandar Kojic | Magali De Koninck | Daniel Giménez-Llorente | Miriam Rodríguez-Corsino | Ana Losada | M. De Koninck | A. Kojic | D. Giménez-Llorente
[1] Timothy J. Durham,et al. Systematic analysis of chromatin state dynamics in nine human cell types , 2011, Nature.
[2] Boris Lenhard,et al. Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin , 2015 .
[3] A. Valencia,et al. Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy , 2013, Nature Genetics.
[4] David J. Reiss,et al. CTCF physically links cohesin to chromatin , 2008, Proceedings of the National Academy of Sciences.
[5] J. Sedat,et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.
[6] M. Rubin,et al. Frequent truncating mutations of STAG2 in bladder cancer , 2013, Nature Genetics.
[7] Manolis Kellis,et al. ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.
[8] Neva C. Durand,et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.
[9] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[10] D. Pisano,et al. A unique role of cohesin‐SA1 in gene regulation and development , 2012, The EMBO journal.
[11] A. Tanay,et al. Multiscale 3D Genome Rewiring during Mouse Neural Development , 2017, Cell.
[12] Hongtao Yu,et al. ZNF198 Stabilizes the LSD1–CoREST–HDAC1 Complex on Chromatin through Its MYM-Type Zinc Fingers , 2008, PloS one.
[13] J. Ellenberg,et al. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins , 2017, The EMBO journal.
[14] Ilya M. Flyamer,et al. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition , 2017, Nature.
[15] Pedro P. Rocha,et al. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation , 2015, Science.
[16] Maxim I Molodtsov,et al. Rapid movement and transcriptional re‐localization of human cohesin on DNA , 2016, The EMBO journal.
[17] A. Losada,et al. Cohesin Mutations in Cancer. , 2016, Cold Spring Harbor perspectives in medicine.
[18] Sally Temple,et al. A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity , 2015, Stem cell reports.
[19] Nuno A. Fonseca,et al. Two independent modes of chromosome organization are revealed by cohesin removal , 2016, bioRxiv.
[20] Jennifer E. Phillips-Cremins,et al. Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment , 2013, Cell.
[21] 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.
[22] R. Kobayashi,et al. Identification and Characterization of Sa/Scc3p Subunits in the Xenopus and Human Cohesin Complexes , 2000, The Journal of cell biology.
[23] G. Mandel,et al. REST and Its Corepressors Mediate Plasticity of Neuronal Gene Chromatin throughout Neurogenesis , 2005, Cell.
[24] J. Ellenberg,et al. Wapl is an essential regulator of chromatin structure and chromosome segregation , 2013, Nature.
[25] Pedro P. Rocha,et al. Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms , 2015, The Journal of experimental medicine.
[26] Nuno A. Fonseca,et al. Two independent modes of chromatin organization revealed by cohesin removal , 2017, Nature.
[27] H. Aburatani,et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor , 2008, Nature.
[28] M. Corces,et al. The three-dimensional cancer genome. , 2016, Current opinion in genetics & development.
[29] L. Mirny,et al. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization , 2017, Cell.
[30] François Serra,et al. Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling , 2016, bioRxiv.
[31] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[32] Chris Berdik. Bladder cancer: 4 big questions , 2017, Nature.
[33] David A. Orlando,et al. Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.
[34] M. Mann,et al. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.
[35] Andre J. Faure,et al. 3D structure of individual mammalian genomes studied by single cell Hi-C , 2017, Nature.
[36] Susan Smith,et al. Differential regulation of telomere and centromere cohesion by the Scc3 homologues SA1 and SA2, respectively, in human cells , 2009, The Journal of cell biology.
[37] Masao Nagasaki,et al. Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms , 2012, Nature Genetics.
[38] Christopher J. Ott,et al. Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis , 2015, The Journal of experimental medicine.
[39] R. Shiekhattar,et al. A core–BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[40] Marco Y. Hein,et al. The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.
[41] C. Glass,et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation , 2013, Nature.
[42] F. Uhlmann,et al. Establishment of DNA-DNA Interactions by the Cohesin Ring , 2018, Cell.
[43] Michael D. Wilson,et al. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules , 2012, Genome research.
[44] Petra C. Schwalie,et al. A CTCF-independent role for cohesin in tissue-specific transcription. , 2010, Genome research.
[45] Jill P. Mesirov,et al. GSEA-P: a desktop application for Gene Set Enrichment Analysis , 2007, Bioinform..
[46] M. Blasco,et al. Cohesin‐SA1 deficiency drives aneuploidy and tumourigenesis in mice due to impaired replication of telomeres , 2012, The EMBO journal.
[47] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[48] D. Pisano,et al. The specific contributions of cohesin-SA1 to cohesion and gene expression , 2012, Cell cycle.
[49] Erez Lieberman Aiden,et al. Cohesin Loss Eliminates All Loop Domains , 2017, Cell.
[50] 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.
[51] A. Bishop,et al. Cohesin SA2 is a sequence-independent DNA-binding protein that recognizes DNA replication and repair intermediates , 2017, The Journal of Biological Chemistry.
[52] David A. Orlando,et al. Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.
[53] Boris Lenhard,et al. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments , 2013, Genome research.
[54] Kim Nasmyth,et al. Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq , 2015, Nucleic acids research.
[55] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[56] Mikael Bodén,et al. MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..
[57] L. Mirny,et al. Formation of Chromosomal Domains in Interphase by Loop Extrusion , 2015, bioRxiv.
[58] Michael Q. Zhang,et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function , 2015, Cell.
[59] A. Cuadrado,et al. Essential role of p18Hamlet/SRCAP‐mediated histone H2A.Z chromatin incorporation in muscle differentiation , 2010, The EMBO journal.
[60] Susan Smith,et al. Protein requirements for sister telomere association in human cells , 2007, The EMBO journal.
[61] A. Losada,et al. Pds5B is required for cohesion establishment and Aurora B accumulation at centromeres , 2013, The EMBO journal.
[62] M. Mann,et al. Universal sample preparation method for proteome analysis , 2009, Nature Methods.
[63] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[64] Marc A. Martí-Renom,et al. Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors , 2017, PLoS Comput. Biol..
[65] Kim Nasmyth,et al. Cohesin: its roles and mechanisms. , 2009, Annual review of genetics.
[66] Jing Liang,et al. Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.
[67] Raymond K. Auerbach,et al. Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.
[68] P. Fraser,et al. Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus , 2009, Nature.
[69] Fidel Ramírez,et al. deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..
[70] Peter H. L. Krijger,et al. The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension , 2017, Cell.
[71] Bruce Stillman,et al. Chromatin Association of Human Origin Recognition Complex, Cdc6, and Minichromosome Maintenance Proteins during the Cell Cycle: Assembly of Prereplication Complexes in Late Mitosis , 2000, Molecular and Cellular Biology.
[72] Catarina P. Santos,et al. Synthetic lethality between the cohesin subunits STAG1 and STAG2 in diverse cancer contexts , 2017, bioRxiv.
[73] M. Mann,et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.
[74] Amos Tanay,et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions , 2012, Nature Methods.
[75] D. Lim,et al. Mechanical cue‐induced YAP instructs Skp2‐dependent cell cycle exit and oncogenic signaling , 2017, The EMBO journal.
[76] Stephan Sauer,et al. Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms , 2008, Cell.
[77] Peter H. L. Krijger,et al. CTCF Binding Polarity Determines Chromatin Looping. , 2015, Molecular cell.