HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types.

[1]  Martin J. Aryee,et al.  hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data , 2018, Nature Methods.

[2]  S. Melov,et al.  Unmasking Transcriptional Heterogeneity in Senescent Cells , 2017, Current Biology.

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

[4]  William Stafford Noble,et al.  HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient , 2017, bioRxiv.

[5]  R. Young,et al.  A Phase Separation Model for Transcriptional Control , 2017, Cell.

[6]  M. Narita,et al.  NOTCH and the 2 SASPs of senescence , 2017, Cell cycle.

[7]  V. Beneš,et al.  Senescence‐associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells , 2016, Aging cell.

[8]  Benjamin G. Bitler,et al.  HMGB2 orchestrates the chromatin landscape of senescence-associated secretory phenotype gene loci , 2016, The Journal of cell biology.

[9]  Panagiotis Kotsantis,et al.  Increased global transcription activity as a mechanism of replication stress in cancer , 2016, Nature Communications.

[10]  Howard Y. Chang,et al.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.

[11]  R. Tjian,et al.  A dynamic mode of mitotic bookmarking by transcription factors , 2016, bioRxiv.

[12]  Juan M. Vaquerizas,et al.  TADtool: visual parameter identification for TAD-calling algorithms , 2016, Bioinform..

[13]  Davide Marenduzzo,et al.  Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains , 2016, Nucleic acids research.

[14]  Fabian J Theis,et al.  Diffusion pseudotime robustly reconstructs lineage branching , 2016, Nature Methods.

[15]  K. Rippe,et al.  Isolation of the protein and RNA content of active sites of transcription from mammalian cells , 2016, Nature Protocols.

[16]  Nicola Neretti,et al.  Reorganization of chromosome architecture in replicative cellular senescence , 2016, Science Advances.

[17]  Christina Backes,et al.  EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test , 2016, Genom. Proteom. Bioinform..

[18]  Davide Marenduzzo,et al.  Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models , 2016, Genome Biology.

[19]  Sebastian A. Leidel,et al.  Stepwise Clearance of Repressive Roadblocks Drives Cardiac Induction in Human ESCs. , 2016, Cell stem cell.

[20]  P. D. de Keizer.  The Fountain of Youth by Targeting Senescent Cells? , 2016, Trends in molecular medicine.

[21]  Gwendolyn M. Jang,et al.  Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. , 2015, Cell host & microbe.

[22]  Sigal Shachar,et al.  Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping , 2015, Cell.

[23]  Peter Frommolt,et al.  QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation , 2015, BMC Genomics.

[24]  Philip A. Ewels,et al.  Global Reorganization of the Nuclear Landscape in Senescent Cells , 2015, Cell reports.

[25]  Tom Misteli,et al.  Cell cycle staging of individual cells by fluorescence microscopy , 2015, Nature Protocols.

[26]  S. Mandrup,et al.  iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data , 2015, Nucleic acids research.

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

[28]  John J. Cole,et al.  HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia , 2014, Genes & development.

[29]  Ivan G. Costa,et al.  Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications , 2014, Bioinform..

[30]  David A. Orlando,et al.  Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. , 2014, Cell reports.

[31]  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.

[32]  S. Dudoit,et al.  Normalization of RNA-seq data using factor analysis of control genes or samples , 2014, Nature Biotechnology.

[33]  J. Deursen.  The role of senescent cells in ageing , 2014, Nature.

[34]  Eric Nestler,et al.  ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases , 2014, BMC Genomics.

[35]  M. Tyers,et al.  BoxPlotR: a web tool for generation of box plots , 2014, Nature Methods.

[36]  S. Tsirka,et al.  Aberrant Neural Stem Cell Proliferation and Increased Adult Neurogenesis in Mice Lacking Chromatin Protein HMGB2 , 2013, PloS one.

[37]  J. Lawrence,et al.  Higher-order unfolding of satellite heterochromatin is a consistent and early event in cell senescence , 2013, The Journal of cell biology.

[38]  Peter D. Adams,et al.  Senescent cells harbour features of the cancer epigenome , 2013, Nature Cell Biology.

[39]  Job Dekker,et al.  Organization of the Mitotic Chromosome , 2013, Science.

[40]  P. A. Pérez-Mancera,et al.  Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence , 2013, Genes & development.

[41]  Kajia Cao,et al.  Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape , 2013, Genes & development.

[42]  A. Dejean,et al.  Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation , 2013, Genome research.

[43]  Kelly J. Morris,et al.  A complex secretory program orchestrated by the inflammasome controls paracrine senescence , 2013, Nature Cell Biology.

[44]  Sara Hillenmeyer,et al.  Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements , 2013, Aging cell.

[45]  D. Schatz,et al.  Cooperative recruitment of HMGB1 during V(D)J recombination through interactions with RAG1 and DNA , 2013, Nucleic acids research.

[46]  N. Schaum,et al.  p53-dependent release of Alarmin HMGB1 is a central mediator of senescent phenotypes , 2011, The Journal of cell biology.

[47]  J. Dekker,et al.  Hi-C: a comprehensive technique to capture the conformation of genomes. , 2012, Methods.

[48]  Emmanuel Barillot,et al.  HiTC - Exploration of High Throughput ’C’ experiments , 2013 .

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

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

[51]  J. Fajkus,et al.  HMGB1 gene knockout in mouse embryonic fibroblasts results in reduced telomerase activity and telomere dysfunction , 2012, Chromosoma.

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

[53]  P. Adams,et al.  Lessons from senescence: Chromatin maintenance in non-proliferating cells. , 2012, Biochimica et biophysica acta.

[54]  Jung-Hee Kwon,et al.  HMGB2 stabilizes p53 by interfering with E6/E6AP-mediated p53 degradation in human papillomavirus-positive HeLa cells. , 2010, Cancer letters.

[55]  V. Maréchal,et al.  High-mobility group protein HMGB2 regulates human erythroid differentiation through trans-activation of GFI1B transcription. , 2010, Blood.

[56]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[57]  M. Štros.  HMGB proteins: interactions with DNA and chromatin. , 2010, Biochimica et biophysica acta.

[58]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[59]  M. Lotz,et al.  Aging-related loss of the chromatin protein HMGB2 in articular cartilage is linked to reduced cellularity and osteoarthritis , 2009, Proceedings of the National Academy of Sciences.

[60]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[61]  S. Lowe,et al.  A Novel Role for High-Mobility Group A Proteins in Cellular Senescence and Heterochromatin Formation , 2006, Cell.

[62]  Adrian A Canutescu,et al.  Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. , 2005, Developmental cell.

[63]  John M Sedivy,et al.  Telomere shortening triggers senescence of human cells through a pathway involving ATM, p53, and p21(CIP1), but not p16(INK4a). , 2004, Molecular cell.

[64]  P. Nordmann,et al.  Association of chromatin proteins high mobility group box (HMGB) 1 and HMGB2 with mitotic chromosomes. , 2003, Molecular biology of the cell.

[65]  G. Längst,et al.  The DNA chaperone HMGB1 facilitates ACF/CHRAC‐dependent nucleosome sliding , 2002, The EMBO journal.

[66]  D. Lockhart,et al.  Mitotic misregulation and human aging. , 2000, Science.

[67]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[68]  J. R. Smith,et al.  Intraclonal variation in proliferative potential of human diploid fibroblasts: stochastic mechanism for cellular aging. , 1980, Science.

[69]  L. Hayflick.  THE LIMITED IN VITRO LIFETIME OF HUMAN DIPLOID CELL STRAINS. , 1965, Experimental cell research.