Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging.

[1]  Haoteng Yan,et al.  BMAL1 moonlighting as a gatekeeper for LINE1 repression and cellular senescence in primates , 2022, Nucleic acids research.

[2]  Derek T. Peters,et al.  HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. , 2022, Molecules and Cells.

[3]  J. Qu,et al.  Cross-species metabolomic analysis identifies uridine as a potent regeneration promoting factor , 2022, Cell discovery.

[4]  S. Horvath,et al.  DNA methylation signatures in Blood DNA of Hutchinson–Gilford Progeria syndrome , 2022, Aging cell.

[5]  M. Lei,et al.  Stage-resolved Hi-C analyses reveal meiotic chromosome organizational features influencing homolog alignment , 2021, Nature Communications.

[6]  Luyang Sun,et al.  Altered chromatin states drive cryptic transcription in aging mammalian stem cells , 2021, Nature Aging.

[7]  Sara B. Linker,et al.  The role of retrotransposable elements in ageing and age-associated diseases , 2021, Nature.

[8]  J. Sedivy,et al.  Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention , 2021, Signal Transduction and Targeted Therapy.

[9]  Michael Q. Zhang,et al.  The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence , 2021, Genome research.

[10]  Weiwei Dang,et al.  Loosening chromatin and dysregulated transcription: a perspective on cryptic transcription during mammalian aging. , 2021, Briefings in Functional Genomics.

[11]  J. I. Izpisúa Belmonte,et al.  In vivo partial reprogramming of myofibers promotes muscle regeneration by remodeling the stem cell niche , 2021, Nature Communications.

[12]  C. López-Otín,et al.  Hallmarks of health , 2021, Cell.

[13]  F. Tang,et al.  Resurrection of endogenous retroviruses during aging reinforces senescence , 2021, Cell.

[14]  Wei Xie,et al.  Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome , 2021, Cell Research.

[15]  Elzo de Wit,et al.  Hi-C analyses with GENOVA: a case study with cohesin variants , 2021, bioRxiv.

[16]  F. Tang,et al.  A genome-wide CRISPR-based screen identifies KAT7 as a driver of cellular senescence , 2021, Science Translational Medicine.

[17]  Jesse R. Dixon,et al.  Promoter-proximal CTCF-binding promotes long-range-enhancer dependent gene activation , 2021, Nature structural & molecular biology.

[18]  R. DePinho,et al.  Telomeres: history, health, and hallmarks of aging , 2021, Cell.

[19]  Margarita V. Meer,et al.  Reprogramming to recover youthful epigenetic information and restore vision , 2020, Nature.

[20]  Mengwei Hu,et al.  Chromatin Tracing: Imaging 3D Genome and Nucleome. , 2020, Trends in cell biology.

[21]  Aibin He,et al.  Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells , 2020, Protein & Cell.

[22]  Shuling Song,et al.  Targeting Senescent Cells for a Healthier Aging: Challenges and Opportunities , 2020, Advanced science.

[23]  Cheng Li,et al.  Senescence-activated enhancer landscape orchestrates the senescence-associated secretory phenotype in murine fibroblasts , 2020, Nucleic acids research.

[24]  J. Qu,et al.  METTL3 counteracts premature aging via m6A-dependent stabilization of MIS12 mRNA , 2020, Nucleic acids research.

[25]  T. Misteli.  The Self-Organizing Genome: Principles of Genome Architecture and Function , 2020, Cell.

[26]  Fidel Ramírez,et al.  pyGenomeTracks: reproducible plots for multivariate genomic datasets , 2020, Bioinform..

[27]  J. C. Belmonte,et al.  Stabilization of heterochromatin by CLOCK promotes stem cell rejuvenation and cartilage regeneration , 2020, Cell Research.

[28]  Irving L. Weissman,et al.  A single-cell transcriptomic atlas characterizes ageing tissues in the mouse , 2020, Nature.

[29]  J. Qu,et al.  Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming. , 2020, Cell reports.

[30]  J. Qu,et al.  SIRT7 antagonizes human stem cell aging as a heterochromatin stabilizer , 2020, Protein & Cell.

[31]  Daniel Jost,et al.  4D Genome Rewiring during Oncogene-Induced and Replicative Senescence , 2020, Molecular cell.

[32]  B. Kennedy,et al.  Aging Biomarkers: From Functional Tests to Multi‐Omics Approaches , 2020, Proteomics.

[33]  J. Qu,et al.  The ageing epigenome and its rejuvenation , 2020, Nature Reviews Molecular Cell Biology.

[34]  A. Korobeynikov,et al.  Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.

[35]  Mark I. McCarthy,et al.  A brief history of human disease genetics , 2020, Nature.

[36]  A. Pombo,et al.  Methods for mapping 3D chromosome architecture , 2019, Nature Reviews Genetics.

[37]  James B. Brewer,et al.  Brain cell type–specific enhancer–promoter interactome maps and disease-risk association , 2019, Science.

[38]  Kyle Xiong,et al.  Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions , 2019, Nature Communications.

[39]  Andreas Keller,et al.  Undulating changes in human plasma proteome profiles across the lifespan , 2019, Nature Medicine.

[40]  C. Mendelson,et al.  HUMAN TROPHOBLAST DIFFERENTIATION IS ASSOCIATED WITH PROFOUND GENE REGULATORY AND EPIGENETIC CHANGES. , 2019, Endocrinology.

[41]  D. Marenduzzo,et al.  Polymer Modeling Predicts Chromosome Reorganization in Senescence , 2019, Cell reports.

[42]  Guangchuang Yu,et al.  RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms , 2019, PeerJ Prepr..

[43]  J. I. Izpisúa Belmonte,et al.  Stabilizing heterochromatin by DGCR8 alleviates senescence and osteoarthritis , 2019, Nature Communications.

[44]  Elie N. Farah,et al.  Transcriptionally Active HERV-H Retrotransposons Demarcate Topologically Associating Domains in Human Pluripotent Stem Cells , 2019, Nature Genetics.

[45]  Kotb Abdelmohsen,et al.  Transcriptome signature of cellular senescence. , 2019, Nucleic acids research.

[46]  Ting Wang,et al.  WashU Epigenome Browser update 2019 , 2019, Nucleic Acids Res..

[47]  Shane A. Evans,et al.  The three-dimensional organization of the genome in cellular senescence and age-associated diseases. , 2019, Seminars in cell & developmental biology.

[48]  L. Mirny,et al.  Two major mechanisms of chromosome organization. , 2019, Current opinion in cell biology.

[49]  Christophe Zimmer,et al.  How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization. , 2019, Annual review of biophysics.

[50]  M. Torres-Padilla,et al.  Genome-lamina interactions are established de novo in the early mouse embryo , 2019, Nature.

[51]  Olga Tanaseichuk,et al.  Metascape provides a biologist-oriented resource for the analysis of systems-level datasets , 2019, Nature Communications.

[52]  Ilya M. Flyamer,et al.  Coolpup.py: versatile pile-up analysis of Hi-C data , 2019, bioRxiv.

[53]  Eileen E M Furlong,et al.  The role of transcription in shaping the spatial organization of the genome , 2019, Nature Reviews Molecular Cell Biology.

[54]  J. I. Izpisúa Belmonte,et al.  FOXO3-Engineered Human ESC-Derived Vascular Cells Promote Vascular Protection and Regeneration. , 2019, Cell stem cell.

[55]  Nezar Abdennur,et al.  Cooler: scalable storage for Hi-C data and other genomically-labeled arrays , 2019, bioRxiv.

[56]  D. Sinclair,et al.  Epigenetic changes during aging and their reprogramming potential , 2019, Critical reviews in biochemistry and molecular biology.

[57]  Jun-Ping Liu,et al.  Roles of Telomere Biology in Cell Senescence, Replicative and Chronological Ageing , 2019, Cells.

[58]  Saket Navlakha,et al.  Predicting age from the transcriptome of human dermal fibroblasts , 2018, Genome Biology.

[59]  J. Han,et al.  Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions , 2018, Genome research.

[60]  Kerstin B. Meyer,et al.  Single-cell reconstruction of the early maternal–fetal interface in humans , 2018, Nature.

[61]  V. Corces,et al.  Organizational principles of 3D genome architecture , 2018, Nature Reviews Genetics.

[62]  E. Lam,et al.  Targeting SPINK1 in the damaged tumour microenvironment alleviates therapeutic resistance , 2018, Nature Communications.

[63]  Martin Vingron,et al.  Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis , 2018, Nature Genetics.

[64]  Max W. Chang,et al.  Transcription Elongation Can Affect Genome 3D Structure , 2018, Cell.

[65]  J. Qu,et al.  Chemical screen identifies a geroprotective role of quercetin in premature aging , 2018, Protein & Cell.

[66]  Q. Gao,et al.  An intercross population study reveals genes associated with body size and plumage color in ducks , 2018, Nature Communications.

[67]  Zev J. Gartner,et al.  DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors , 2018, bioRxiv.

[68]  M. Demaria,et al.  Hallmarks of Cellular Senescence. , 2018, Trends in cell biology.

[69]  K. Rippe,et al.  HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types. , 2018, Molecular cell.

[70]  E. Lam,et al.  The senescence-associated secretory phenotype is potentiated by feedforward regulatory mechanisms involving Zscan4 and TAK1 , 2018, Nature Communications.

[71]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[72]  Shane A. Evans,et al.  Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage-and Histone Methylation-Dependent Pathways , 2018, Cell reports.

[73]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[74]  J. Qu,et al.  Differential stem cell aging kinetics in Hutchinson-Gilford progeria syndrome and Werner syndrome , 2018, Protein & Cell.

[75]  Cizhong Jiang,et al.  Genome-wide DNA methylation analysis reveals that mouse chemical iPSCs have closer epigenetic features to mESCs than OSKM-integrated iPSCs , 2018, Cell Death & Disease.

[76]  Hui Shen,et al.  DNA methylation loss in late-replicating domains is linked to mitotic cell division , 2018, Nature Genetics.

[77]  Manolis Kellis,et al.  Chromatin-state discovery and genome annotation with ChromHMM , 2017, Nature Protocols.

[78]  D. Peeper,et al.  Massive reshaping of genome–nuclear lamina interactions during oncogene-induced senescence , 2017, Genome research.

[79]  R. David Hawkins,et al.  Three-dimensional genome architecture and emerging technologies: looping in disease , 2017, Genome Medicine.

[80]  J. I. Izpisúa Belmonte,et al.  Regulation of Stem Cell Aging by Metabolism and Epigenetics. , 2017, Cell metabolism.

[81]  Erez Lieberman Aiden,et al.  Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. , 2017, Molecular cell.

[82]  Wei Zhu,et al.  3D Chromatin Structures of Mature Gametes and Structural Reprogramming during Mammalian Embryogenesis , 2017, Cell.

[83]  Bas van Steensel,et al.  Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression , 2017, Cell.

[84]  Naoki Nariai,et al.  Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data , 2017, BMC Bioinformatics.

[85]  Andrew P. Feinberg,et al.  Potential energy landscapes identify the information-theoretic nature of the epigenome , 2017, Nature Genetics.

[86]  Yuying Zhang,et al.  The decay of Redox-stress Response Capacity is a substantive characteristic of aging: Revising the redox theory of aging , 2016, Redox biology.

[87]  C. R. Esteban,et al.  In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming , 2016, Cell.

[88]  R. Brunauer,et al.  Stem Cell Models: A Guide to Understand and Mitigate Aging? , 2016, Gerontology.

[89]  Giacomo Cavalli,et al.  Organization and function of the 3D genome , 2016, Nature Reviews Genetics.

[90]  S. Berger,et al.  Epigenetic Mechanisms of Longevity and Aging , 2016, Cell.

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

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

[93]  B. Meyer,et al.  Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPRmt , 2016, Cell.

[94]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[95]  L. Mirny,et al.  The 3D Genome as Moderator of Chromosomal Communication , 2016, Cell.

[96]  A. Seluanov,et al.  DNA double strand break repair, aging and the chromatin connection. , 2016, Mutation research.

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

[98]  S. Gasser,et al.  Histones and histone modifications in perinuclear chromatin anchoring: from yeast to man , 2016, EMBO reports.

[99]  D. Guan,et al.  SIRT6 safeguards human mesenchymal stem cells from oxidative stress by coactivating NRF2 , 2016, Cell Research.

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

[101]  Geir Kjetil Sandve,et al.  In the loop: promoter–enhancer interactions and bioinformatics , 2015, Briefings Bioinform..

[102]  Siddharth S. Dey,et al.  Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells , 2015, Cell.

[103]  Aaron T. L. Lun,et al.  diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data , 2015, BMC Bioinformatics.

[104]  R. Shiekhattar,et al.  Integrator mediates the biogenesis of enhancer RNAs , 2015, Nature.

[105]  B. Kennedy,et al.  H3K36 methylation promotes longevity by enhancing transcriptional fidelity , 2015, Genes & development.

[106]  F. Tang,et al.  A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging , 2015, Science.

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

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

[109]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[110]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

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

[112]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[113]  Manolis Kellis,et al.  Large-scale epigenome imputation improves data quality and disease variant enrichment , 2015, Nature Biotechnology.

[114]  Howard Y. Chang,et al.  ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide , 2015, Current protocols in molecular biology.

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

[116]  Tom Moore,et al.  Pregnancy-specific glycoproteins: complex gene families regulating maternal-fetal interactions. , 2014, The International journal of developmental biology.

[117]  Zhaohui S. Qin,et al.  Insulator function and topological domain border strength scale with architectural protein occupancy , 2014, Genome Biology.

[118]  S. Berger,et al.  Epigenetics of aging and aging-related disease. , 2014, The journals of gerontology. Series A, Biological sciences and medical sciences.

[119]  S. Fisher,et al.  Reversal of gene dysregulation in cultured cytotrophoblasts reveals possible causes of preeclampsia. , 2013, The Journal of clinical investigation.

[120]  L. Partridge,et al.  The Hallmarks of Aging , 2013, Cell.

[121]  C. Glass,et al.  Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation , 2013, Nature.

[122]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[123]  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.

[124]  W. Bickmore,et al.  Single-Cell Dynamics of Genome-Nuclear Lamina Interactions , 2013, Cell.

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

[126]  Rachel Patton McCord,et al.  Correlated alterations in genome organization, histone methylation, and DNA–lamin A/C interactions in Hutchinson-Gilford progeria syndrome , 2013, Genome research.

[127]  Manolis Kellis,et al.  Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence , 2013, Genome research.

[128]  Dan Liu,et al.  Telomeres-structure, function, and regulation. , 2013, Experimental cell research.

[129]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[130]  Bradley E. Bernstein,et al.  DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina , 2012, Cell.

[131]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

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

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

[134]  Manolis Kellis,et al.  ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.

[135]  Howard Y. Chang,et al.  Aging, Rejuvenation, and Epigenetic Reprogramming: Resetting the Aging Clock , 2012, Cell.

[136]  I. Ellis,et al.  Differential oestrogen receptor binding is associated with clinical outcome in breast cancer , 2011, Nature.

[137]  C. Glass,et al.  Reprogramming Transcription via Distinct Classes of Enhancers Functionally Defined by eRNA , 2011, Nature.

[138]  J. Yates,et al.  Recapitulation of premature aging with iPSCs from Hutchinson-Gilford progeria syndrome , 2011, Nature.

[139]  P. Flicek,et al.  Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. , 2010, Molecular cell.

[140]  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.

[141]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[142]  Dustin E. Schones,et al.  A clustering approach for identification of enriched domains from histone modification ChIP-Seq data , 2009, Bioinform..

[143]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[144]  Dan Liu,et al.  The telosome/shelterin complex and its functions , 2008, Genome Biology.

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

[146]  L. Wessels,et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions , 2008, Nature.

[147]  Bas van Steensel,et al.  Detection of in vivo protein–DNA interactions using DamID in mammalian cells , 2007, Nature Protocols.

[148]  T. Misteli,et al.  Lamin A-Dependent Nuclear Defects in Human Aging , 2006, Science.

[149]  Yosef Gruenbaum,et al.  Accumulation of mutant lamin A causes progressive changes in nuclear architecture in Hutchinson–Gilford progeria syndrome , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[150]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[151]  P. Ho,et al.  Pregnancy-specific beta 1-glycoprotein as a prognostic indicator in complications of early pregnancy. , 1980, American journal of obstetrics and gynecology.

[152]  O. Medalia,et al.  Nuclear Lamins: Thin Filaments with Major Functions. , 2018, Trends in cell biology.

[153]  Yuanxin Xi,et al.  BMC Bioinformatics BioMed Central Methodology article BSMAP: whole genome bisulfite sequence MAPping program , 2009 .

[154]  S. Hoehme,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[155]  Y. Wan,et al.  Characterization of pregnancy-specific beta 1-glycoprotein synthesized by human placental fibroblasts. , 1989, Molecular endocrinology.

[156]  I. Amit,et al.  Supporting Online Material Materials and Methods Som Text Comprehensive Mapping of Long-range Interactions Reveals Folding Principles of the Human Genome , 2022 .