The sirtuin-associated human senescence program converges on the activation of placenta-specific gene PAPPA.

[1]  J. Qu,et al.  Stress, epigenetics, and aging: Unraveling the intricate crosstalk. , 2023, Molecular cell.

[2]  J. Qu,et al.  SIRT2 counteracts primate cardiac aging via deacetylation of STAT3 that silences CDKN2B , 2023, Nature Aging.

[3]  J. Qu,et al.  MAVS Antagonizes Human Stem Cell Senescence as a Mitochondrial Stabilizer , 2023, Research.

[4]  Jiawei Han,et al.  Biomarkers of aging , 2023, Science China Life Sciences.

[5]  J. Qu,et al.  APOE-mediated suppression of the lncRNA MEG3 protects human cardiovascular cells from chronic inflammation , 2023, Protein & cell.

[6]  J. Qu,et al.  CRISPR-based screening identifies XPO7 as a positive regulator of senescence , 2023, Protein & cell.

[7]  D. Guallar,et al.  Chromatin 3D Structure, Phase Separation and Disease , 2023, Life Medicine.

[8]  Xinyi Lu,et al.  Endogenous retroviruses make aging go viral , 2023, Life Medicine.

[9]  Andreas R. Pfenning,et al.  Loss of epigenetic information as a cause of mammalian aging , 2023, Cell.

[10]  C. Conover,et al.  Senescence induces proteolytically-active PAPP-A secretion and association with extracellular vesicles in human pre-adipocytes , 2022, Experimental Gerontology.

[11]  M. Ji,et al.  Sirt6 attenuates chondrocyte senescence and osteoarthritis progression , 2022, Nature communications.

[12]  Yashu Liu,et al.  The sirtuin family in health and disease , 2022, Signal Transduction and Targeted Therapy.

[13]  Danica Chen.  MITOCHONDRIAL METABOLIC CHECKPOINT, STEM CELL AGING AND REJUVENATION , 2022, Innovation in Aging.

[14]  Ilya M. Flyamer,et al.  Cooltools: Enabling high-resolution Hi-C analysis in Python , 2022, bioRxiv.

[15]  Xingguo Liu,et al.  NAD + is critical for maintaining acetyl-CoA and H3K27ac in embryonic stem cells by Sirt1-dependent deacetylation of AceCS1 , 2022, Life Medicine.

[16]  E. Nora,et al.  New insights into genome folding by loop extrusion from inducible degron technologies , 2022, Nature Reviews Genetics.

[17]  Q. Kong,et al.  The landscape of aging , 2022, Science China Life Sciences.

[18]  Q. Lu,et al.  3D genome alterations in T cells associated with disease activity of systemic lupus erythematosus , 2022, Annals of the Rheumatic Diseases.

[19]  J. Qu,et al.  4E-BP1 counteracts human mesenchymal stem cell senescence via maintaining mitochondrial homeostasis , 2022, Protein & cell.

[20]  J. Kirkland,et al.  Targeting senescent cells for a healthier longevity: the roadmap for an era of global aging , 2022, Life medicine.

[21]  Dongxin Zhao,et al.  Failures at every level: breakdown of the epigenetic machinery of aging , 2022, Life Medicine.

[22]  J. Qu,et al.  Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging. , 2022, Developmental cell.

[23]  J. Qu,et al.  Destabilizing heterochromatin by APOE mediates senescence , 2022, Nature Aging.

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

[25]  Kang Zhang,et al.  Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity , 2022, Nature Communications.

[26]  Sharon Y. R. Dent,et al.  Now open: Evolving insights to the roles of lysine acetylation in chromatin organization and function. , 2022, Molecular cell.

[27]  C. Chabot,et al.  3D chromatin remodeling potentiates transcriptional programs driving cell invasion , 2021, Proceedings of the National Academy of Sciences of the United States of America.

[28]  J. Qu,et al.  Large-scale chemical screen identifies Gallic acid as a geroprotector for human stem cells , 2021, Protein & Cell.

[29]  S. Orkin,et al.  Reactivation of a developmentally silenced embryonic globin gene , 2021, Nature Communications.

[30]  Leng Han,et al.  ADEIP: an integrated platform of age-dependent expression and immune profiles across human tissues , 2021, Briefings Bioinform..

[31]  Wenming Zhao,et al.  The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types , 2021, bioRxiv.

[32]  Hening Lin,et al.  Understanding the Function of Mammalian Sirtuins and Protein Lysine Acylation. , 2021, Annual review of biochemistry.

[33]  J. Qu,et al.  SIRT3 consolidates heterochromatin and counteracts senescence , 2021, Nucleic acids research.

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

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

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

[37]  J. I. Izpisúa Belmonte,et al.  A Single-Cell Transcriptomic Atlas of Human Skin Aging. , 2020, Developmental cell.

[38]  A. Moore,et al.  Plasma proteomic biomarker signature of age predicts health and life span , 2020, eLife.

[39]  C. Redman,et al.  Syncytiotrophoblast stress in preeclampsia: the convergence point for multiple pathways. , 2020, American journal of obstetrics and gynecology.

[40]  G. Mazzoccoli,et al.  Melatonin and Sirtuins in Buccal Epithelium: Potential Biomarkers of Aging and Age-Related Pathologies , 2020, International journal of molecular sciences.

[41]  Jing Qu,et al.  Aging Atlas: a multi-omics database for aging biology , 2020, Nucleic Acids Res..

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

[43]  Jorja G Henikoff,et al.  Efficient low-cost chromatin profiling with CUT&Tag , 2020, Nature Protocols.

[44]  Chao Zhang,et al.  ATF3 drives senescence by reconstructing accessible chromatin profiles , 2020, bioRxiv.

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

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

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

[48]  J. Qu,et al.  ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin , 2020, Nucleic acids research.

[49]  A. S. Hansen,et al.  CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism , 2020, Nucleus.

[50]  J. Danesh,et al.  Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases , 2019, Nature Metabolism.

[51]  B. Deplancke,et al.  Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons , 2019, Science Advances.

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

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

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

[55]  H. Kashima,et al.  Trophoblast type-specific expression of senescence markers in the human placenta. , 2019, Placenta.

[56]  Wei Xie,et al.  The role of 3D genome organization in development and cell differentiation , 2019, Nature Reviews Molecular Cell Biology.

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

[58]  Margarita V. Meer,et al.  LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation. , 2019, Cell metabolism.

[59]  J. I. Izpisúa Belmonte,et al.  Up-regulation of FOXD1 by YAP alleviates senescence and osteoarthritis , 2019, PLoS biology.

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

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

[62]  Danica Chen,et al.  Mitochondrial Stress-Initiated Aberrant Activation of the NLRP3 Inflammasome Regulates the Functional Deterioration of Hematopoietic Stem Cell Aging , 2019, Cell reports.

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

[64]  Qi Zhou,et al.  SIRT6 deficiency results in developmental retardation in cynomolgus monkeys , 2018, Nature.

[65]  Cheng Zhu,et al.  Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta , 2018, Cell Research.

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

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

[68]  Daniel S. Day,et al.  YY1 Is a Structural Regulator of Enhancer-Promoter Loops , 2017, Cell.

[69]  Matthew E. Gosden,et al.  Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo , 2017, Nature Cell Biology.

[70]  Guo-Cheng Yuan,et al.  Dissecting super-enhancer hierarchy based on chromatin interactions , 2017, Nature Communications.

[71]  L. Mirny,et al.  Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization , 2017, Cell.

[72]  Jonathan M. Cairns,et al.  Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation. , 2017, Molecular cell.

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

[74]  Neville E. Sanjana,et al.  Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening , 2017, Nature Protocols.

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

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

[77]  Jesse R. Dixon,et al.  Chromatin Domains: The Unit of Chromosome Organization. , 2016, Molecular cell.

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

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

[80]  X. Zhou,et al.  TopDom: an efficient and deterministic method for identifying topological domains in genomes , 2015, Nucleic acids research.

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

[82]  P. Wierzbicki,et al.  Age-Related Changes in Sirtuin 7 Expression in Calorie-Restricted and Refed Rats , 2015, Gerontology.

[83]  Timothy E. Reddy,et al.  Highly Specific Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements , 2015, Nature Methods.

[84]  P. Kharchenko,et al.  The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains , 2015, Genes & development.

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

[86]  Danica Chen,et al.  A mitochondrial UPR-mediated metabolic checkpoint regulates hematopoietic stem cell aging , 2015, Science.

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

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

[89]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[90]  Anthony J. Geneva,et al.  SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age , 2014, Nature Communications.

[91]  D. Sinclair,et al.  Aging-like Phenotype and Defective Lineage Specification in SIRT1-Deleted Hematopoietic Stem and Progenitor Cells , 2014, Stem cell reports.

[92]  H. Gal,et al.  Cell fusion induced by ERVWE1 or measles virus causes cellular senescence , 2013, Genes & development.

[93]  Frank Fischer,et al.  An acetylome peptide microarray reveals specificities and deacetylation substrates for all human sirtuin isoforms , 2013, Nature Communications.

[94]  J. Coppee,et al.  A Role for SIRT2-Dependent Histone H3K18 Deacetylation in Bacterial Infection , 2013, Science.

[95]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[96]  Jennifer E. Phillips-Cremins,et al.  Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment , 2013, Cell.

[97]  J. Kopchick,et al.  The GH/IGF-1 axis in ageing and longevity , 2013, Nature Reviews Endocrinology.

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

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

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

[101]  Kevin Struhl,et al.  SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation , 2012, Nature.

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

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

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

[105]  Robert V Farese,et al.  SIRT3 deficiency and mitochondrial protein hyperacetylation accelerate the development of the metabolic syndrome. , 2011, Molecular cell.

[106]  J. Auwerx,et al.  Sir-two-homolog 2 (Sirt2) modulates peripheral myelination through polarity protein Par-3/atypical protein kinase C (aPKC) signaling , 2011, Proceedings of the National Academy of Sciences.

[107]  Enxuan Jing,et al.  Sirtuin-3 (Sirt3) regulates skeletal muscle metabolism and insulin signaling via altered mitochondrial oxidation and reactive oxygen species production , 2011, Proceedings of the National Academy of Sciences.

[108]  N. Uldbjerg,et al.  Biology of pregnancy‐associated plasma protein‐A in relation to prenatal diagnostics: an overview , 2010, Acta obstetricia et gynecologica Scandinavica.

[109]  C. Conover,et al.  Longevity and age-related pathology of mice deficient in pregnancy-associated plasma protein-A. , 2010, The journals of gerontology. Series A, Biological sciences and medical sciences.

[110]  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.

[111]  F. Mulero,et al.  Sirt1 improves healthy ageing and protects from metabolic syndrome-associated cancer. , 2010, Nature communications.

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

[113]  Or Gozani,et al.  Cell cycle-dependent deacetylation of telomeric histone H3 lysine K56 by human SIRT6 , 2009, Cell cycle.

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

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

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

[117]  P. Pfluger,et al.  Sirt1 protects against high-fat diet-induced metabolic damage , 2008, Proceedings of the National Academy of Sciences.

[118]  E. Bober,et al.  Sirt7 Increases Stress Resistance of Cardiomyocytes and Prevents Apoptosis and Inflammatory Cardiomyopathy in Mice , 2008, Circulation research.

[119]  Howard Y. Chang,et al.  SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin , 2008, Nature.

[120]  C. Conover,et al.  Loss of pregnancy‐associated plasma protein A extends lifespan in mice , 2007, Aging cell.

[121]  C. Conover,et al.  Pregnancy-associated plasma protein-A (PAPP-A): a local regulator of IGF bioavailability through cleavage of IGFBPs. , 2007, Growth hormone & IGF research : official journal of the Growth Hormone Research Society and the International IGF Research Society.

[122]  D. Reinberg,et al.  Human SirT1 interacts with histone H1 and promotes formation of facultative heterochromatin. , 2004, Molecular cell.

[123]  R. Frye,et al.  Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. , 2000, Biochemical and biophysical research communications.

[124]  C. Conover,et al.  Messenger ribonucleic acid levels of pregnancy-associated plasma protein-A and the proform of eosinophil major basic protein: expression in human reproductive and nonreproductive tissues. , 1999, Biology of reproduction.

[125]  C. Conover,et al.  Characterization and partial purification of the insulin-like growth factor (IGF)-dependent IGF binding protein-4-specific protease from human fibroblast conditioned media. , 1999, Growth hormone & IGF research : official journal of the Growth Hormone Research Society and the International IGF Research Society.

[126]  J. Boeke,et al.  An unusual form of transcriptional silencing in yeast ribosomal DNA. , 1997, Genes & development.

[127]  I. Herskowitz,et al.  Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. , 1987, Genetics.

[128]  J. Grudzinskas,et al.  Pregnancy-associated plasma protein A: circulating levels during normal pregnancy. , 1981, American journal of obstetrics and gynecology.

[129]  W. Spellacy,et al.  Characterization of four human pregnancy-associated plasma proteins. , 1974, American journal of obstetrics and gynecology.

[130]  D. Haldar,et al.  Human sirtuin 3 (SIRT3) deacetylates histone H3 lysine 56 to promote nonhomologous end joining repair. , 2018, DNA repair.

[131]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

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

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

[134]  Heng Li,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .