Loss of epigenetic information as a cause of mammalian aging

Inference of CRISPR Edits from Sanger Trace Data

(2022) David Conant et al.   CRISPR Journal

Semirational bioengineering of AAV vectors with increased potency and specificity for systemic gene therapy of muscle disorders

(2022) Jihad El Andari et al.   Science Advances

Unlike dietary restriction, rapamycin fails to extend lifespan and reduce transcription stress in progeroid DNA repair‐deficient mice

(2021) María B. Birkisdóttir et al.   AGING CELL

Genomic instability in the naturally and prematurely aged myocardium

(2021) Federica De Majo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increased somatic mutation burdens in normal human cells due to defective DNA polymerases

(2021) Philip S. Robinson et al.   NATURE GENETICS

The Pathobiology of Skin Aging

(2020) Eleanor Russell-Goldman et al.   AMERICAN JOURNAL OF PATHOLOGY

Transient non-integrative expression of nuclear reprogramming factors promotes multifaceted amelioration of aging in human cells

(2020) Tapash Jay Sarkar et al.   Nature Communications

Reprogramming to recover youthful epigenetic information and restore vision

(2020) Yuancheng Lu et al.   NATURE

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

L1 drives IFN in senescent cells and promotes age-associated inflammation

(2019) Marco De Cecco et al.   NATURE

Retrospective Analysis of the Effects of Identification Procedures and Cage Changing by Using Data from Automated, Continuous Monitoring

(2019) Maria A Lim et al.   Journal of the American Association for Laboratory Animal Science

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

(2019) Bérénice A. Benayoun et al.   GENOME RESEARCH

Epigenetic changes during aging and their reprogramming potential

(2019) Alice E. Kane et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation

(2019) Matthew Simon et al.   Cell Metabolism

Impairment of an Endothelial NAD+-H2S Signaling Network Is a Reversible Cause of Vascular Aging

(2019) Abhirup Das et al.   CELL

SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species

(2019) Xiao Tian et al.   CELL

Stem cell competition orchestrates skin homeostasis and ageing

(2019) Nan Liu et al.   NATURE

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Methylation of the genes ROD1, NLRC5, and HKR1 is associated with aging in Hainan centenarians

(2018) Qian Zeng et al.   BMC Medical Genomics

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

(2018) Peggie Cheung et al.   CELL

Neuronal hypothalamic regulation of body metabolism and bone density is galanin dependent

(2018) Anna Idelevich et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2018) Anne Zirkel et al.   MOLECULAR CELL

Wnt signaling induces radioresistance through upregulating HMGB1 in esophageal squamous cell carcinoma

(2018) Yuanyuan Zhao et al.   Cell Death & Disease

The Aging Astrocyte Transcriptome from Multiple Regions of the Mouse Brain

(2018) Matthew M. Boisvert et al.   Cell Reports

Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression

(2018) I-Hsuan Lin et al.   BMC GENETICS

Increased epigenetic age in normal breast tissue from luminal breast cancer patients

(2018) Erin W. Hofstatter et al.   Clinical Epigenetics

A multi-tissue full lifespan epigenetic clock for mice

(2018) Michael J. Thompson et al.   Aging-US

Identity Noise and Adipogenic Traits Characterize Dermal Fibroblast Aging

(2018) Marion Claudia Salzer et al.   CELL

Architects meets Repairers: The interplay between homeobox genes and DNA repair

(2018) Bruno César Feltes   DNA REPAIR

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

A whole lifespan mouse multi-tissue DNA methylation clock

(2018) Margarita V Meer et al.   eLife

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

(2017) Sharmistha Kundu et al.   MOLECULAR CELL

Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape

(2017) Andrey Tvardovskiy et al.   NUCLEIC ACIDS RESEARCH

Individual CpG sites that are associated with age and life expectancy become hypomethylated upon aging

(2017) Yan Zhang et al.   Clinical Epigenetics

Development of the Digital Arthritis Index, a Novel Metric to Measure Disease Parameters in a Rat Model of Rheumatoid Arthritis

(2017) Maria A. Lim et al.   Frontiers in Pharmacology

Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming

(2017) Li Tan et al.   Stem Cell Reports

Cerebromicrovascular dysfunction predicts cognitive decline and gait abnormalities in a mouse model of whole brain irradiation-induced accelerated brain senescence

(2017) Zoltan Ungvari et al.   GeroScience

Epigenetic Mechanisms of Longevity and Aging

(2016) Payel Sen et al.   CELL

In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming

(2016) Alejandro Ocampo et al.   CELL

Impaired DNA double-strand break repair contributes to the age-associated rise of genomic instability in humans

(2016) Z Li et al.   CELL DEATH AND DIFFERENTIATION

Hallmarks of progeroid syndromes: lessons from mice and reprogrammed cells

(2016) Dido Carrero et al.   Disease Models & Mechanisms

Aging of Cloned Animals: A Mini-Review

(2016) Jörg Patrick Burgstaller et al.   GERONTOLOGY

Mouse models of ageing and their relevance to disease

(2016) Sulev Kõks et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Do DNA Double-Strand Breaks Drive Aging?

(2016) Ryan R. White et al.   MOLECULAR CELL

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Chromatin-modifying genetic interventions suppress age-associated transposable element activation and extend life span inDrosophila

(2016) Jason G. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NLRC5/MHC class I transactivator is a target for immune evasion in cancer

(2016) Sayuri Yoshihama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hair follicle aging is driven by transepidermal elimination of stem cells via COL17A1 proteolysis

(2016) H. Matsumura et al.   SCIENCE

Pathology of Mouse Models of Accelerated Aging

(2016) L. Harkema et al.   VETERINARY PATHOLOGY

Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells

(2016) Lacey J. Luense et al.   Epigenetics & Chromatin

Small nucleoli are a cellular hallmark of longevity

(2016) Varnesh Tiku et al.   Nature Communications

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Epigenetics and aging

(2016) S. Pal et al.   Science Advances

SIRT6 stabilizes DNA-dependent Protein Kinase at chromatin for DNA double-strand break repair

(2016) Ronald A. McCord et al.   Aging-US

Dietary and genetic effects on age-related loss of gene silencing reveal epigenetic plasticity of chromatin repression during aging

(2016) Nan Jiang et al.   Aging-US

Evidence that mutation accumulation does not cause aging inSaccharomyces cerevisiae

(2015) Alaattin Kaya et al.   AGING CELL

Reduced Expression of MYC Increases Longevity and Enhances Healthspan

(2015) Jeffrey W. Hofmann et al.   CELL

Small-Molecule-Driven Direct Reprogramming of Mouse Fibroblasts into Functional Neurons

(2015) Xiang Li et al.   Cell Stem Cell

Optic nerve head biomechanics in aging and disease

(2015) J. Crawford Downs   EXPERIMENTAL EYE RESEARCH

H3K36 methylation promotes longevity by enhancing transcriptional fidelity

(2015) Payel Sen et al.   GENES & DEVELOPMENT

HIV-1 Infection Accelerates Age According to the Epigenetic Clock

(2015) Steve Horvath et al.   JOURNAL OF INFECTIOUS DISEASES

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epigenetic regulation of ageing: linking environmental inputs to genomic stability

(2015) Bérénice A. Benayoun et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Mitochondrial morphology is altered in atrophied skeletal muscle of aged mice

(2015) Jean-Philippe Leduc-Gaudet et al.   Oncotarget

APOE Stabilization by Exercise Prevents Aging Neurovascular Dysfunction and Complement Induction

(2015) Ileana Soto et al.   PLOS BIOLOGY

Loss of the Set2 histone methyltransferase increases cellular lifespan in yeast cells

(2014) Hong-Yeoul Ryu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The 3D Genome in Transcriptional Regulation and Pluripotency

(2014) David U. Gorkin et al.   Cell Stem Cell

Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

(2014) Z. Hu et al.   GENES & DEVELOPMENT

REST and stress resistance in ageing and Alzheimer’s disease

(2014) Tao Lu et al.   NATURE

Quantifying DNA double-strand breaks induced by site-specific endonucleases in living cells by ligation-mediated purification

(2014) Catherine Chailleux et al.   Nature Protocols

ChIP-Enrich: gene set enrichment testing for ChIP-seq data

(2014) Ryan P. Welch et al.   NUCLEIC ACIDS RESEARCH

Aging-induced type I interferon response at the choroid plexus negatively affects brain function

(2014) K. Baruch et al.   SCIENCE

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

Aging of blood can be tracked by DNA methylation changes at just three CpG sites

(2014) Carola Weidner et al.   GENOME BIOLOGY

Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements

(2013) Marco De Cecco et al.   AGING CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Successful Serial Recloning in the Mouse over Multiple Generations

(2013) Sayaka Wakayama et al.   Cell Stem Cell

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape

(2013) P. P. Shah et al.   GENES & DEVELOPMENT

The histone demethylase LSD1/KDM1A promotes the DNA damage response

(2013) Nima Mosammaparast et al.   JOURNAL OF CELL BIOLOGY

Estimating Podocyte Number and Density Using a Single Histologic Section

(2013) M. Venkatareddy et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

A Clinical Frailty Index in Aging Mice: Comparisons With Frailty Index Data in Humans

(2013) Jocelyne C. Whitehead et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

A canonical to non-canonical Wnt signalling switch in haematopoietic stem-cell ageing

(2013) Maria Carolina Florian et al.   NATURE

SIRT1 collaborates with ATM and HDAC1 to maintain genomic stability in neurons

(2013) Matthew M Dobbin et al.   NATURE NEUROSCIENCE

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Lamin B1 loss is a senescence-associated biomarker

(2012) Adam Freund et al.   MOLECULAR BIOLOGY OF THE CELL

Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates

(2012) Gregory Hannum et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Review: Microglia of the aged brain: primed to be activated and resistant to regulation

(2012) D. M. Norden et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells

(2011) Roberto Chiarle et al.   CELL

Cutting Edge: Ku70 Is a Novel Cytosolic DNA Sensor That Induces Type III Rather Than Type I IFN

(2011) X. Zhang et al.   JOURNAL OF IMMUNOLOGY

Age-Related Alterations in Neurons of the Mouse Retina

(2011) M. A. Samuel et al.   JOURNAL OF NEUROSCIENCE

Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans

(2011) Eric L. Greer et al.   NATURE

The metabolic footprint of aging in mice

(2011) Riekelt H. Houtkooper et al.   Scientific Reports

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Bridging Neurocognitive Aging and Disease Modification: Targeting Functional Mechanisms of Memory Impairment

(2010) M. Gallagher et al.   Current Alzheimer Research

Statistical and visual crossdating in R using the dplR library

(2010) Andrew G. Bunn   DENDROCHRONOLOGIA

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Age-Related Hyperkyphosis: Its Causes, Consequences, and Management

(2010) Wendy B. Katzman et al.   JOURNAL OF ORTHOPAEDIC & SPORTS PHYSICAL THERAPY

Elevated Histone Expression Promotes Life Span Extension

(2010) Jason Feser et al.   MOLECULAR CELL

Members of the H3K4 trimethylation complex regulate lifespan in a germline-dependent manner in C. elegans

(2010) Eric L. Greer et al.   NATURE

A novel pathway regulates memory and plasticity via SIRT1 and miR-134

(2010) Jun Gao et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Myogenic transcriptional activation of MyoD mediated by replication-independent histone deposition

(2010) J.-H. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Histone H4 lysine 16 acetylation regulates cellular lifespan

(2009) Weiwei Dang et al.   NATURE

Telomere length measurement by a novel monochrome multiplex quantitative PCR method

(2009) R. M. Cawthon   NUCLEIC ACIDS RESEARCH

Increased muscle PGC-1  expression protects from sarcopenia and metabolic disease during aging

(2009) T. Wenz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The Adaptive Brain: Aging and Neurocognitive Scaffolding

(2008) Denise C. Park et al.   Annual Review of Psychology

An elt-3/elt-5/elt-6 GATA Transcription Circuit Guides Aging in C. elegans

(2008) Yelena V. Budovskaya et al.   CELL

SIRT1 Redistribution on Chromatin Promotes Genomic Stability but Alters Gene Expression during Aging

(2008) Philipp Oberdoerffer et al.   CELL

A dendrochronology program library in R (dplR)

(2008) Andrew G. Bunn   DENDROCHRONOLOGIA

macroH2A1-Dependent Silencing of Endogenous Murine Leukemia Viruses

(2008) L. N. Changolkar et al.   MOLECULAR AND CELLULAR BIOLOGY

Double Strand Breaks Can Initiate Gene Silencing and SIRT1-Dependent Onset of DNA Methylation in an Exogenous Promoter CpG Island

(2008) Heather M. O'Hagan et al.   PLoS Genetics