Genome-wide RNA polymerase stalling shapes the transcriptome during aging

Proper control of R‐loop homeostasis is required for maintenance of gene expression and neuronal function during aging

(2022) Juan Jauregui‐Lozano et al.   AGING CELL

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice

(2021) Matias Fuentealba et al.   MECHANISMS OF AGEING AND DEVELOPMENT

DNA damage—how and why we age?

(2021) Matt Yousefzadeh et al.   eLife

Gene Size Matters: An Analysis of Gene Length in the Human Genome

(2021) Inês Lopes et al.   Frontiers in Genetics

The central role of DNA damage in the ageing process

(2021) Björn Schumacher et al.   NATURE

Deletion of Nrf2 shortens lifespan in C57BL6/J male mice but does not alter the health and survival benefits of caloric restriction

(2020) Laura C.D. Pomatto et al.   FREE RADICAL BIOLOGY AND MEDICINE

Temporal changes in the gene expression heterogeneity during brain development and aging

(2020) Ulaş Işıldak et al.   Scientific Reports

Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair

(2020) Yuka Nakazawa et al.   CELL

Regulation of the RNAPII Pool Is Integral to the DNA Damage Response

(2020) Ana Tufegdžić Vidaković et al.   CELL

Ageing hallmarks exhibit organ-specific temporal signatures

(2020) Nicholas Schaum et al.   NATURE

Long genes are more frequently affected by somatic mutations and show reduced expression in Alzheimer's disease: Implications for disease etiology

(2020) Sourena Soheili‐Nezhad et al.   Alzheimers & Dementia

High levels of oxidatively generated DNA damage 8,5’-cyclo-2’-deoxyadenosine accumulate in the brain tissues of xeroderma pigmentosum group A gene-knockout mice

(2019) Toshio Mori et al.   DNA REPAIR

Comparison of multi-tissue aging between human and mouse

(2019) Jujuan Zhuang et al.   Scientific Reports

The role of lipid metabolism in aging, lifespan regulation, and age‐related disease

(2019) Adiv A. Johnson et al.   AGING CELL

DNA Damage and Associated DNA Repair Defects in Disease and Premature Aging

(2019) Vinod Tiwari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The DNA damage response to transcription stress

(2019) Hannes Lans et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA damage and transcription stress cause ATP-mediated redesign of metabolism and potentiation of anti-oxidant buffering

(2019) Chiara Milanese et al.   Nature Communications

Global accumulation of circRNAs during aging in Caenorhabditis elegans

(2018) Mariela Cortés-López et al.   BMC GENOMICS

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II

(2018) Barbara Steurer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunosenescence and Inflamm-Aging As Two Sides of the Same Coin: Friends or Foes?

(2018) Tamas Fulop et al.   Frontiers in Immunology

Spontaneous DNA damage to the nuclear genome promotes senescence, redox imbalance and aging

(2018) Andria R. Robinson et al.   Redox Biology

Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans

(2017) Khyobeni Mozhui et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Reference ranges for serum insulin-like growth factor I (IGF-I) in healthy Chinese adults

(2017) Huijuan Zhu et al.   PLoS One

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

Longer lifespan in male mice treated with a weakly estrogenic agonist, an antioxidant, an α-glucosidase inhibitor or a Nrf2-inducer

(2016) Randy Strong et al.   AGING CELL

Genome Integrity in Aging: Human Syndromes, Mouse Models, and Therapeutic Options

(2016) Wilbert P. Vermeij et al.   Annual Review of Pharmacology and Toxicology

Epigenetic Mechanisms of Longevity and Aging

(2016) Payel Sen et al.   CELL

Restricted diet delays accelerated ageing and genomic stress in DNA-repair-deficient mice

(2016) W. P. Vermeij et al.   NATURE

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

(2015) Jinchuan Hu et al.   GENES & DEVELOPMENT

The core spliceosome as target and effector of non-canonical ATM signalling

(2015) Maria Tresini et al.   NATURE

Deciphering the RNA landscape by RNAome sequencing

(2015) Kasper WJ Derks et al.   RNA Biology

Transcriptome analysis of ageing in uninjured human Achilles tendon

(2015) Mandy Peffers et al.   ARTHRITIS RESEARCH & THERAPY

Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality

(2015) Sunitha Rangaraju et al.   eLife

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Senescence and apoptosis: dueling or complementary cell fates?

(2014) B. G. Childs et al.   EMBO REPORTS

Changes in Nucleosome Occupancy Associated with Metabolic Alterations in Aged Mammalian Liver

(2014) Irina M. Bochkis et al.   Cell Reports

UVB Induces a Genome-Wide Acting Negative Regulatory Mechanism That Operates at the Level of Transcription Initiation in Human Cells

(2014) Ákos Gyenis et al.   PLoS Genetics

Cell-Autonomous Progeroid Changes in Conditional Mouse Models for Repair Endonuclease XPG Deficiency

(2014) Sander Barnhoorn et al.   PLoS Genetics

MicroRNAs as Mediators of the Ageing Process

(2014) Lorna Harries   Genes

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

The GH/IGF-1 axis in ageing and longevity

(2013) Riia K. Junnila et al.   Nature Reviews Endocrinology

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

The oxidative DNA lesions 8,5′-cyclopurines accumulate with aging in a tissue-specific manner

(2012) Jin Wang et al.   AGING CELL

Aging, Cellular Senescence, and Cancer

(2012) Judith Campisi   Annual Review of Physiology

MicroRNA in Aging: From Discovery to Biology

(2012) Hwa Jin Jung et al.   CURRENT GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mutagenesis and Repair Induced by the DNA Advanced Glycation End ProductN2-1-(Carboxyethyl)-2′-deoxyguanosine in Human Cells

(2011) Daniel Tamae et al.   BIOCHEMISTRY

Liver-Derived IGF-I Regulates Mean Life Span in Mice

(2011) Johan Svensson et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Aging in inbred strains of mice: study design and interim report on median lifespans and circulating IGF1 levels

(2009) Rong Yuan et al.   AGING CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genes and gene expression modules associated with caloric restriction and aging in the laboratory mouse

(2009) William R Swindell   BMC GENOMICS

Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity

(2009) George A. Garinis et al.   NATURE CELL BIOLOGY

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

(2008) Philipp Oberdoerffer et al.   CELL

Delayed and Accelerated Aging Share Common Longevity Assurance Mechanisms

(2008) Björn Schumacher et al.   PLoS Genetics