Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The epigenetic tracks of aging

(2014) Carola Ingrid Weidner et al.   BIOLOGICAL CHEMISTRY

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

(2014) Carola Weidner et al.   GENOME BIOLOGY

The GATA transcription factor/MTA-1 homologegr-1promotes longevity and stress resistance inCaenorhabditis elegans

(2013) Stephanie M. Zimmerman et al.   AGING CELL

Closing the (nuclear) envelope on the genome: How nuclear lamins interact with promoters and modulate gene expression

(2013) Philippe Collas et al.   BIOESSAYS

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   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

Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes

(2013) E. Lund et al.   GENOME RESEARCH

Age-associated epigenetic drift: implications, and a case of epigenetic thrift?

(2013) A. E. Teschendorff et al.   HUMAN MOLECULAR GENETICS

A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects

(2013) Joseph L. McClay et al.   HUMAN MOLECULAR GENETICS

MYCN/LIN28B/Let-7/HMGA2 pathway implicated by meta-analysis of GWAS in suppression of post-natal proliferation thereby potentially contributing to aging

(2013) Michael Keane et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Senescent cells harbour features of the cancer epigenome

(2013) Hazel A. Cruickshanks et al.   NATURE CELL BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

Conditional TRF1 knockout in the hematopoietic compartment leads to bone marrow failure and recapitulates clinical features of dyskeratosis congenita

(2012) F. Beier et al.   BLOOD

Pluripotent stem cells escape from senescence-associated DNA methylation changes

(2012) C. M. Koch 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

Donor Age of Human Platelet Lysate Affects Proliferation and Differentiation of Mesenchymal Stem Cells

(2012) Michael Lohmann et al.   PLoS One

Human Telomeres Are Tethered to the Nuclear Envelope during Postmitotic Nuclear Assembly

(2012) Laure Crabbe et al.   Cell Reports

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

Monitoring of cellular senescence by DNA-methylation at specific CpG sites

(2011) Carmen M. Koch et al.   AGING CELL

Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging

(2011) M. T. Bocker et al.   BLOOD

Population dynamics of mesenchymal stromal cells during culture expansion

(2011) Anne Schellenberg et al.   CYTOTHERAPY

The role of nuclear lamin B1 in cell proliferation and senescence

(2011) T. Shimi et al.   GENES & DEVELOPMENT

Specific Age-Associated DNA Methylation Changes in Human Dermal Fibroblasts

(2011) Carmen M. Koch et al.   PLoS One

Different telomere-length dynamics at the inner cell mass versus established embryonic stem (ES) cells

(2011) E. Varela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene expression, chromosome position and lamin A/C mutations

(2011) Megan J. Puckelwartz et al.   Nucleus

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

(2010) A. E. Teschendorff et al.   GENOME RESEARCH

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

(2010) M. D. Robinson et al.   GENOME RESEARCH

Widespread and tissue specific age-related DNA methylation changes in mice

(2010) S. Maegawa et al.   GENOME RESEARCH

Whole-genome DNA methylation profiling using MethylCap-seq

(2010) Arie B. Brinkman et al.   METHODS

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Altered Chromosomal Positioning, Compaction, and Gene Expression with a Lamin A/C Gene Mutation

(2010) Stephanie K. Mewborn et al.   PLoS One

DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells

(2009) Simone Bork et al.   AGING CELL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs

(2009) Bartek Wilczynski et al.   BMC BIOINFORMATICS

Novel roles for A-type lamins in telomere biology and the DNA damage response pathway

(2009) Ignacio Gonzalez-Suarez et al.   EMBO JOURNAL

Interaction between the inner nuclear membrane lamin B receptor and the heterochromatic methyl binding protein, MeCP2

(2009) Alessia Guarda et al.   EXPERIMENTAL CELL RESEARCH

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

(2009) David Serre et al.   NUCLEIC ACIDS RESEARCH

Ah receptor and NF-κB interplay on the stage of epigenome

(2008) Yanan Tian   BIOCHEMICAL PHARMACOLOGY

Telomeres, stem cells, and hematology

(2008) P. M. Lansdorp   BLOOD

The nuclear lamina promotes telomere aggregation and centromere peripheral localization during senescence of human mesenchymal stem cells

(2008) V. Raz et al.   JOURNAL OF CELL SCIENCE

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Replicative Senescence of Mesenchymal Stem Cells: A Continuous and Organized Process

(2008) Wolfgang Wagner et al.   PLoS One

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY