Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome

Epigenetic signatures of Werner syndrome occur early in life and are distinct from normal epigenetic aging processes

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DNA methylation loss in late-replicating domains is linked to mitotic cell division

(2018) Wanding Zhou et al.   NATURE GENETICS

Epigenetic clock for skin and blood cells applied to Hutchinson Gilford Progeria Syndrome and ex vivo studies

(2018) Steve Horvath et al.   Aging-US

ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

(2018) Tiago C Silva et al.   BIOINFORMATICS

Systematic evaluation of DNA methylation age estimation with common preprocessing methods and the Infinium MethylationEPIC BeadChip array

(2018) Lisa M McEwen et al.   Clinical Epigenetics

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle

(2017) Wen Jun Xie et al.   Scientific Reports

Repression of the Antioxidant NRF2 Pathway in Premature Aging

(2016) Nard Kubben et al.   CELL

Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis

(2016) Lorenzo Rinaldi et al.   Cell Stem Cell

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

(2016) Xingqi Chen et al.   NATURE METHODS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

Reconfiguration of DNA methylation in aging

(2015) Michele Zampieri et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

(2015) Tuncay Baubec et al.   NATURE

Global Reorganization of the Nuclear Landscape in Senescent Cells

(2015) Tamir Chandra et al.   Cell Reports

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

(2015) Lijing Yao et al.   GENOME BIOLOGY

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

(2015) Eivind G Lund et al.   Nucleus

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

(2015) Eivind G Lund et al.   Nucleus

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(2015) Arthur Liberzon et al.   Cell Systems

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

The p.R482W substitution in A-type lamins deregulates SREBP1 activity in Dunnigan-type familial partial lipodystrophy

(2014) Nathalie Vadrot et al.   HUMAN MOLECULAR GENETICS

Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations

(2014) Eivind Lund et al.   NUCLEIC ACIDS RESEARCH

The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts

(2014) James R Wagner et al.   GENOME BIOLOGY

Depleting the methyltransferase Suv39h1 improves DNA repair and extends lifespan in a progeria mouse model

(2013) Baohua Liu et al.   Nature Communications

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Aberrant DNA methylation profiles in the premature aging disorders Hutchinson-Gilford Progeria and Werner syndrome

(2012) Holger Heyn et al.   Epigenetics

Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome

(2012) R. P. McCord et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Distinct DNA methylomes of newborns and centenarians

(2012) H. Heyn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recapitulation of premature ageing with iPSCs from Hutchinson–Gilford progeria syndrome

(2011) Guang-Hui Liu et al.   NATURE

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Farnesyltransferase inhibitor treatment restores chromosome territory positions and active chromosome dynamics in Hutchinson-Gilford progeria syndrome cells

(2011) Ishita S Mehta et al.   GENOME BIOLOGY

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

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

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

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

Telomere length in Hutchinson-Gilford Progeria Syndrome

(2009) Michelle L. Decker et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Effect of progerin on the accumulation of oxidized proteins in fibroblasts from Hutchinson Gilford progeria patients

(2009) Gabriela Viteri et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

(2009) Bo Wen et al.   NATURE GENETICS

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Oncogenic BRAF Induces Senescence and Apoptosis through Pathways Mediated by the Secreted Protein IGFBP7

(2008) Narendra Wajapeyee et al.   CELL

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

(2008) Lars Guelen et al.   NATURE

Phenotype and Course of Hutchinson–Gilford Progeria Syndrome

(2008) Melissa A. Merideth et al.   NEW ENGLAND JOURNAL OF MEDICINE

Glioblastoma-secreted factors induce IGFBP7 and angiogenesis by modulating Smad-2-dependent TGF-β signaling

(2008) A Pen et al.   ONCOGENE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY