Reorganization of chromosome architecture in replicative cellular senescence

Nuclear protein accumulation in cellular senescence and organismal aging revealed with a novel single-cell resolution fluorescence microscopy assay

(2016) Marco De Cecco et al.   Aging-US

How to measure RNA expression in rare senescent cells expressing any specific protein such as p16Ink4a

(2016) Jessie C. Jeyapalan et al.   Aging-US

Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues

(2016) Marco De Cecco et al.   Aging-US

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Long-Range Chromatin Interactions

(2015) Job Dekker et al.   Cold Spring Harbor Perspectives in Biology

Global Reorganization of the Nuclear Landscape in Senescent Cells

(2015) Tamir Chandra et al.   Cell Reports

A comparison of oncogene-induced senescence and replicative senescence: implications for tumor suppression and aging

(2014) David M. Nelson et al.   AGE

A genomics approach identifies senescence-specific gene expression regulation

(2014) Daniel H. Lackner et al.   AGING CELL

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

A statistical approach for inferring the 3D structure of the genome

(2014) N. Varoquaux et al.   BIOINFORMATICS

Irreparable telomeric DNA damage and persistent DDR signalling as a shared causative mechanism of cellular senescence and ageing

(2014) Francesca Rossiello et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cellular senescence and its effector programs

(2014) R. Salama et al.   GENES & DEVELOPMENT

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Hutchinson-Gilford progeria syndrome through the lens of transcription

(2013) Miron Prokocimer et al.   AGING CELL

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

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Programmed Cell Senescence during Mammalian Embryonic Development

(2013) Daniel Muñoz-Espín et al.   CELL

Senescence Is a Developmental Mechanism that Contributes to Embryonic Growth and Patterning

(2013) Mekayla Storer et al.   CELL

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence

(2013) M. Sadaie et al.   GENES & DEVELOPMENT

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

Higher-order unfolding of satellite heterochromatin is a consistent and early event in cell senescence

(2013) Eric C. Swanson et al.   JOURNAL OF CELL BIOLOGY

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Senescent cells harbour features of the cancer epigenome

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

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

Binary Interval Search: a scalable algorithm for counting interval intersections

(2012) Ryan M. Layer et al.   BIOINFORMATICS

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

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

(2012) Yin C Lin et al.   NATURE IMMUNOLOGY

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

Senescence-associated heterochromatin foci are dispensable for cellular senescence, occur in a cell type- and insult-dependent manner and follow expression of p16ink4a

(2011) Martin Kosar et al.   CELL CYCLE

Control of the senescence-associated secretory phenotype by NF- B promotes senescence and enhances chemosensitivity

(2011) Y. Chien et al.   GENES & DEVELOPMENT

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Clearance of p16Ink4a-positive senescent cells delays ageing-associated disorders

(2011) Darren J. Baker et al.   NATURE

Interplay between oncogene-induced DNA damage response and heterochromatin in senescence and cancer

(2011) Raffaella Di Micco et al.   NATURE CELL BIOLOGY

Age-associated increase in heterochromatic marks in murine and primate tissues

(2010) Jill A. Kreiling et al.   AGING CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The matricellular protein CCN1 induces fibroblast senescence and restricts fibrosis in cutaneous wound healing

(2010) Joon-Il Jun et al.   NATURE CELL BIOLOGY

Senescent mouse cells fail to overtly regulate the HIRA histone chaperone and do not form robust Senescence Associated Heterochromatin Foci

(2010) Alyssa L Kennedy et al.   Cell Division

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

(2009) R. S. Hansen 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

Senescence of Activated Stellate Cells Limits Liver Fibrosis

(2008) Valery Krizhanovsky et al.   CELL

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

(2008) Lars Guelen et al.   NATURE

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor

(2008) Jean-Philippe Coppé et al.   PLOS BIOLOGY