Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy

DNA Damage Response/TP53 Pathway Is Activated and Contributes to the Pathogenesis of Dilated Cardiomyopathy Associated With LMNA (Lamin A/C) Mutations

(2019) Suet Nee Chen et al.   CIRCULATION RESEARCH

Suppression of Activated FOXO Transcription Factors in the Heart Prolongs Survival in a Mouse Model of LaminopathiesNovelty and Significance

(2018) Gaelle Auguste et al.   CIRCULATION RESEARCH

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

(2018) Ralf Gilsbach et al.   Nature Communications

Transcriptome analysis of human heart failure reveals dysregulated cell adhesion in dilated cardiomyopathy and activated immune pathways in ischemic heart failure

(2018) Mary E. Sweet et al.   BMC GENOMICS

p53 regulates the cardiac transcriptome

(2017) Tak W. Mak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

(2017) Judith F. Kribelbauer et al.   Cell Reports

Current insights into LMNA cardiomyopathies: Existing models and missing LINCs

(2017) Daniel Brayson et al.   Nucleus

Current insights into LMNA cardiomyopathies: Existing models and missing LINCs

(2017) Daniel Brayson et al.   Nucleus

Knockdown of Plakophilin 2 Downregulates miR-184 Through CpG Hypermethylation and Suppression of the E2F1 Pathway and Leads to Enhanced Adipogenesis In VitroNovelty and Significance

(2016) Priyatansh Gurha et al.   CIRCULATION RESEARCH

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha

(2016) Kevin Gesson et al.   GENOME RESEARCH

Molecular insights into the premature aging disease progeria

(2016) Sandra Vidak et al.   HISTOCHEMISTRY AND CELL BIOLOGY

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Lamins: Nuclear Intermediate Filament Proteins with Fundamental Functions in Nuclear Mechanics and Genome Regulation

(2015) Yosef Gruenbaum et al.   Annual Review of Biochemistry

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

(2015) Jop Kind et al.   CELL

Dynamics of Cell Generation and Turnover in the Human Heart

(2015) Olaf Bergmann et al.   CELL

Deciphering the Epigenetic Code of Cardiac Myocyte TranscriptionNovelty and Significance

(2015) Sebastian Preissl et al.   CIRCULATION RESEARCH

Revisiting Cardiac Cellular CompositionNovelty and Significance

(2015) Alexander R. Pinto et al.   CIRCULATION RESEARCH

Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B

(2015) Torunn Rønningen et al.   GENOME RESEARCH

RNA-Seq identifies novel myocardial gene expression signatures of heart failure

(2015) Yichuan Liu et al.   GENOMICS

Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

(2015) Jennifer C. Harr et al.   JOURNAL OF CELL BIOLOGY

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

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

Role of nuclear Lamin A/C in cardiomyocyte functions

(2014) Monica Carmosino et al.   BIOLOGY OF THE CELL

Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNAs in Failing Human Heart and Remodeling With Mechanical Circulatory Support

(2014) Kai-Chien Yang et al.   CIRCULATION

Linker of Nucleoskeleton and Cytoskeleton Complex Proteins in Cardiac Structure, Function, and Disease

(2014) Matthew J Stroud et al.   CIRCULATION RESEARCH

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

(2014) Eivind Lund et al.   NUCLEIC ACIDS RESEARCH

Robustly detecting differential expression in RNA sequencing data using observation weights

(2014) Xiaobei Zhou et al.   NUCLEIC ACIDS RESEARCH

Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease

(2014) Aibin He et al.   Nature Communications

GATA-dependent regulatory switches establish atrioventricular canal specificity during heart development

(2014) Sonia Stefanovic et al.   Nature Communications

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

When Lamins Go Bad: Nuclear Structure and Disease

(2013) Katherine H. Schreiber et al.   CELL

Circulating p53-Responsive MicroRNAs Are Predictive Indicators of Heart Failure After Acute Myocardial Infarction

(2013) Sen Matsumoto et al.   CIRCULATION RESEARCH

ATM Mediates pRB Function To Control DNMT1 Protein Stability and DNA Methylation

(2013) Awad Shamma et al.   MOLECULAR AND CELLULAR BIOLOGY

Senescent cells harbour features of the cancer epigenome

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

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

(2012) Joseph M. Zullo et al.   CELL

Mapping of lamin A- and progerin-interacting genome regions

(2012) Nard Kubben et al.   CHROMOSOMA

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Histone modifications and lamin A regulate chromatin protein dynamics in early embryonic stem cell differentiation

(2012) Shai Melcer et al.   Nature Communications

Isolation of Cardiomyocyte Nuclei from Post-mortem Tissue

(2012) Olaf Bergmann et al.   Jove-Journal of Visualized Experiments

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

LMNA cardiomyopathy: cell biology and genetics meet clinical medicine

(2011) J. T. Lu et al.   Disease Models & Mechanisms

Mutations in the Lamin A/C gene mimic arrhythmogenic right ventricular cardiomyopathy

(2011) Giovanni Quarta et al.   EUROPEAN HEART JOURNAL

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

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Identification of cardiomyocyte nuclei and assessment of ploidy for the analysis of cell turnover

(2010) Olaf Bergmann et al.   EXPERIMENTAL CELL RESEARCH

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

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

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

(2010) Kohta Ikegami et al.   GENOME BIOLOGY

A transcription factor affinity-based code for mammalian transcription initiation

(2009) M. Megraw et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Elevated p53 expression is associated with dysregulation of the ubiquitin-proteasome system in dilated cardiomyopathy

(2008) E. J. Birks et al.   CARDIOVASCULAR RESEARCH

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

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE