Elucidating the mechanisms of transcription regulation during heart development by next-generation sequencing

Brg1 modulates enhancer activation in mesoderm lineage commitment

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15q11.2 microdeletion (BP1–BP2) and developmental delay, behaviour issues, epilepsy and congenital heart disease: A series of 52 patients

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Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

Increased Frequency of De Novo Copy Number Variants in Congenital Heart Disease by Integrative Analysis of Single Nucleotide Polymorphism Array and Exome Sequence Data

(2014) Joseph T. Glessner et al.   CIRCULATION RESEARCH

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

A long noncoding RNA protects the heart from pathological hypertrophy

(2014) Pei Han et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

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Advances in the profiling of DNA modifications: cytosine methylation and beyond

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Histone H3 Lysine 36 Methyltransferase Whsc1 Promotes the Association of Runx2 and p300 in the Activation of Bone-Related Genes

(2014) Yu Fei Lee et al.   PLoS One

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

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

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure

(2013) Priti Anand et al.   CELL

De novo mutations in histone-modifying genes in congenital heart disease

(2013) Samir Zaidi et al.   NATURE

A genome-wide association study identifies two risk loci for congenital heart malformations in Han Chinese populations

(2013) Zhibin Hu et al.   NATURE GENETICS

Genome-wide association study of multiple congenital heart disease phenotypes identifies a susceptibility locus for atrial septal defect at chromosome 4p16

(2013) Heather J Cordell et al.   NATURE GENETICS

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

CYFIP1 Coordinates mRNA Translation and Cytoskeleton Remodeling to Ensure Proper Dendritic Spine Formation

(2013) Silvia De Rubeis et al.   NEURON

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

(2012) Sharon L. Paige et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer

(2012) Malou van den Boogaard et al.   JOURNAL OF CLINICAL INVESTIGATION

Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis

(2012) Paul Delgado-Olguín et al.   NATURE GENETICS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Chromatin Remodeling in Cardiovascular Development and Physiology

(2011) Pei Han et al.   CIRCULATION RESEARCH

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5, Srf, Histone Modifications, and MicroRNAs

(2011) Jenny Schlesinger et al.   PLoS Genetics

Reversal of Histone Methylation: Biochemical and Molecular Mechanisms of Histone Demethylases

(2010) Nima Mosammaparast et al.   Annual Review of Biochemistry

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

The spectrum of clinical features in CHARGE syndrome

(2010) Sandra L. H. Davenport et al.   CLINICAL GENETICS

Chromatin remodeling in heart development

(2010) Benoit G Bruneau   CURRENT OPINION IN GENETICS & DEVELOPMENT

Ash2l interacts with Tbx1 and is required during early embryogenesis

(2010) Jason Z Stoller et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Jarid2 and PRC2, partners in regulating gene expression

(2010) G. Li et al.   GENES & DEVELOPMENT

Histone methyltransferases: regulation of transcription and contribution to human disease

(2010) Keisuke Nimura et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Chromatin regulation by Brg1 underlies heart muscle development and disease

(2010) Calvin T. Hang et al.   NATURE

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

Histone deacetylases facilitate sodium/calcium exchanger up-regulation in adult cardiomyocytes

(2009) Sangeetha Chandrasekaran et al.   FASEB JOURNAL

Deletion of ETS-1, a gene in the Jacobsen syndrome critical region, causes ventricular septal defects and abnormal ventricular morphology in mice

(2009) Maoqing Ye et al.   HUMAN MOLECULAR GENETICS

A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf–Hirschhorn syndrome

(2009) Keisuke Nimura et al.   NATURE

Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors

(2009) Jun K. Takeuchi et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Quantitative Control of Adaptive Cardiac Hypertrophy by Acetyltransferase p300

(2008) Jian Qin Wei et al.   CIRCULATION

The developmental genetics of congenital heart disease

(2008) Benoit G. Bruneau   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

(2008) William F. Marzluff et al.   NATURE REVIEWS GENETICS

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

MCAT Elements and the TEF-1 Family of Transcription Factors in Muscle Development and Disease

(2007) Tadashi Yoshida   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY