A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples.

PubWeight™: 0.87‹?›

🔗 View Article (PMC 3680319)

Published in Epigenetics Chromatin on June 07, 2013

Authors

Verity F Oliver1, Jun Wan, Saurabh Agarwal, Donald J Zack, Jiang Qian, Shannath L Merbs

Author Affiliations

1: Department of Ophthalmology, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA. smerbs@jhmi.edu.

Articles cited by this

Genome-wide location and function of DNA binding proteins. Science (2000) 31.25

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A (1992) 29.51

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet (2009) 18.90

Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature (2010) 9.81

Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res (2008) 8.62

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00

Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol (2010) 5.96

Evaluation of the Infinium Methylation 450K technology. Epigenomics (2011) 4.90

The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell (2012) 4.32

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods (2010) 4.30

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc (2011) 4.18

Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Genes Dev (1993) 3.42

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol (2012) 3.31

Polymer-stimulated ligation: enhanced blunt- or cohesive-end ligation of DNA or deoxyribooligonucleotides by T4 DNA ligase in polymer solutions. Nucleic Acids Res (1983) 2.54

MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res (2008) 2.28

Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest (2005) 2.23

Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics (2010) 2.11

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics (2011) 1.76

Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc (2012) 1.70

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res (2012) 1.61

Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics (2011) 1.56

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res (2012) 1.50

The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural Dev (2011) 1.30

HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) assay for DNA methylation profiling of primary normal and malignant B lymphocytes. Methods Mol Biol (2010) 1.03

Cell-specific DNA methylation patterns of retina-specific genes. PLoS One (2012) 1.00

Dynamic usage of alternative splicing exons during mouse retina development. Nucleic Acids Res (2011) 0.97

Changes in retinal gene expression in proliferative vitreoretinopathy: glial cell expression of HB-EGF. Mol Vis (2005) 0.91

RGSZ1 and Ret RGS: two of several splice variants from the gene RGS20. Genomics (2001) 0.89

Adaptation of the CHARM DNA methylation platform for the rat genome reveals novel brain region-specific differences. Epigenetics (2011) 0.84

Characterization and function of the bHLH-O protein XHes2: insight into the mechanisms controlling retinal cell fate decision. Development (2006) 0.81

The cholecystokinin system in the rat retina: receptor expression and in vivo activation of tyrosine phosphorylation pathways. Neuropeptides (2003) 0.77

Articles by these authors

Toll-like receptor 3 and geographic atrophy in age-related macular degeneration. N Engl J Med (2008) 4.46

Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration. Proc Natl Acad Sci U S A (2010) 4.30

Seven new loci associated with age-related macular degeneration. Nat Genet (2013) 3.81

Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell (2009) 3.69

A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet (2011) 3.55

TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics (2008) 3.37

Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC). Proc Natl Acad Sci U S A (2010) 3.33

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27

Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell (2009) 2.99

Phase 3, randomized, controlled trial of atrasentan in patients with nonmetastatic, hormone-refractory prostate cancer. Cancer (2008) 2.86

Clinical and pathological continuum of multisystem TDP-43 proteinopathies. Arch Neurol (2009) 2.68

An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res (2004) 2.56

Enhancement of cardiac function and suppression of heart failure progression by inhibition of protein phosphatase 1. Circ Res (2005) 2.52

Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38

Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res (2006) 2.26

A genomic atlas of mouse hypothalamic development. Nat Neurosci (2010) 2.25

Elongated styloid process (Eagle's syndrome): a clinical study. J Oral Maxillofac Surg (2002) 2.18

Pigment epithelium-derived factor suppresses ischemia-induced retinal neovascularization and VEGF-induced migration and growth. Invest Ophthalmol Vis Sci (2002) 2.03

Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration. Hum Mol Genet (2011) 1.98

Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev (2011) 1.86

Gene therapy with brain-derived neurotrophic factor as a protection: retinal ganglion cells in a rat glaucoma model. Invest Ophthalmol Vis Sci (2003) 1.83

Genetic and functional dissection of HTRA1 and LOC387715 in age-related macular degeneration. PLoS Genet (2010) 1.83

Caspase activation and amyloid precursor protein cleavage in rat ocular hypertension. Invest Ophthalmol Vis Sci (2002) 1.82

Changes in gene expression in experimental glaucoma and optic nerve transection: the equilibrium between protective and detrimental mechanisms. Invest Ophthalmol Vis Sci (2007) 1.74

Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics (2012) 1.65

Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.65

DNA methylation presents distinct binding sites for human transcription factors. Elife (2013) 1.63

Hsp20-engineered mesenchymal stem cells are resistant to oxidative stress via enhanced activation of Akt and increased secretion of growth factors. Stem Cells (2009) 1.60

Novel cardioprotective role of a small heat-shock protein, Hsp20, against ischemia/reperfusion injury. Circulation (2005) 1.60

Construction of human activity-based phosphorylation networks. Mol Syst Biol (2013) 1.59

Inducible expression of vascular endothelial growth factor in adult mice causes severe proliferative retinopathy and retinal detachment. Am J Pathol (2002) 1.59

Fine mapping of chromosome 3 in uveal melanoma: identification of a minimal region of deletion on chromosomal arm 3p25.1-p25.2. Cancer Res (2003) 1.59

The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biol (2002) 1.59

Integration of genomic datasets to predict protein complexes in yeast. J Struct Funct Genomics (2002) 1.58

AAV-mediated gene transfer of pigment epithelium-derived factor inhibits choroidal neovascularization. Invest Ophthalmol Vis Sci (2002) 1.58

Inducible expression of active protein phosphatase-1 inhibitor-1 enhances basal cardiac function and protects against ischemia/reperfusion injury. Circ Res (2009) 1.52

Severe subcortical TDP-43 pathology in sporadic frontotemporal lobar degeneration with motor neuron disease. Acta Neuropathol (2007) 1.51

Oncomodulin links inflammation to optic nerve regeneration. Proc Natl Acad Sci U S A (2009) 1.50

Myelination transition zone astrocytes are constitutively phagocytic and have synuclein dependent reactivity in glaucoma. Proc Natl Acad Sci U S A (2011) 1.47

A model to study differences between primary and secondary degeneration of retinal ganglion cells in rats by partial optic nerve transection. Invest Ophthalmol Vis Sci (2003) 1.46

A splice-site mutation in a retina-specific exon of BBS8 causes nonsyndromic retinitis pigmentosa. Am J Hum Genet (2010) 1.46

Increased expression of brain-derived neurotrophic factor preserves retinal function and slows cell death from rhodopsin mutation or oxidative damage. J Neurosci (2003) 1.44

Definitions and standardization of a new grading scheme for eyelid contour abnormalities after trichiasis surgery. PLoS Negl Trop Dis (2012) 1.44

Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication. Cell Host Microbe (2011) 1.43

Inducible expression of cre recombinase in the retinal pigmented epithelium. Invest Ophthalmol Vis Sci (2008) 1.41

G-CSF receptor positive neuroblastoma subpopulations are enriched in chemotherapy-resistant or relapsed tumors and are highly tumorigenic. Cancer Res (2013) 1.41

Analysis of the VMD2 promoter and implication of E-box binding factors in its regulation. J Biol Chem (2004) 1.41

Heat shock protein 20 interacting with phosphorylated Akt reduces doxorubicin-triggered oxidative stress and cardiotoxicity. Circ Res (2008) 1.40

Targeting iron homeostasis induces cellular differentiation and synergizes with differentiating agents in acute myeloid leukemia. J Exp Med (2010) 1.39

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol (2011) 1.39

The dorsal root ganglion in Friedreich's ataxia. Acta Neuropathol (2009) 1.38

Isoform-specific regulation of Akt by PDGF-induced reactive oxygen species. Proc Natl Acad Sci U S A (2011) 1.38

Functional analysis of cone-rod homeobox (CRX) mutations associated with retinal dystrophy. Hum Mol Genet (2002) 1.37

hPDI: a database of experimental human protein-DNA interactions. Bioinformatics (2009) 1.37

Functional genomic screening identifies dual leucine zipper kinase as a key mediator of retinal ganglion cell death. Proc Natl Acad Sci U S A (2013) 1.36

Analysis of regulatory network topology reveals functionally distinct classes of microRNAs. Nucleic Acids Res (2008) 1.36

Small heat-shock protein Hsp20 attenuates beta-agonist-mediated cardiac remodeling through apoptosis signal-regulating kinase 1. Circ Res (2006) 1.35

The pathology of superficial siderosis of the central nervous system. Acta Neuropathol (2008) 1.34

Identification of gene expression changes associated with the progression of retinal degeneration in the rd1 mouse. Invest Ophthalmol Vis Sci (2004) 1.33

Nonredundant role of Akt2 for neuroprotection of rod photoreceptor cells from light-induced cell death. J Neurosci (2007) 1.33

Effect of CNTF on retinal ganglion cell survival in experimental glaucoma. Invest Ophthalmol Vis Sci (2008) 1.31

Inactivation of the microRNA-183/96/182 cluster results in syndromic retinal degeneration. Proc Natl Acad Sci U S A (2013) 1.31

A functional variant in the CFI gene confers a high risk of age-related macular degeneration. Nat Genet (2013) 1.29

Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers. Glycobiology (2008) 1.28

MiR-124 suppresses growth of human colorectal cancer by inhibiting STAT3. PLoS One (2013) 1.28

Iron and iron-responsive proteins in the cardiomyopathy of Friedreich's ataxia. Cerebellum (2006) 1.28

The dentate nucleus in Friedreich's ataxia: the role of iron-responsive proteins. Acta Neuropathol (2007) 1.27

Vitreous levels of pigment epithelium-derived factor and vascular endothelial growth factor: implications for ocular angiogenesis. Am J Ophthalmol (2004) 1.26

Lack of BRAF mutation in primary uveal melanoma. Invest Ophthalmol Vis Sci (2003) 1.26

Phase 2 trial of linifanib (ABT-869) in patients with advanced renal cell cancer after sunitinib failure. Eur J Cancer (2011) 1.26

Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis. Nat Chem Biol (2012) 1.24

Identification of miR-130a, miR-27b and miR-210 as serum biomarkers for atherosclerosis obliterans. Clin Chim Acta (2010) 1.20

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors. BMC Bioinformatics (2007) 1.20

Silencing of the inhibitor of DNA binding protein 4 (ID4) contributes to the pathogenesis of mouse and human CLL. Blood (2010) 1.19

Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol Syst Biol (2009) 1.19

Increased expression of VEGF in retinal pigmented epithelial cells is not sufficient to cause choroidal neovascularization. J Cell Physiol (2004) 1.19

Generation of Cre transgenic mice with postnatal RPE-specific ocular expression. Invest Ophthalmol Vis Sci (2011) 1.18

Malignant gliomas with primitive neuroectodermal tumor-like components: a clinicopathologic and genetic study of 53 cases. Brain Pathol (2008) 1.18

betaA3/A1-crystallin in astroglial cells regulates retinal vascular remodeling during development. Mol Cell Neurosci (2007) 1.18

Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics (2007) 1.17

Relationship between gene co-expression and probe localization on microarray slides. BMC Genomics (2003) 1.16

An integrated approach to identifying cis-regulatory modules in the human genome. PLoS One (2009) 1.16

Heritability and genome-wide association study to assess genetic differences between advanced age-related macular degeneration subtypes. Ophthalmology (2012) 1.16

Functional analysis of the rod photoreceptor cGMP phosphodiesterase alpha-subunit gene promoter: Nrl and Crx are required for full transcriptional activity. J Biol Chem (2004) 1.15

MicroRNA profile of the developing mouse retina. Invest Ophthalmol Vis Sci (2009) 1.14

Identification of miR-508-3p and miR-509-3p that are associated with cell invasion and migration and involved in the apoptosis of renal cell carcinoma. Biochem Biophys Res Commun (2012) 1.14

Phase 2 trial of linifanib (ABT-869) in patients with unresectable or metastatic hepatocellular carcinoma. Cancer (2012) 1.12