Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach.

PubWeight™: 0.80‹?›

🔗 View Article (PMC 4243378)

Published in Genome Biol on January 01, 2014

Authors

Daniel Wong1, Wanseon Lee, Peter Humburg, Seiko Makino, Evelyn Lau, Vivek Naranbhai, Benjamin P Fairfax, Kenneth Chan, Katharine Plant, Julian C Knight

Author Affiliations

1: Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt, Drive, Oxford OX3 7BN, UK.

Articles cited by this

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99

An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83

Rapid detection of octamer binding proteins with 'mini-extracts', prepared from a small number of cells. Nucleic Acids Res (1989) 22.73

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20

An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96

Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res (2010) 9.55

Variation in transcription factor binding among humans. Science (2010) 9.33

Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet (2013) 7.13

MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics (2011) 6.52

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res (2013) 6.12

ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res (2012) 4.91

Complementation cloning of an MHC class II transactivator mutated in hereditary MHC class II deficiency (or bare lymphocyte syndrome). Cell (1993) 4.80

Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat Genet (2012) 3.77

Regulation of major histocompatibility complex class-II genes: X, Y and other letters of the alphabet. Annu Rev Immunol (1990) 3.68

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics (2010) 3.47

Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science (2014) 3.16

Selective and ATP-dependent translocation of peptides by the MHC-encoded transporter. Science (1993) 3.06

Expression of MHC class II molecules in different cellular and functional compartments is controlled by differential usage of multiple promoters of the transactivator CIITA. EMBO J (1997) 2.52

The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions. J Exp Med (2008) 2.50

Regulation of MHC class II gene expression by the class II transactivator. Nat Rev Immunol (2005) 2.44

Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res (2012) 2.41

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding. Nat Immunol (2011) 1.72

Transcriptional scaffold: CIITA interacts with NF-Y, RFX, and CREB to cause stereospecific regulation of the class II major histocompatibility complex promoter. Mol Cell Biol (2000) 1.62

Complex NF-kappaB interactions at the distal tumor necrosis factor promoter region in human monocytes. J Biol Chem (1998) 1.54

Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis. BMC Bioinformatics (2008) 1.51

The chromatin-remodeling enzyme BRG1 coordinates CIITA induction through many interdependent distal enhancers. Nat Immunol (2008) 1.44

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

A novel variant marking HLA-DP expression levels predicts recovery from hepatitis B virus infection. J Virol (2012) 1.24

NLRC5: a key regulator of MHC class I-dependent immune responses. Nat Rev Immunol (2012) 1.17

Modulation of gene expression by the MHC class II transactivator. J Immunol (2002) 1.16

The protein phosphatase 1 regulator PNUTS is a new component of the DNA damage response. EMBO Rep (2010) 1.10

Isolation of a B-cell-specific promoter for the human class II transactivator. Immunogenetics (1997) 1.03

Long distance control of MHC class II expression by multiple distal enhancers regulated by regulatory factor X complex and CIITA. J Immunol (2004) 1.01

CIITA and Its Dual Roles in MHC Gene Transcription. Front Immunol (2013) 0.95

Expression of the MHC class II transactivator (CIITA) type IV promoter in B lymphocytes and regulation by IFN-gamma. Mol Immunol (2005) 0.94

From transcription to cell surface expression, the induction of MHC class II I-A alpha by interferon-gamma in macrophages is regulated at different levels. Immunogenetics (2001) 0.91

Identification of CIITA regulated genetic module dedicated for antigen presentation. PLoS Genet (2008) 0.91

Characterization of mononuclear cells remaining in the leukoreduction system chambers of apheresis instruments after routine platelet collection: a new source of viable human blood cells. Transfusion (2007) 0.91

Enrichment of cell subpopulations applying automated MACS technique: purity, recovery and applicability for PCR-based chimerism analysis. Bone Marrow Transplant (2009) 0.84

Articles by these authors

MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1. Blood (2009) 5.87

A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res (2010) 4.77

Common variants in KCNN3 are associated with lone atrial fibrillation. Nat Genet (2010) 3.97

Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat Genet (2012) 3.77

Cardiotoxicity of histone deacetylase inhibitor depsipeptide in patients with metastatic neuroendocrine tumors. Clin Cancer Res (2006) 3.72

A fine-scale chimpanzee genetic map from population sequencing. Science (2012) 2.83

Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature (2012) 2.66

Phospho-dependent functional modulation of GABA(B) receptors by the metabolic sensor AMP-dependent protein kinase. Neuron (2007) 2.38

Expression of the multiple sclerosis-associated MHC class II Allele HLA-DRB1*1501 is regulated by vitamin D. PLoS Genet (2009) 2.23

The chromosome 6p22 haplotype associated with dyslexia reduces the expression of KIAA0319, a novel gene involved in neuronal migration. Hum Mol Genet (2006) 2.14

Large scale replication and meta-analysis of variants on chromosome 4q25 associated with atrial fibrillation. Eur Heart J (2009) 2.06

Increased CDA expression/activity in males contributes to decreased cytidine analog half-life and likely contributes to worse outcomes with 5-azacytidine or decitabine therapy. Clin Cancer Res (2013) 2.00

Independent susceptibility markers for atrial fibrillation on chromosome 4q25. Circulation (2010) 1.90

Mutation in the S3 segment of KCNQ1 results in familial lone atrial fibrillation. Heart Rhythm (2009) 1.87

Genetic variation in the alternative splicing regulator RBM20 is associated with dilated cardiomyopathy. Heart Rhythm (2011) 1.85

Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex. Genome Res (2011) 1.80

Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proc Natl Acad Sci U S A (2013) 1.75

Major histocompatibility complex genomics and human disease. Annu Rev Genomics Hum Genet (2013) 1.75

CCancer: a bird's eye view on gene lists reported in cancer-related studies. Nucleic Acids Res (2010) 1.62

Lack of replication in polymorphisms reported to be associated with atrial fibrillation. Heart Rhythm (2010) 1.58

ACE I/D polymorphism associated with abnormal atrial and atrioventricular conduction in lone atrial fibrillation and structural heart disease: implications for electrical remodeling. Heart Rhythm (2009) 1.55

Clinical and mycological predictors of cryptococcosis-associated immune reconstitution inflammatory syndrome. AIDS (2013) 1.46

Increased prevalence of sex chromosome aneuploidies in specific language impairment and dyslexia. Dev Med Child Neurol (2013) 1.44

Non-destructive clinical assessment of occlusal caries lesions using near-IR imaging methods. Lasers Surg Med (2011) 1.43

Comparative phloem chemistry of Manchurian (Fraxinus mandshurica) and two North American ash species (Fraxinus americana and Fraxinus pennsylvanica). J Chem Ecol (2007) 1.42

Optic disc area and correlation with central corneal thickness, corneal hysteresis and ocular pulse amplitude in glaucoma patients and controls. Clin Experiment Ophthalmol (2010) 1.42

Leprosy and the adaptation of human toll-like receptor 1. PLoS Pathog (2010) 1.41

Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol (2011) 1.40

FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. Nucleic Acids Res (2010) 1.35

Development of methods for cross-sectional HIV incidence estimation in a large, community randomized trial. PLoS One (2013) 1.24

Blocking telomerase by dietary polyphenols is a major mechanism for limiting the growth of human cancer cells in vitro and in vivo. Cancer Res (2003) 1.24

Functional analyses of coronary artery disease associated variation on chromosome 9p21 in vascular smooth muscle cells. Hum Mol Genet (2012) 1.24

A common variant associated with dyslexia reduces expression of the KIAA0319 gene. PLoS Genet (2009) 1.20

Multiple sclerosis and the major histocompatibility complex. Curr Opin Neurol (2009) 1.19

Phase II trial of temsirolimus in patients with relapsed or refractory multiple myeloma. Leuk Res (2009) 1.16

The ratio of monocytes to lymphocytes in peripheral blood correlates with increased susceptibility to clinical malaria in Kenyan children. PLoS One (2013) 1.16

Transcriptome analysis of nitrate assimilation in Aspergillus nidulans reveals connections to nitric oxide metabolism. Mol Microbiol (2010) 1.12

The human Major Histocompatibility Complex as a paradigm in genomics research. Brief Funct Genomic Proteomic (2009) 1.11

HLA class I alleles tag HLA-DRB1*1501 haplotypes for differential risk in multiple sclerosis susceptibility. Proc Natl Acad Sci U S A (2008) 1.11

Effects of maternal obesity on tissue concentrations of prophylactic cefazolin during cesarean delivery. Obstet Gynecol (2011) 1.09

IFITM3 and susceptibility to respiratory viral infections in the community. J Infect Dis (2013) 1.06

Phase I study of GTI-2040, an antisense to ribonucleotide reductase, in combination with high-dose cytarabine in patients with acute myeloid leukemia. Clin Cancer Res (2008) 1.05

CAPRISA 004 tenofovir microbicide trial: no impact of tenofovir gel on the HIV transmission bottleneck. J Infect Dis (2012) 0.99

ADAMTS7 cleavage and vascular smooth muscle cell migration is affected by a coronary-artery-disease-associated variant. Am J Hum Genet (2013) 0.97

Preservation HIV-1-specific IFNγ+ CD4+ T-cell responses in breakthrough infections after exposure to tenofovir gel in the CAPRISA 004 microbicide trial. J Acquir Immune Defic Syndr (2012) 0.97

A systematic review of definitions of extreme phenotypes of HIV control and progression. AIDS (2014) 0.96

Associations of HLA alleles with specific language impairment. J Neurodev Disord (2014) 0.95

Novel candidate virulence factors in rice pathogen Xanthomonas oryzae pv. oryzicola as revealed by mutational analysis. Appl Environ Microbiol (2007) 0.95

An integrated expression phenotype mapping approach defines common variants in LEP, ALOX15 and CAPNS1 associated with induction of IL-6. Hum Mol Genet (2009) 0.95

Validation and functional annotation of expression-based clusters based on gene ontology. BMC Bioinformatics (2006) 0.94

High-speed scanning ablation of dental hard tissues with a λ = 9.3 μm CO2 laser: adhesion, mechanical strength, heat accumulation, and peripheral thermal damage. J Biomed Opt (2011) 0.94

An integrated approach to defining genetic and environmental determinants for major clinical outcomes involving vitamin D. Mol Diagn Ther (2014) 0.91

A randomized, double-blinded, controlled trial comparing parenteral normal saline with and without dextrose on the course of labor in nulliparas. Am J Obstet Gynecol (2009) 0.90

The association between the ratio of monocytes:lymphocytes at age 3 months and risk of tuberculosis (TB) in the first two years of life. BMC Med (2014) 0.90

HIV disease progression in seroconvertors from the CAPRISA 004 tenofovir gel pre-exposure prophylaxis trial. J Acquir Immune Defic Syndr (2015) 0.90

Longitudinal changes in the B-type natriuretic peptide levels in normal pregnancy and postpartum. Clin Cardiol (2009) 0.89

Neuropilin 1 directly interacts with Fer kinase to mediate semaphorin 3A-induced death of cortical neurons. J Biol Chem (2010) 0.89

Vitamin D receptor gene methylation is associated with ethnicity, tuberculosis, and TaqI polymorphism. Hum Immunol (2010) 0.89

Sustainability of task-shifting for antiretroviral treatment. Lancet (2012) 0.87

No evidence for selection of HIV-1 with enhanced gag-protease or Nef function among breakthrough infections in the CAPRISA 004 tenofovir microbicide trial. PLoS One (2013) 0.86

Electrophoresis-assisted open-tubular liquid chromatography/mass spectrometry for the analysis of lipooligosaccharide expressed by Campylobacter jejuni. Electrophoresis (2005) 0.86

A common haplotype of the TNF receptor 2 gene modulates endotoxin tolerance. J Immunol (2011) 0.84

Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1). J Allergy Clin Immunol (2011) 0.84

Chromatin profiling across the human tumour necrosis factor gene locus reveals a complex, cell type-specific landscape with novel regulatory elements. Nucleic Acids Res (2008) 0.84

Interdelivery interval and the success of vaginal birth after cesarean delivery. Obstet Gynecol (2002) 0.84

Common variant on chromosome 9p21 predicts severity of coronary artery disease. J Am Coll Cardiol (2011) 0.83

Systems biology of infectious diseases: a focus on fungal infections. Immunobiology (2011) 0.83

Identification of a novel beta-cell glucokinase (GCK) promoter mutation (-71G>C) that modulates GCK gene expression through loss of allele-specific Sp1 binding causing mild fasting hyperglycemia in humans. Diabetes (2009) 0.83

Global catastrophizing vs catastrophizing subdomains: assessment and associations with patient functioning. Pain Med (2012) 0.82

"One-pot" methylation in glycomics application: esterification of sialic acids and permanent charge construction. Anal Chem (2007) 0.81

Genetic determinants of HSP70 gene expression following heat shock. Hum Mol Genet (2010) 0.81

Angiotensin-(1-7) regulates Angiotensin II-induced VCAM-1 expression on vascular endothelial cells. Biochem Biophys Res Commun (2012) 0.80

Transcriptomic profiling facilitates classification of response to influenza challenge. J Mol Med (Berl) (2014) 0.80

Nitric oxide and carbon monoxide production and metabolism in preeclampsia. Reprod Sci (2012) 0.79

Fatal chloroquine poisoning: a rare cause of sudden cardiac arrest. Ann Acad Med Singapore (2011) 0.79

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes. EBioMedicine (2015) 0.78

A randomized, double-masked trial of prophylactic indomethacin tocolysis versus placebo in women with premature rupture of membranes. Am J Perinatol (2010) 0.78

Microwave-assisted sample preparation for rapid and sensitive analysis of H. pylori lipid A applicable to a single colony. J Lipid Res (2009) 0.78

TRIM5α and TRIM22 are differentially regulated according to HIV-1 infection phase and compartment. J Virol (2014) 0.78

HIV prevention and treatment research in sub-Saharan Africa: where are the adolescents? AIDS (2006) 0.78

Analysis of nitrosamines by capillary electrospray-high-field asymmetric waveform ion mobility spectrometry-MS with programmed compensation voltage. Electrophoresis (2007) 0.77

Microwave-assisted nonspecific proteolytic digestion and controlled methylation for glycomics applications. Carbohydr Res (2008) 0.76

Academics and competing interests in H1N1 influenza media reporting. J Epidemiol Community Health (2013) 0.76

Women's attitudes regarding mode of delivery and cesarean delivery on maternal request. J Matern Fetal Neonatal Med (2011) 0.76

Corrigendum: T-cell activation is an immune correlate of risk in BCG vaccinated infants. Nat Commun (2016) 0.75

An allele-specific gene expression assay to test the functional basis of genetic associations. J Vis Exp (2010) 0.75

Origins of magic: review of genetic and epigenetic effects. BMJ (2007) 0.75

Insights into the nature and consequences of our variable genome. Brief Funct Genomic Proteomic (2009) 0.75

Subchronic oral toxicity study of decitabine in combination with tetrahydrouridine in CD-1 mice. Int J Toxicol (2014) 0.75

Investigation of Acid-Etched CO2 Laser Ablated Enamel Surfaces Using Polarization Sensitive Optical Coherence Tomography. Proc SPIE Int Soc Opt Eng (2012) 0.75

111In-DTPA-Octreotide SPECT (OctreoScan) Uptake in Metastatic Renal Cell Carcinoma to the Pancreas. Clin Nucl Med (2018) 0.75