Autosomal monoallelic expression in the mouse.

PubWeight™: 1.30‹?› | Rank: Top 10%

🔗 View Article (PMID 22348269)

Published in Genome Biol on February 20, 2012

Authors

Lillian M Zwemer1, Alexander Zak, Benjamin R Thompson, Andrew Kirby, Mark J Daly, Andrew Chess, Alexander A Gimelbrant

Author Affiliations

1: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.

Articles citing this

Recurrent hemizygous deletions in cancers may optimize proliferative potential. Science (2012) 3.41

Mechanisms and consequences of widespread random monoallelic expression. Nat Rev Genet (2012) 1.81

Random monoallelic gene expression increases upon embryonic stem cell differentiation. Dev Cell (2014) 1.17

Random monoallelic expression: regulating gene expression one allele at a time. Trends Genet (2014) 1.12

Smchd1 regulates a subset of autosomal genes subject to monoallelic expression in addition to being critical for X inactivation. Epigenetics Chromatin (2013) 1.06

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation. Nat Rev Genet (2015) 1.05

Chromatin signature of widespread monoallelic expression. Elife (2013) 1.03

Using next-generation RNA sequencing to identify imprinted genes. Heredity (Edinb) (2014) 0.99

Extensive variation between tissues in allele specific expression in an outbred mammal. BMC Genomics (2015) 0.96

Random or stochastic monoallelic expressed genes are enriched for neurodevelopmental disorder candidate genes. PLoS One (2013) 0.90

Genetic basis of neuronal individuality in the mammalian brain. J Neurogenet (2013) 0.86

Asynchronous replication, mono-allelic expression, and long range Cis-effects of ASAR6. PLoS Genet (2013) 0.85

Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. Nat Genet (2016) 0.84

Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. Genetics (2015) 0.84

Epigenetic regulation of monoallelic rearrangement (allelic exclusion) of antigen receptor genes. Front Immunol (2014) 0.82

Chromatin Signature Identifies Monoallelic Gene Expression Across Mammalian Cell Types. G3 (Bethesda) (2015) 0.81

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. Nat Genet (2016) 0.80

The origin of the RB1 imprint. PLoS One (2013) 0.80

Evolution of vertebrate sex chromosomes and dosage compensation. Nat Rev Genet (2015) 0.80

ASAR15, A cis-acting locus that controls chromosome-wide replication timing and stability of human chromosome 15. PLoS Genet (2015) 0.79

dbMAE: the database of autosomal monoallelic expression. Nucleic Acids Res (2015) 0.78

Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Res (2015) 0.77

Monoallelic expression of the human FOXP2 speech gene. Proc Natl Acad Sci U S A (2014) 0.77

Emerging Skin T-Cell Functions in Response to Environmental Insults. J Invest Dermatol (2016) 0.76

The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits. BMC Genomics (2016) 0.76

Known unknowns for allele-specific expression and genomic imprinting effects. F1000Prime Rep (2014) 0.76

A monoallelic-to-biallelic T-cell transcriptional switch regulates GATA3 abundance. Genes Dev (2015) 0.76

RNA as a fundamental component of interphase chromosomes: could repeats prove key? Curr Opin Genet Dev (2016) 0.75

Erasure and reestablishment of random allelic expression imbalance after epigenetic reprogramming. RNA (2016) 0.75

Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders. Mol Psychiatry (2017) 0.75

Genome-wide identification of autosomal genes with allelic imbalance of chromatin state. PLoS One (2017) 0.75

Articles cited by this

Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature (1961) 23.98

Genomic imprinting: parental influence on the genome. Nat Rev Genet (2001) 11.50

Clonal selection and learning in the antibody system. Nature (1996) 9.58

Widespread monoallelic expression on human autosomes. Science (2007) 7.12

Cellular localization of immunoglobulins with different allotypic specificities in rabbit lymphoid tissues. J Exp Med (1965) 6.93

Allelic inactivation regulates olfactory receptor gene expression. Cell (1994) 5.93

Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat Rev Genet (2009) 4.05

Preferential inactivation of the paternally derived X chromosome in the extraembryonic membranes of the mouse. Nature (1975) 3.75

In vitro transformation of lymphoid cells by Abelson murine leukemia virus. Proc Natl Acad Sci U S A (1975) 3.47

Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science (1999) 2.90

Monoallelic expression of the interleukin-2 locus. Science (1998) 2.58

Independent and epigenetic regulation of the interleukin-4 alleles in CD4+ T cells. Science (1998) 2.13

Regulation of expression of IL-4 alleles: analysis using a chimeric GFP/IL-4 gene. Immunity (2001) 1.97

Regulation of IL-4 expression by activation of individual alleles. Immunity (1998) 1.84

Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics (2010) 1.71

Monoallelic expression and asynchronous replication of p120 catenin in mouse and human cells. J Biol Chem (2004) 1.42

Evidence of non-random X chromosome activity in the mouse. Genet Res (1972) 1.39

Allele-specific expression patterns of interleukin-2 and Pax-5 revealed by a sensitive single-cell RT-PCR analysis. Curr Biol (2000) 1.31

Genome-wide assessment of imprinted expression in human cells. Genome Biol (2011) 1.22

Autosomal dominant mutations affecting X inactivation choice in the mouse. Science (2002) 1.12

Monoallelic expression of multiple genes in the CNS. PLoS One (2007) 0.96

Differentially methylated alleles in a distinct region of the human interleukin-1alpha promoter are associated with allele-specific expression of IL-1alpha in CD4+ T cells. Blood (2006) 0.87

Articles by these authors

PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet (2007) 209.92

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39

A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59

Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science (2007) 51.70

The structure of haplotype blocks in the human genome. Science (2002) 50.88

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet (2008) 35.06

Genome-wide association studies for common diseases and complex traits. Nat Rev Genet (2005) 33.96

Integrating common and rare genetic variation in diverse human populations. Nature (2010) 32.30

The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet (2008) 30.20

A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science (2006) 27.49

Efficiency and power in genetic association studies. Nat Genet (2005) 25.56

Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04

Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med (2008) 19.71

Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet (2008) 19.55

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet (2007) 19.08

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet (2010) 17.38

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet (2008) 15.89

Common deletion polymorphisms in the human genome. Nat Genet (2006) 15.66

A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet (2006) 15.63

Genetic mapping in human disease. Science (2008) 15.12

Calibrating a coalescent simulation of human genome sequence variation. Genome Res (2005) 15.04

Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat Genet (2006) 14.76

Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature (2012) 13.71

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature (2011) 13.23

Efficient control of population structure in model organism association mapping. Genetics (2008) 12.32

Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet (2009) 12.19

Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study. Lancet (2012) 12.10

Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat Genet (2008) 12.07

Methods for high-density admixture mapping of disease genes. Am J Hum Genet (2004) 12.02

Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol (2008) 11.28

Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder. Nat Genet (2008) 10.49

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet (2008) 9.52

Testing for an unusual distribution of rare variants. PLoS Genet (2011) 9.28

Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet (2007) 8.74

Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet (2009) 8.39

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nat Genet (2013) 8.02

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet (2011) 7.98

Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration. Nat Genet (2006) 7.49

Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nat Genet (2009) 7.16

Widespread monoallelic expression on human autosomes. Science (2007) 7.12

Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet (2008) 7.07

Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med (2010) 6.84

A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature (2007) 6.77

The mosaic structure of variation in the laboratory mouse genome. Nature (2002) 6.54

Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet (2008) 6.42

Parental phenotypes in family-based association analysis. Am J Hum Genet (2004) 6.35

Gene body-specific methylation on the active X chromosome. Science (2007) 6.33

A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics (2007) 6.28

Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet (2011) 6.20

An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell (2009) 6.08

Ascertainment through family history of disease often decreases the power of family-based association studies. Behav Genet (2007) 6.06

Genetic architectures of psychiatric disorders: the emerging picture and its implications. Nat Rev Genet (2012) 5.99

Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits. PLoS Genet (2010) 5.79

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet (2011) 5.58

Synaptic, transcriptional and chromatin genes disrupted in autism. Nature (2014) 5.30

Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet (2008) 5.08

Disruption of neurexin 1 associated with autism spectrum disorder. Am J Hum Genet (2008) 5.04

Transferability of tag SNPs in genetic association studies in multiple populations. Nat Genet (2006) 4.78

A genome-wide linkage and association scan reveals novel loci for autism. Nature (2009) 4.76

Whole population, genome-wide mapping of hidden relatedness. Genome Res (2008) 4.72

Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci U S A (2007) 4.71

Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet (2010) 4.65

Validating, augmenting and refining genome-wide association signals. Nat Rev Genet (2009) 4.56

Ipr1 gene mediates innate immunity to tuberculosis. Nature (2005) 4.53

Pervasive sharing of genetic effects in autoimmune disease. PLoS Genet (2011) 4.42

Common single nucleotide polymorphisms in TCF7L2 are reproducibly associated with type 2 diabetes and reduce the insulin response to glucose in nondiabetic individuals. Diabetes (2006) 4.36

Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell (2010) 4.32

Variation in complement factor 3 is associated with risk of age-related macular degeneration. Nat Genet (2007) 4.23

HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat Genet (2009) 4.11

Evaluation of common variants in the six known maturity-onset diabetes of the young (MODY) genes for association with type 2 diabetes. Diabetes (2007) 3.84

Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet (2009) 3.82

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

Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. Nat Genet (2009) 3.65

Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis. Proc Natl Acad Sci U S A (2008) 3.56

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

Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nat Genet (2009) 3.52

Searching for missing heritability: designing rare variant association studies. Proc Natl Acad Sci U S A (2014) 3.47

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol (2012) 3.39

Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant. PLoS One (2008) 3.36

WHAP: haplotype-based association analysis. Bioinformatics (2006) 3.36

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

High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet (2010) 3.31

Variation near complement factor I is associated with risk of advanced AMD. Eur J Hum Genet (2008) 3.29

Stochastic yet biased expression of multiple Dscam splice variants by individual cells. Nat Genet (2004) 3.27