title: The landscape of genomic imprinting across diverse adult human tissues.
abstract: Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project. We characterize imprinting in 42 genes, including both novel and previously identified genes. Tissue specificity of imprinting is widespread, and gender-specific effects are revealed in a small number of genes in muscle with stronger imprinting in males. IGF2 shows maternal expression in the brain instead of the canonical paternal expression elsewhere. Imprinting appears to have only a subtle impact on tissue-specific expression levels, with genes lacking a systematic expression difference between tissues with imprinted and biallelic expression. In summary, our systematic characterization of imprinting in adult tissues highlights variation in imprinting between genes, individuals, and tissues.
authors.affiliation: The Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel;
authors.forename: Yael
authors.initials: Y
authors.lastname: Baran
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
authors.forename: Meena
authors.initials: M
authors.lastname: Subramaniam
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
authors.forename: Anne
authors.initials: A
authors.lastname: Biton
authors.affiliation: Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA;
authors.forename: Taru
authors.initials: T
authors.lastname: Tukiainen
authors.affiliation: Department of Pathology, Stanford University, Stanford, California 94305, USA; Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA;
authors.forename: Emily K
authors.initials: EK
authors.lastname: Tsang
authors.affiliation: Wellcome Trust Center for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom;
authors.forename: Manuel A
authors.initials: MA
authors.lastname: Rivas
authors.affiliation: Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland;
authors.forename: Matti
authors.initials: M
authors.lastname: Pirinen
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland;
authors.forename: Maria
authors.initials: M
authors.lastname: Gutierrez-Arcelus
authors.affiliation: Department of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA;
authors.forename: Kevin S
authors.initials: KS
authors.lastname: Smith
authors.affiliation: Department of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA;
authors.forename: Kim R
authors.initials: KR
authors.lastname: Kukurba
authors.affiliation: Department of Genetics, Stanford University, Stanford, California 94305, USA;
authors.forename: Rui
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
authors.forename: Celeste
authors.initials: C
authors.lastname: Eng
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
authors.forename: Dara G
authors.initials: DG
authors.lastname: Torgerson
authors.affiliation: Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA;
authors.forename: Cydney
authors.initials: C
authors.lastname: Urbanek
authors.affiliation: Department of Genetics, Stanford University, Stanford, California 94305, USA;
authors.forename: Jin Billy
authors.initials: JB
authors.lastname: Li
authors.affiliation: Centro de Neumología Pediátrica, San Juan, Puerto Rico, 00917;
authors.forename: Jose R
authors.initials: JR
authors.lastname: Rodriguez-Santana
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA;
authors.forename: Esteban G
authors.initials: EG
authors.lastname: Burchard
authors.affiliation: Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA; Department of Pediatrics, National Jewish Health, Denver, Colorado 80206, USA; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado-Denver, Denver, Colorado 80045, USA;
authors.forename: Max A
authors.initials: MA
authors.lastname: Seibold
authors.affiliation: Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
authors.forename: Daniel G
authors.initials: DG
authors.lastname: MacArthur
authors.affiliation: Department of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA;
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Montgomery
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
authors.forename: Noah A
authors.initials: NA
authors.lastname: Zaitlen
authors.affiliation: New York Genome Center, New York, New York 10013, USA; Department of Systems Biology, Columbia University, New York, New York 10032, USA.
authors.forename: Tuuli
authors.initials: T
authors.lastname: Lappalainen
mesh_terms: D000328:Adult; D000483:Alleles; D016000:Cluster Analysis; D019175:DNA Methylation; D030561:Databases, Nucleic Acid; D005260:Female; D005786:Gene Expression Regulation; D014644:Genetic Variation; D018392:Genomic Imprinting; D023281:Genomics; D005838:Genotype; D006801:Humans; D008297:Male; D009928:Organ Specificity / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012737:Sex Factors