Research

The landscape of genomic imprinting across diverse adult human tissues

    • 1The Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel;
    • 2Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
    • 3Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA;
    • 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA;
    • 5Department of Pathology, Stanford University, Stanford, California 94305, USA;
    • 6Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA;
    • 7Wellcome Trust Center for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom;
    • 8Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland;
    • 9Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland;
    • 10Department of Genetics, Stanford University, Stanford, California 94305, USA;
    • 11Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA;
    • 12Centro de Neumología Pediátrica, San Juan, Puerto Rico, 00917;
    • 13Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA;
    • 14Department of Pediatrics, National Jewish Health, Denver, Colorado 80206, USA;
    • 15Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado-Denver, Denver, Colorado 80045, USA;
    • 16Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
    • 17New York Genome Center, New York, New York 10013, USA;
    • 18Department of Systems Biology, Columbia University, New York, New York 10032, USA
    • 19 These authors contributed equally to this work.
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cover of Genome Research Vol 36 Issue 6
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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.

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