The landscape of genomic imprinting across diverse adult human tissues
- Yael Baran1,
- Meena Subramaniam2,
- Anne Biton2,
- Taru Tukiainen3,4,
- Emily K. Tsang5,6,
- Manuel A. Rivas7,
- Matti Pirinen8,
- Maria Gutierrez-Arcelus9,
- Kevin S. Smith5,10,
- Kim R. Kukurba5,10,
- Rui Zhang10,
- Celeste Eng2,
- Dara G. Torgerson2,
- Cydney Urbanek11,
- the GTEx Consortium,
- Jin Billy Li10,
- Jose R. Rodriguez-Santana12,
- Esteban G. Burchard2,13,
- Max A. Seibold11,14,15,
- Daniel G. MacArthur3,4,16,
- Stephen B. Montgomery5,10,
- Noah A. Zaitlen2,19 and
- Tuuli Lappalainen17,18,19
- 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
- Corresponding authors: tlappalainen{at}nygenome.org, noah.zaitlen{at}ucsf.edu
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↵19 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.192278.115.
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Freely available online through the Genome Research Open Access option.
- Received March 23, 2015.
- Accepted May 7, 2015.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.