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Genome Res. 2015 Jul;25(7):927-36. doi: 10.1101/gr.192278.115. Epub 2015 May 7.

The landscape of genomic imprinting across diverse adult human tissues.

Author information

1
The Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel;
2
Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
3
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;
4
Department of Pathology, Stanford University, Stanford, California 94305, USA; Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA;
5
Wellcome Trust Center for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom;
6
Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland;
7
Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland;
8
Department of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA;
9
Department of Genetics, Stanford University, Stanford, California 94305, USA;
10
Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA;
11
Centro de Neumología Pediátrica, San Juan, Puerto Rico, 00917;
12
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;
13
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;
14
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;
15
New York Genome Center, New York, New York 10013, USA; Department of Systems Biology, Columbia University, New York, New York 10032, USA.

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.

PMID:
25953952
PMCID:
PMC4484390
DOI:
10.1101/gr.192278.115
[Indexed for MEDLINE]
Free PMC Article

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