The landscape of genomic imprinting across diverse adult human tissues

  1. Tuuli Lappalainen17,18,19
  1. 1The Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel;
  2. 2Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA;
  3. 3Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA;
  4. 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA;
  5. 5Department of Pathology, Stanford University, Stanford, California 94305, USA;
  6. 6Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA;
  7. 7Wellcome Trust Center for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom;
  8. 8Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland;
  9. 9Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland;
  10. 10Department of Genetics, Stanford University, Stanford, California 94305, USA;
  11. 11Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA;
  12. 12Centro de Neumología Pediátrica, San Juan, Puerto Rico, 00917;
  13. 13Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA;
  14. 14Department of Pediatrics, National Jewish Health, Denver, Colorado 80206, USA;
  15. 15Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado-Denver, Denver, Colorado 80045, USA;
  16. 16Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
  17. 17New York Genome Center, New York, New York 10013, USA;
  18. 18Department of Systems Biology, Columbia University, New York, New York 10032, USA
  1. Corresponding authors: tlappalainen{at}nygenome.org, noah.zaitlen{at}ucsf.edu
  1. 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

  • [Supplemental material is available for this article.]

  • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.192278.115.

  • 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/.

| Table of Contents
OPEN ACCESS ARTICLE

Preprint Server