The landscape of genomic imprinting across diverse adult human tissues
- Yael Baran1,
- Meena Subramaniam2,
- Anne Biton2,
- Taru Tukiainen3,
- Emily K Tsang4,
- Manuel A Rivas5,
- Matti Pirinen6,
- Maria Gutierrez-Arcelus7,
- Kevin S Smith4,
- Kim R Kukurba4,
- Rui Zhang4,
- Celeste Eng2,
- Dara G Torgerson2,
- Cydney Urbanek8,
- GTEx Consortium9,
- Jin Billy Li4,
- Jose R Rodriguez-Santana10,
- Esteban G Burchard2,
- Max A Seibold8,
- Daniel G MacArthur3,
- Stephen B Montgomery4,
- Noah A Zaitlen2 and
- Tuuli Lappalainen11,12
- 1 Tel-Aviv University;
- 2 University of California San Francisco;
- 3 Massachusetts General Hospital;
- 4 Stanford University;
- 5 Wellcome Trust Center for Human Genetics;
- 6 University of Helsinki;
- 7 University of Geneva;
- 8 National Jewish Health;
- 9 -;
- 10 Centro de Neumología Pediátrica, San Juan;
- 11 NY Genome Center
- ↵* Corresponding author; email: tlappalainen{at}nygenome.org
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.
- Received March 23, 2015.
- Accepted May 7, 2015.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at http://creativecommons.org/licenses/by-nc/4.0/.
