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DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

Kaie Lokk123, Vijayachitra Modhukur4, Balaji Rajashekar4, Kaspar Märtens4, Reedik Mägi5, Raivo Kolde4, Marina Koltšina1, Torbjörn K Nilsson6, Jaak Vilo4, Andres Salumets789* and Neeme Tõnisson125*

Author Affiliations

1 Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia

2 Department of Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia

3 Estonian Biocentre, Tartu, Estonia

4 Institute of Computer Science, University of Tartu, Tartu, Estonia

5 Estonian Genome Center, University of Tartu, Tartu, Estonia

6 Department of Medical Biosciences, Clinical Chemistry, Umeå University, Umeå, Sweden

7 Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia

8 Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia

9 Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia

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Genome Biology 2014, 15:r54  doi:10.1186/gb-2014-15-4-r54

Published: 1 April 2014

Abstract

Background

DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites.

Results

Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases.

Conclusions

This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms.