The correlation of genome size and DNA methylation rate in metazoans
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ORIGINAL PAPER
The correlation of genome size and DNA methylation rate in metazoans Marcus Lechner • Manja Marz • Christian Ihling Andrea Sinz • Peter F. Stadler • Veiko Krauss
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Received: 17 May 2012 / Accepted: 3 October 2012 / Published online: 7 November 2012 Ó Springer-Verlag Berlin Heidelberg 2012
Abstract Total DNA methylation rates are well known to vary widely between different metazoans. The phylogenetic distribution of this variation, however, has not been investigated systematically. We combine here publicly available data on methylcytosine content with the analysis of nucleotide compositions of genomes and transcriptomes of 78 metazoan species to trace the evolution of abundance
Electronic supplementary material The online version of this article (doi:10.1007/s12064-012-0167-y) contains supplementary material, which is available to authorized users. M. Lechner Institut fu¨r Pharmazeutische Chemie, Philipps-Universita¨t Marburg, Marbacher Weg 6, 35037 Marburg, Germany e-mail: [email protected] M. Marz RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Leutragraben 1, 07743 Jena, Germany e-mail: [email protected] C. Ihling A. Sinz Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle, Germany e-mail: [email protected] A. Sinz e-mail: [email protected] P. F. Stadler Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Ha¨rtelstraße 16-18, 04107 Leipzig, Germany P. F. Stadler Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany
and distribution of DNA methylation. The depletion of CpG and the associated enrichment of TpG and CpA dinucleotides are used to infer the intensity and localization of germline CpG methylation and to estimate its evolutionary dynamics. We observe a positive correlation of the relative methylation of CpG motifs with genome size. We tested this trend successfully by measuring total DNA methylation with LC/MS in orthopteran insects with very different genome sizes: house crickets, migratory locusts and meadow grasshoppers. We hypothesize that the observed correlation between methylation rate and genome P. F. Stadler RNomics Group, Fraunhofer Institut fu¨r Zelltherapie und Immunologie, Deutscher Platz 5e, 04103 Leipzig, Germany P. F. Stadler Department of Theoretical Chemistry, University of Vienna, Wa¨hringerstraße 17, 1090 Wien, Austria P. F. Stadler Center for Non-coding RNA in Technology and Health, University of Copenhagen, Grønnega˚rdsvej 3, 1870 Frederiksberg, Denmark P. F. Stadler (&) Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA e-mail: [email protected] V. Krauss (&) Bioinformatics Group, Department of Computer Science, University of Leipzig, Ha¨rtelstraße 16-18, 04107 Leipzig, Germany e-mail: [email protected] V. Krauss Group of Develo
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