Falckenhayn, 2016

Falckenhayn C. 2016. The methylome of the marbled crayfish Procambarus virginalis. Doctoral dissertation, Combined Faculties for the Natural Sciences and for Mathematics, University of Heidelberg, Heidelberg. http://archiv.ub.uni-heidelberg.de/volltextserver/22489/1/Falckenhayn_Cassandra_PhDThesis.pdf

Abstract

DNA methylation in invertebrates seems to play a different role as in mammals and its evolutionary conservation among invertebrates is unclear. Only two studies describe crustacean methylomes giving just a small overview. The parthenogenetic reproducing marbled crayfish display a high environmental adaptability besides its genetic uniformity and thus, possess the necessary attributes of a laboratory model organism. The aim of this work was to characterize the methylome of the marbled crayfish at single-base resolution using whole-genome bisulfite sequencing in an attempt to give new insights into DNA methylation in crustaceans and thus, in the evolutionary conservation among invertebrates. Analysis of the mitochondrial DNA of different marbled crayfish strains revealed a single origin and suggests to consider the marbled crayfish as independent asexual species Procambarus virginalis. Furthermore, since the P. virginalis possess a large genome size, the transcriptome was assembled and comparison to other species revealed a relative good quality of the first draft transcriptome as well as the presence of a conserved DNA methylation system in P. virginalis. Analysis of the CpG depletion in protein-coding sequences and mass spectrometry confirmed historical germline and current DNA methylation in various tissues of P. virginalis. The methylome was characterized by the key features of animal methylomes with methylation targeted to gene bodies. The gene bodies displayed the typical pattern of a mosaically methylated invertebrate genome and a bimodal distribution of their methylation levels. Targeted gene bodies were annotated as housekeeping genes and methylation showed a parabolic relationship to housekeeping gene expression suggesting that the DNA methylation of housekeeping genes might fine-tune their expression. Additionally, repeats were generally hypomethylated and the methylation of repeats depended on their position to gene bodies. Finally, inter-individual and inter-tissue comparison of gene body methylation revealed a high reproducibility of the methylation patterns, while inter-species comparison between P. fallax and P. virginalis displayed an overall hypomethylation in the P. virginalis genes which however, could not explain the by mass spectrometry detected global hypomethylation in P. virginalis. These findings uncovered that the P. virginalis methylome is characterized by tissue-invariant housekeeping gene methylation. This thesis describes novel insights into the evolutionary conservation of gene body and repeat methylation in invertebrates, especially crustaceans, and the preferential methylation of housekeeping genes highlights a functional difference to the tissue-specific methylation in mammals.

Keywords: None provided.