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Application of the LU minometric M ethylation A ssay to ecological species: tissue quality requirements and a survey of DNA methylation levels in animals
Author(s) -
Head Jessica A.,
Mittal Krittika,
Basu Niladri
Publication year - 2014
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12244
Subject(s) - biology , dna methylation , methylation , dna , zoology , biochemistry , gene , gene expression
The LU minometric M ethylation A ssay ( LUMA ) measures global DNA methylation. LUMA depends on digestion of DNA with methyl‐sensitive and methyl‐insensitive restriction enzymes, followed by pyrosequencing. Until recently, LUMA has been principally used for biomedical research. Here, we use chickens as a model to investigate sample quality issues relating to LUMA and then apply the method to ecological species. First, we assessed the effect of tissue storage conditions on DNA methylation values. This is an important consideration for ecological species because samples are not always ideally preserved and LUMA is sensitive to poor DNA quality. We found that good quality LUMA data could be obtained from chicken liver and brain tissues stored at 21 °C for at least 2 and 12 h, respectively. Longer storage times introduced nonspecific peaks to pyrograms which were associated with reduced DNA methylation. Repeatedly, freezing and thawing the tissues did not affect LUMA data. Second, we measured DNA methylation in 12 species representing five animal classes: amphibians ( A frican and W estern clawed frog), reptiles (green anole lizard), fish (yellow perch, goldfish, lake trout), mammals ( A merican mink, polar bear, short‐beaked common dolphin, A tlantic white‐sided dolphin) and birds (chicken, J apanese quail). We saw a pattern of high DNA methylation in fish (84–87%), and intermediate levels in mammals (68–72%) and birds (52–71%). This pattern corresponds well with previous measures of DNA methylation generated by HPLC . Our data represent the first C p G methylation values to be reported in several species and provide a basis for studying patterns of epigenetic inheritance in an ecological context.