DNA methylation of the LIN28 pseudogene familyReport as inadecuate

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BMC Genomics

, 16:287

First Online: 11 April 2015Received: 15 August 2014Accepted: 25 March 2015DOI: 10.1186-s12864-015-1487-3

Cite this article as: Davis, A.P., Benninghoff, A.D., Thomas, A.J. et al. BMC Genomics 2015 16: 287. doi:10.1186-s12864-015-1487-3


BackgroundDNA methylation directs the epigenetic silencing of selected regions of DNA, including the regulation of pseudogenes, and is widespread throughout the genome. Pseudogenes are decayed copies of duplicated genes that have spread throughout the genome by transposition. Pseudogenes are transcriptionally silenced by DNA methylation, but little is known about how pseudogenes are targeted for methylation or how methylation levels are maintained in different tissues.

ResultsWe employed bisulfite next generation sequencing to examine the methylation status of the LIN28 gene and four processed pseudogenes derived from LIN28. The objective was to determine whether LIN28 pseudogenes maintain the same pattern of methylation as the parental gene or acquire a methylation pattern independent of the gene of origin. In this study, we determined that the methylation status of LIN28 pseudogenes does not resemble the pattern evident for the LIN28 gene, but rather these pseudogenes appear to acquire methylation patterns independent of the parental gene. Furthermore, we observed that methylation levels of the examined pseudogenes correlate to the location of insertion within the genome. LIN28 pseudogenes inserted into gene bodies were highly methylated in all tissues examined. In contrast, pseudogenes inserted into genomic regions that are not proximal to genes were differentially methylated in various tissue types.

ConclusionsOur analysis suggests that Lin28 pseudogenes do not aquire patterns of tissue-specific methylation as for the parental gene, but rather are methylated in patterns specific to the local genomic environment into which they were inserted.

KeywordsDNA methylation Pseudogene LIN28 Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1487-3 contains supplementary material, which is available to authorized users.

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Author: Aaron P Davis - Abby D Benninghoff - Aaron J Thomas - Benjamin R Sessions - Kenneth L White

Source: https://link.springer.com/

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