title: DNA methylation of the LIN28 pseudogene family.
abstract: BACKGROUND
  DNA 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Our analysis suggests that Lin28 pseudogenes do not acquire 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.
authors.affiliation: Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA. adavis@uwsp.edu.
authors.forename: Aaron P
authors.initials: AP
authors.lastname: Davis
authors.affiliation: Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA. abby.benninghoff@usu.edu.|School of Veterinary Medicine, Utah State University, Logan, UT, USA. abby.benninghoff@usu.edu.|USTAR Applied Nutrition Research, Utah State University, Logan, UT, USA. abby.benninghoff@usu.edu.
authors.forename: Abby D
authors.initials: AD
authors.lastname: Benninghoff
authors.affiliation: Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA. aaron.thomas@usu.edu.
authors.forename: Aaron J
authors.initials: AJ
authors.lastname: Thomas
authors.affiliation: Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA. brsessions@gmail.com.
authors.forename: Benjamin R
authors.initials: BR
authors.lastname: Sessions
authors.affiliation: Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA. ken.white@usu.edu.|School of Veterinary Medicine, Utah State University, Logan, UT, USA. ken.white@usu.edu.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: White
mesh_terms: D000818:Animals; D002417:Cattle; D018899:CpG Islands; D019175:DNA Methylation; D005347:Fibroblasts; D059014:High-Throughput Nucleotide Sequencing; D005810:Multigene Family; D009865:Oocytes / Q000166:cytology / Q000378:metabolism; D011544:Pseudogenes; D016601:RNA-Binding Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012867:Skin / Q000166:cytology
chemical_list: D016601:RNA-Binding Proteins