Genome-wide methylation analysis of retrocopy-associated CpG islands and their genomic environment

Abstract

Gene duplication by retrotransposition, i.e., the reverse transcription of an mRNA and integration of the cDNA into the genome, is an important mechanism in evolution. Based on whole-genome bisulfite sequencing of monocyte DNA, we have investigated the methylation state of all CpG islands (CGIs) associated with a retrocopy (n D 1,319), their genomic environment, as well as the CGIs associated with the ancestral genes. Approximately 10% of retrocopies are associated with a CGI. Whereas almost all CGIs of the human genome are unmethylated, 68% of the CGIs associated with a retrocopy are methylated. In retrocopies resulting from multiple retrotranspositions of the same ancestral gene, the methylation state of the CGI often differs. There is a strong positive correlation between the methylation state of the CGI/ retrocopy and their genomic environment, suggesting that the methylation state of the integration site determined the methylation state of the CGI/retrocopy, or that methylation of the retrocopy by a host defense mechanism has spread into the adjacent regions. Only a minor fraction of CGI/retrocopies (n D 195) has intermediate methylation levels. Among these, the previously reported CGI/retrocopy in intron 2 of the RB1 gene (PPP1R26P1) as well as the CGI associated with the retrocopy RPS2P32 identified in this study carry a maternal methylation imprint. In conclusion, these findings shed light on the evolutionary dynamics and constraints of DNA methylation.

Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements

“…In this study, we employed pyrosequencing at 18 CpG rich UCNEs to determine the pattern of methylation conservation using 56 representative species covering 300–400 million years of evolution. We expected DNA methylation at UCNEs to be either near 0% or near 100%, since the overwhelming majority of CpG sites within the genome exhibit one of these maxima [ 30 ]. Unexpectedly, we found that several UCNEs exhibited intermediate DNA methylation consistently across their embedded CpG sites.…”

New insights into the imprinted MEG8-DMR in 14q32 and clinical and molecular description of novel patients with Temple syndrome

“…Placenta samples were obtained from the Institute of Molecular Biology/Department of Gynecology and Obstetrics, University Hospital Essen, Germany after informed consent. 21 First trimester placenta samples (Placenta 1-3) were taken at week 9, 10 and 11 of gestation, respectively, after abortions that were not medically indicated. Third trimester placenta samples (Placenta 4 and 5) were taken after the birth of healthy babies at week 36 and 37 of gestation.…”

“…For subsequent data analysis the Amplikyzer software was used. 21 Only reads with a conversion rate over 95% were considered.…”

The maternal uniparental disomy of chromosome 6 (upd(6)mat) “phenotype”: result of placental trisomy 6 mosaicism?

“…Methylation analysis of the CUL7 DMR described by Hamada et al (2016) was conducted in DNA from blood of normal controls, three first and three third-term placenta samples (Grothaus et al 2016) (Beygo et al, submitted; maternal contamination was excluded before) by next-generation bisulfite sequencing on the Roche/454 GS junior system (Branford, CT, USA) as described previously (Beygo et al 2013) using tagged primers F1 5 0 -CTTGCTTCCTGGCACGAG-GGGTAGGGTGTATAG ATTAGGTAGG-3 0 with R1 5 0 -CAGGAAACAGCTAT GAC-CCCTTACTCTATAAAAAACAAACCTC-3 0 and F2 5 0 -CTTGCTTCCTGGCACGAG-GAGGTTTGTTTTTTATA GAGTAAGGGA-3 0 with R2 5 0 -CAGGAAACAGCTATGAC-TCCAAAATCTTTTCCAATTCTAACTT-3 0 .…”