Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements |
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Authors: | Sebastian Szpakowski,Xueguang Sun,José M. Lage,Andrew Dyer,Jill Rubinstein,Diane Kowalski,Clarence Sasaki,Jose Costa,Paul M. Lizardi |
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Affiliation: | 1. Interdepartmental Program in Computational, Biology and Bioinformatics, Yale University School of Medicine, Room LH-208, 310 Cedar Street, New Haven, CT 06520, USA;2. Department of Pathology, Yale University School of Medicine, Room LH-208, 310 Cedar Street, New Haven, CT 06520, USA;3. M.D.-Ph.D. Program, Yale University School of Medicine, Room LH-208, 310 Cedar Street, New Haven, CT 06520, USA;4. Department of Surgery, Yale University School of Medicine, Room LH-208, 310 Cedar Street, New Haven, CT 06520, USA |
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Abstract: | Close to 50% of the human genome harbors repetitive sequences originally derived from mobile DNA elements, and in normal cells, this sequence compartment is tightly regulated by epigenetic silencing mechanisms involving chromatin-mediated repression. In cancer cells, repetitive DNA elements suffer abnormal demethylation, with potential loss of silencing. We used a genome-wide microarray approach to measure DNA methylation changes in cancers of the head and neck and to compare these changes to alterations found in adjacent non-tumor tissues. We observed specific alterations at thousands of small clusters of CpG dinucleotides associated with DNA repeats. Among the 257,599 repetitive elements probed, 5% to 8% showed disease-related DNA methylation alterations. In dysplasia, a large number of local events of loss of methylation appear in apparently stochastic fashion. Loss of DNA methylation is most pronounced for certain members of the SVA, HERV, LINE-1P, AluY, and MaLR families. The methylation levels of retrotransposons are discretely stratified, with younger elements being highly methylated in healthy tissues, while in tumors, these young elements suffer the most dramatic loss of methylation. Wilcoxon test statistics reveals that a subset of primate LINE-1 elements is demethylated preferentially in tumors, as compared to non-tumoral adjacent tissue. Sequence analysis of these strongly demethylated elements reveals genomic loci harboring full length, as opposed to truncated elements, while possible enrichment for functional LINE-1 ORFs is weaker. Our analysis suggests that, in non-tumor adjacent tissues, there is generalized and highly variable disruption of epigenetic control across the repetitive DNA compartment, while in tumor cells, a specific subset of LINE-1 retrotransposons that arose during primate evolution suffers the most dramatic DNA methylation alterations. |
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Keywords: | DSB, double-strand break EIDR, endonuclease-independent DNA repair ERV, endogenous retrovirus HERV, human endogenous retrovirus HNSCC, head and neck squamous cell carcinoma LINE, long interspersed nuclear element LTR, long terminal repeat MaLR, mammalian apparent LTR retrotransposons MDA, multiple displacement amplification MPSS, massively parallel sequencing ORF, open reading frame SINE, short interspersed nuclear element SVA, SINE-VNTR-Alu VNTR, variable-number tandem repeat |
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