Please use this identifier to cite or link to this item: http://hdl.handle.net/2445/101440
Title: Disclosing bias in bisulfite assay: MethPrimers underestimate high DNA methylation
Author: Fuso, Andrea
Ferraguti, Giampiero
Scarpa, Sigfrido
Ferrer, Isidro (Ferrer Abizanda)
Lucarelli, Marco
Keywords: ADN
Metilació
Àcids nucleics
Clonatge
Epigènesi
Bioinformàtica
DNA
Methylation
Nucleic acids
Cloning
Epigenesis
Bioinformatics
Issue Date: 18-Feb-2015
Publisher: Public Library of Science (PLoS)
Abstract: Discordant results obtained in bisulfite assays using MethPrimers (PCR primers designed using MethPrimer software or assuming that non-CpGs cytosines are non methylated) versus primers insensitive to cytosine methylation lead us to hypothesize a technical bias. We therefore used the two kinds of primers to study different experimental models and methylation statuses. We demonstrated that MethPrimers negatively select hypermethylated DNA sequences in the PCR step of the bisulfite assay, resulting in CpG methylation underestimation and non-CpG methylation masking, failing to evidence differential methylation statuses. We also describe the characteristics of "Methylation-Insensitive Primers" (MIPs), having degenerated bases (G/A) to cope with the uncertain C/U conversion. As CpG and non-CpG DNA methylation patterns are largely variable depending on the species, developmental stage, tissue and cell type, a variable extent of the bias is expected. The more the methylome is methylated, the greater is the extent of the bias, with a prevalent effect of non-CpG methylation. These findings suggest a revision of several DNA methylation patterns so far documented and also point out the necessity of applying unbiased analyses to the increasing number of epigenomic studies.
Note: Reproducció del document publicat a: http://dx.doi.org/10.1371/journal.pone.0118318
It is part of: PLoS One, 2015, vol. 10, num. 2, p. e0118318
Related resource: http://dx.doi.org/10.1371/journal.pone.0118318
URI: http://hdl.handle.net/2445/101440
ISSN: 1932-6203
Appears in Collections:Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))
Articles publicats en revistes (Patologia i Terapèutica Experimental)

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