title: Focussing reduced representation CpG sequencing through judicious restriction enzyme choice.
abstract: Current restriction enzyme based reduced representation methylation analyses aim for limited, but unbiased, methylome coverage. As the current best estimate suggests that only ~20% of CpGs are dynamically regulated, we characterised the CpG and genomic context surrounding all suitable restriction enzyme sites to identify those that were located in regions rich in dynamically methylated CpGs. The restriction-site distributions for MspI, BstUI, and HhaI were non-random. CpGs in CGI and shelf+shore could be enriched, particularly in gene bodies for all genomic regions, promoters (TSS1500, TSS200), intra- (1st exon, gene body, 3'UTR, 5'UTR) and inter-genic regions. HpyCH4IV enriched CpG elements in the open sea for all genomic elements. Judicious restriction enzyme choice improves the focus of reduced representation approaches by avoiding the monopolization of read coverage by genomic regions that are irrelevant, unwanted or difficult to map, and only sequencing the most informative fraction of CpGs.
authors.affiliation: Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg; Department of Immunology, Research Institute of Psychobiology, University of Trier, D-54290, Germany.
authors.forename: Sophie A
authors.initials: SA
authors.lastname: Kirschner
authors.affiliation: Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg.
authors.forename: Oliver
authors.initials: O
authors.lastname: Hunewald
authors.affiliation: Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg.
authors.forename: Sophie B
authors.initials: SB
authors.lastname: Mériaux
authors.affiliation: Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg.
authors.forename: Regina
authors.initials: R
authors.lastname: Brunnhoefer
authors.affiliation: Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg; Department of Immunology, Research Institute of Psychobiology, University of Trier, D-54290, Germany.
authors.forename: Claude P
authors.initials: CP
authors.lastname: Muller
authors.affiliation: Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg. Electronic address: jonathan.turner@lih.lu.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Turner
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000737:chemistry*; D015723:Gene Library; D023281:Genomics / Q000379:methods; D051379:Mice; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D004262:DNA Restriction Enzymes
keywords: CpG; DNA methylation; Next-generation sequencing; Restriction enzyme