Focussing reduced representation CpG sequencing through judicious restriction enzyme choice.

Autor: Kirschner SA; 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., Hunewald O; 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., Mériaux SB; 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., Brunnhoefer R; 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., Muller CP; 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., Turner JD; 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.
Jazyk: angličtina
Zdroj: Genomics [Genomics] 2016 Apr; Vol. 107 (4), pp. 109-19. Date of Electronic Publication: 2016 Mar 03.
DOI: 10.1016/j.ygeno.2016.03.001
Abstrakt: 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.
(Copyright © 2016 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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