TY - JOUR
T1 - Focussing reduced representation CpG sequencing through judicious restriction enzyme choice
AU - Kirschner, Sophie A.
AU - Hunewald, Oliver
AU - Mériaux, Sophie B.
AU - Brunnhoefer, Regina
AU - Muller, Claude P.
AU - Turner, Jonathan D.
N1 - Funding Information:
This work was financially supported by AFR PhD grant No. 1176135 and C12/BM/3985792 “EpiPath” from the Fonds National de la Recherche (FNR), the Luxembourg Institute of Health (LIH) and the Ministry of Higher Education and Research of Luxembourg. We thank both Francisco Azuaje and William J. Faison for their critical reading of, and helpful comments on, this manuscript (NorLux Neuro-Oncology Laboratory, and Dept. of Infection and Immunity, LIH, Luxembourg, respectively).
Publisher Copyright:
© 2016 Elsevier Inc.
PY - 2016/4/1
Y1 - 2016/4/1
N2 - 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.
AB - 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.
KW - CpG
KW - DNA methylation
KW - Next-generation sequencing
KW - Restriction enzyme
UR - http://www.scopus.com/inward/record.url?scp=84959459582&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2016.03.001
DO - 10.1016/j.ygeno.2016.03.001
M3 - Article
C2 - 26945642
AN - SCOPUS:84959459582
SN - 0888-7543
VL - 107
SP - 109
EP - 119
JO - Genomics
JF - Genomics
IS - 4
ER -