Focussing reduced representation CpG sequencing through judicious restriction enzyme choice.
Identifieur interne : 000137 ( Main/Exploration ); précédent : 000136; suivant : 000138Focussing reduced representation CpG sequencing through judicious restriction enzyme choice.
Auteurs : Sophie A. Kirschner [Allemagne] ; Oliver Hunewald [Luxembourg (pays)] ; Sophie B. Mériaux [Luxembourg (pays)] ; Regina Brunnhoefer [Luxembourg (pays)] ; Claude P. Muller [Allemagne] ; Jonathan D. Turner [Luxembourg (pays)]Source :
- Genomics [ 1089-8646 ] ; 2016.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA Restriction Enzymes.
- chemical : 3' Untranslated Regions, 5' Untranslated Regions.
- methods : Genomics, Sequence Analysis, DNA.
- Animals, CpG Islands, DNA Methylation, Gene Library, Mice, Promoter Regions, Genetic.
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.
DOI: 10.1016/j.ygeno.2016.03.001
PubMed: 26945642
Affiliations:
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Mériaux</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Luxembourg (pays)</country><wicri:regionArea>Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette</wicri:regionArea><wicri:noRegion>L-4354 Esch-sur-Alzette</wicri:noRegion></affiliation></author><author><name sortKey="Brunnhoefer, Regina" sort="Brunnhoefer, Regina" uniqKey="Brunnhoefer R" first="Regina" last="Brunnhoefer">Regina Brunnhoefer</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Luxembourg (pays)</country><wicri:regionArea>Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette</wicri:regionArea><wicri:noRegion>L-4354 Esch-sur-Alzette</wicri:noRegion></affiliation></author><author><name sortKey="Muller, Claude P" sort="Muller, Claude P" uniqKey="Muller C" first="Claude P" last="Muller">Claude P. Muller</name><affiliation wicri:level="4"><nlm: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.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>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</wicri:regionArea><wicri:noRegion>54290</wicri:noRegion><orgName type="university">Université de Trèves</orgName><placeName><settlement type="city">Trèves (Allemagne)</settlement><region type="land" nuts="1">Rhénanie-Palatinat</region></placeName></affiliation></author><author><name sortKey="Turner, Jonathan D" sort="Turner, Jonathan D" uniqKey="Turner J" first="Jonathan D" last="Turner">Jonathan D. Turner</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Luxembourg (pays)</country><wicri:regionArea>Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette</wicri:regionArea><wicri:noRegion>L-4354 Esch-sur-Alzette</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genomics</title><idno type="eISSN">1089-8646</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>3' Untranslated Regions</term><term>5' Untranslated Regions</term><term>Animals</term><term>CpG Islands</term><term>DNA Methylation</term><term>DNA Restriction Enzymes (chemistry)</term><term>Gene Library</term><term>Genomics (methods)</term><term>Mice</term><term>Promoter Regions, Genetic</term><term>Sequence Analysis, DNA (methods)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA Restriction Enzymes</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>3' Untranslated Regions</term><term>5' Untranslated Regions</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>CpG Islands</term><term>DNA Methylation</term><term>Gene Library</term><term>Mice</term><term>Promoter Regions, Genetic</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Luxembourg (pays)</li></country><region><li>Rhénanie-Palatinat</li></region><settlement><li>Trèves (Allemagne)</li></settlement><orgName><li>Université de Trèves</li></orgName></list><tree><country name="Allemagne"><region name="Rhénanie-Palatinat"><name sortKey="Kirschner, Sophie A" sort="Kirschner, Sophie A" uniqKey="Kirschner S" first="Sophie A" last="Kirschner">Sophie A. Kirschner</name></region><name sortKey="Muller, Claude P" sort="Muller, Claude P" uniqKey="Muller C" first="Claude P" last="Muller">Claude P. Muller</name></country><country name="Luxembourg (pays)"><noRegion><name sortKey="Hunewald, Oliver" sort="Hunewald, Oliver" uniqKey="Hunewald O" first="Oliver" last="Hunewald">Oliver Hunewald</name></noRegion><name sortKey="Brunnhoefer, Regina" sort="Brunnhoefer, Regina" uniqKey="Brunnhoefer R" first="Regina" last="Brunnhoefer">Regina Brunnhoefer</name><name sortKey="Meriaux, Sophie B" sort="Meriaux, Sophie B" uniqKey="Meriaux S" first="Sophie B" last="Mériaux">Sophie B. Mériaux</name><name sortKey="Turner, Jonathan D" sort="Turner, Jonathan D" uniqKey="Turner J" first="Jonathan D" last="Turner">Jonathan D. Turner</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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