کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
5907688 | 1160856 | 2016 | 11 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Focussing reduced representation CpG sequencing through judicious restriction enzyme choice
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کلمات کلیدی
TSSROIBSPPCpGwhole genome bisulfite sequencingMBDCGIRRBSMethyl-CpG binding domainWGBSMREMeDIPrestriction enzyme - آنزیم محدود کنندهNext-generation sequencing - تعیین توالی نسل بعدیCpG island - جزیره CpGtranscription start site - رونویسی شروع سایتRepetitive element - عنصر تکراریDNA methylation - متیلاسیون DNAUTR یا untranslated regions - منطقه ترجمه نشدهregion of interest - منطقه مورد نظرNucleotide - نوکلئوتید
موضوعات مرتبط
علوم زیستی و بیوفناوری
بیوشیمی، ژنتیک و زیست شناسی مولکولی
ژنتیک
پیش نمایش صفحه اول مقاله
چکیده انگلیسی
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, 3â²UTR, 5â²UTR) 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.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Genomics - Volume 107, Issue 4, April 2016, Pages 109-119
Journal: Genomics - Volume 107, Issue 4, April 2016, Pages 109-119
نویسندگان
Sophie A. Kirschner, Oliver Hunewald, Sophie B. Mériaux, Regina Brunnhoefer, Claude P. Muller, Jonathan D. Turner,