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首页> 外文期刊>Genomics >Focussing reduced representation CpG sequencing through judicious restriction enzyme choice
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Focussing reduced representation CpG sequencing through judicious restriction enzyme choice

机译：通过明智地选择限制性内切酶来集中减少代表性CpG测序

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摘要

Current restriction enzyme based reduced representation methylation analyses aim for limited, but unbiased, methylome coverage. As the current best estimate suggests that only similar to 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. (C) 2016 Elsevier Inc. All rights reserved.
机译：当前基于限制性内切酶的减少表达甲基化分析的目标是有限但无偏见的甲基化组。正如目前的最佳估计表明，只有约20％的CpG受到动态调节，我们对所有合适的限制性酶切位点周围的CpG和基因组背景进行了鉴定，以鉴定出位于富含动态甲基化CpGs的区域中的那些酶。 MspI，BstUI和HhaI的限制性酶切位点分布是非随机的。 CGI和架子+岸上的CpG可能会富集，特别是在所有基因组区域，启动子（TSS1500，TSS200），内部（第一外显子，基因体，3'UTR，5'UTR）和跨基因区域的基因体中。 HpyCH4IV在公海中丰富了所有基因组元素的CpG元素。明智的限制性内切酶选择避免了不相关，不需要或难以作图的基因组区域对阅读范围的垄断，并且仅对信息量最大的CpG进行了测序，从而提高了减少代表性方法的重点。 （C）2016 Elsevier Inc.保留所有权利。

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