Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
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DOI：
10.1371/journal.pone.0042414
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Zhang YX
中科院分区：
文献类型：
--
作者：
Wang YM;Zhou P;Wang LY;Li ZH;Zhang YN;Zhang YX
核染色质内dna酶I超敏感位点（DHSs）定位是一种传统而有效的基因调控元件鉴定方法。通过捕获长DNase I-cut片段（bbb10万bp）或100-1200 bp DNase I-double cleavage片段（也称为double-hit片段）的末端来绘制dhs。但下一代测序需要包含100 - 500bp DNA片段的DNA文库。因此，我们使用DNase I酶切释放的短DNA片段来生成下一代测序的DNA文库。短片段长度为100-300 bp，可直接克隆用于高通量测序。我们在人类基因组的2,343,479个标签中鉴定出83,897个dhs。我们的研究结果表明，通过DHS分析鉴定的DHS与以往研究中通过较长片段鉴定的DHS一致。我们还发现：(1)DHSs在相似表达基因的启动子和其他基因区域的分布在不同染色体间存在差异；(2)沉默基因的染色质结构比先前认为的更开放；(3) 3′非翻译区dhs与基因表达水平呈负相关。
Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100–1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100–500 bp. Therefore, we used short DNA fragments released by DNase I digestion to generate DNA libraries for next generation sequencing. The short segments are 100–300 bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by this DHS assay are consistent with those identified by longer fragments in previous studies. We also found: (1) the distribution of DHSs in promoter and other gene regions of similarly expressed genes differs among different chromosomes; (2) silenced genes had a more open chromatin structure than previously thought; (3) DHSs in 3′untranslated regions (3′UTRs) are negatively correlated with level of gene expression.
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