Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.
Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.
复制标题
通过 DNase I 超敏感位点的平铺阵列作图对秀丽隐杆线虫调控元件进行基因组规模鉴定
DOI：
10.1186/1471-2164-10-92
复制
发表时间：
2009-02-25
期刊：
影响因子：
4.4
通讯作者：
Chen R
中科院分区：
文献类型：
--
作者：
Shi B;Guo X;Wu T;Sheng S;Wang J;Skogerbø G;Zhu X;Chen R
背景
后基因组学研究的一个主要目标是在全基因组范围内对基因、调控元件和染色质结构进行综合分析。在核染色质内绘制DNase I超敏位点是鉴定调控元件候选物的强有力且已确立的方法。
结果
在这里，我们报告的第一个全基因组分析的DNase I超敏位点（DHS）在秀丽隐杆线虫。通过将来自年轻成虫的DNA酶I处理的和末端捕获的材料与高分辨率平铺微阵列杂交来获得数据。数据表明，C.线虫DHSs在位于编码基因上游和下游2kb的基因间区域内显著富集，并且所有DHSs的相当大部分映射到远离注释的编码基因的基因间位置。注释的转录位点通常在DHS中相对于基因间区域被耗尽，但是DHS仍然在编码外显子和UTR中富集，而内含子在DHS中被显著耗尽。许多DHS似乎与注释的非编码RNA和最近检测到的功能未知的转录本有关。有报道表明线虫高度保守的非编码元件与顺式调控元件相关，我们还发现DHSs，特别是远端基因间DHSs，在C. elegans和C.布里格斯基因组。
结论
我们描述了第一个全基因组分析C。elegans DHSs，并显示DHSs的分布与基因组中的功能元件密切相关。
Background
A major goal of post-genomics research is the integrated analysis of genes, regulatory elements and the chromatin architecture on a genome-wide scale. Mapping DNase I hypersensitive sites within the nuclear chromatin is a powerful and well-established method of identifying regulatory element candidates.
Results
Here, we report the first genome-wide analysis of DNase I hypersensitive sites (DHSs) in Caenorhabditis elegans. The data was obtained by hybridizing DNase I-treated and end-captured material from young adult worms to a high-resolution tiling microarray. The data show that C. elegans DHSs were significantly enriched within intergenic regions located 2 kb upstream and downstream of coding genes, and also that a considerable fraction of all DHSs mapped to intergenic positions distant to annotated coding genes. Annotated transcribed loci were generally depleted in DHSs relative to intergenic regions, but DHSs were nonetheless enriched in coding exons and UTRs, whereas introns were significantly depleted in DHSs. Many DHSs appeared to be associated with annotated non-coding RNAs and recently detected transcripts of unknown function. It has been reported that nematode highly conserved non-coding elements were associated with cis-regulatory elements, and we also found that DHSs, particularly distal intergenic DHSs, were significantly enriched in regions that were conserved between the C. elegans and C. briggsae genomes.
Conclusion
We describe the first genome-wide analysis of C. elegans DHSs, and show that the distribution of DHSs is strongly associated with functional elements in the genome.
登录
查看更多内容
影响因子：
14.9
作者：
HEWISH, D
通讯作者：
HEWISH, D
影响因子：
7
作者：
Huang, Peiming;Pleasance, Erin D.;Jones, Steven J. M.
通讯作者：
Jones, Steven J. M.
影响因子：
5.3
作者：
MEHEUS, L;VANFLETEREN, JR
通讯作者：
VANFLETEREN, JR
影响因子：
30.8
作者：
Heintzman, Nathaniel D.;Stuart, Rhona K.;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
7
作者：
He, Housheng;Wang, Jie;Chen, Runsheng
通讯作者：
Chen, Runsheng