Jiang Jiming
Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
Curr Opin Plant Biol. 2015 Apr;24:17-23. doi: 10.1016/j.pbi.2015.01.005. Epub 2015 Jan 24.
Sequencing of complete plant genomes has become increasingly more routine since the advent of the next-generation sequencing technology. Identification and annotation of large amounts of noncoding but functional DNA sequences, including cis-regulatory DNA elements (CREs), have become a new frontier in plant genome research. Genomic regions containing active CREs bound to regulatory proteins are hypersensitive to DNase I digestion and are called DNase I hypersensitive sites (DHSs). Several recent DHS studies in plants illustrate that DHS datasets produced by DNase I digestion followed by next-generation sequencing (DNase-seq) are highly valuable for the identification and characterization of CREs associated with plant development and responses to environmental cues. DHS-based genomic profiling has opened a door to identify and annotate the 'dark matter' in sequenced plant genomes.
自新一代测序技术问世以来，完整植物基因组的测序已变得越来越常规。对大量非编码但具有功能的DNA序列进行鉴定和注释，包括顺式调控DNA元件（CREs），已成为植物基因组研究的一个新前沿。含有与调控蛋白结合的活性CREs的基因组区域对DNase I消化高度敏感，被称为DNase I超敏位点（DHSs）。最近在植物中进行的几项DHS研究表明，通过DNase I消化然后进行新一代测序（DNase-seq）产生的DHS数据集对于鉴定和表征与植物发育及对环境信号响应相关的CREs非常有价值。基于DHS的基因组分析为识别和注释已测序植物基因组中的“暗物质”打开了一扇门。
