Department of Genetics, University of Georgia, Athens, GA, USA.
Department of Plant Biology, University of Georgia, Athens, GA, USA.
Nat Plants. 2019 Dec;5(12):1250-1259. doi: 10.1038/s41477-019-0548-z. Epub 2019 Nov 18.
Chromatin accessibility and modification is a hallmark of regulatory DNA, the study of which led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants, especially in species with large and complex genomes. The majority of distal CREs have been moved away from their target genes by transposable-element (TE) proliferation, but a substantial number of distal CREs also seem to be created by TEs. Finally, plant distal CREs are associated with three major types of chromatin signatures that are distinct from metazoans. Taken together, these results suggest that CREs are prevalent in plants, highly dynamic during evolution and function through distinct chromatin pathways to regulate gene expression.
染色质可及性和修饰是调控 DNA 的标志，对其的研究导致了顺式调控元件 (CREs) 的发现。在这里，我们描述了 13 种植物物种中的染色质可及性、组蛋白修饰和序列保守性。我们鉴定了数千个推定的 CREs，并揭示了远端 CREs 在植物中很普遍，尤其是在基因组较大且复杂的物种中。大多数远端 CREs 已被转座元件 (TE) 的增殖从其靶基因中移开，但相当数量的远端 CREs 似乎也是由 TEs 产生的。最后，植物的远端 CREs 与三种主要的染色质特征类型相关，这些类型与后生动物明显不同。总之，这些结果表明 CREs 在植物中很普遍，在进化过程中高度动态，通过不同的染色质途径发挥作用来调节基因表达。
