Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis

	Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis
	Tan, YJ; Yan, XH; Sun, JL; Wan, J; Li, XX; Huang, YZ; Li, L; Niu, LJ; Hou, CH
	2023
发表期刊	PLANT JOURNAL
ISSN	0960-7412
卷号	116 期号:1 页码:234-250
摘要	Enhancers are critical cis-regulatory elements controlling gene expression during cell development and differentiation. However, genome-wide enhancer characterization has been challenging due to the lack of a well-defined relationship between enhancers and genes. Function-based methods are the gold standard for determining the biological function of cis-regulatory elements; however, these methods have not been widely applied to plants. Here, we applied a massively parallel reporter assay on Arabidopsis to measure enhancer activities across the genome. We identified 4327 enhancers with various combinations of epigenetic modifications distinctively different from animal enhancers. Furthermore, we showed that enhancers differ from promoters in their preference for transcription factors. Although some enhancers are not conserved and overlap with transposable elements forming clusters, enhancers are generally conserved across thousand Arabidopsis accessions, suggesting they are selected under evolution pressure and could play critical roles in the regulation of important genes. Moreover, comparison analysis reveals that enhancers identified by different strategies do not overlap, suggesting these methods are complementary in nature. In sum, we systematically investigated the features of enhancers identified by functional assay in A. thaliana, which lays the foundation for further investigation into enhancers' functional mechanisms in plants.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14362
专题	科研部门_进化发育与四维基因调控（候春晖）
推荐引用方式 GB/T 7714	Tan, YJ,Yan, XH,Sun, JL,et al. Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis[J]. PLANT JOURNAL,2023,116(1):234-250.
APA	Tan, YJ.,Yan, XH.,Sun, JL.,Wan, J.,Li, XX.,...&Hou, CH.(2023).Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis.PLANT JOURNAL,116(1),234-250.
MLA	Tan, YJ,et al."Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis".PLANT JOURNAL 116.1(2023):234-250.

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