植物顺式调控元件研究进展

doi:10.3969/j.issn.1004-1524.20231144

浙江农业学报 ›› 2024, Vol. 36 ›› Issue (8): 1945-1956.DOI: 10.3969/j.issn.1004-1524.20231144

• 综述 • 上一篇

植物顺式调控元件研究进展

张鑫^a(), 刘鹏^b^,^*()

扬州大学 a. 江苏省作物遗传生理国家重点实验室,植物功能基因组学教育部重点实验室,江苏省作物基因组学与分子育种重点实验室,粮食作物现代产业技术协同创新中心;b. 农业科技发展研究院,教育部农业与农产品安全国际合作联合实验室,江苏扬州 225009

收稿日期:2023-09-25 出版日期:2024-08-25 发布日期:2024-09-06
作者简介:*刘鹏,E-mail: pengliu@yzu.edu.cn
张鑫(1998—),男,贵州铜仁人,硕士研究生,研究方向为生物信息学与作物分子进化。E-mail: zx1766952382@qq.com
通讯作者: 刘鹏
基金资助:
扬州大学植物功能基因组学教育部重点实验室开放课题

Research progress of cis-regulatory elements in plants

ZHANG Xin^a(), LIU Peng^b^,^*()

a. State Key Laboratory of Crop Genetic Physiology, Jiangsu Province, Key Laboratory of Plant Functional Genomics, Ministry of Education, Key Laboratory of Crop Genomics and Molecular Breeding in Jiangsu Province, Collaborative Innovation Center for Modern Industrial Technology of Grain Crops; b. Institute of Agricultural Science and Technology Development, Joint Laboratory for International Cooperation in Agricultural and Agricultural Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, Jiangsu, China

Received:2023-09-25 Online:2024-08-25 Published:2024-09-06
Contact: LIU Peng

摘要/Abstract

摘要：

顺式调控元件是具有调控功能的非编码DNA序列,确保植物在不同生长发育阶段和环境应答时相关基因正确的时空表达。目前,植物顺式调控元件的功能研究落后于动物,然而依托较完善的基因组注释信息和开放染色质技术,植物顺式调控元件研究取得了重要进展。文章综述了植物顺式调控元件的相关研究,发现活性顺式调控元件与染色质活性相关联,转录因子和顺式调控元件之间的相互作用决定了基因转录水平,高通量测序技术提供的不同分子层面的组学数据能高效鉴定到顺式调控元件,由转座子衍生的顺式调控元件调控农艺性状基因转录。精准鉴定和深入功能解析顺式调控元件是未来重要的研究方向。植物顺式调控元件的挖掘与功能解析有助于系统阐明农作物重要农艺性状基因的调控机制,更好助力于培育高产、优质、高抗、高效的优良新品种。

关键词: 顺式调控元件, 开放染色质, 转录因子, 染色质活性

Abstract:

Cis-regulatory elements are non-coding DNA sequences serving the key regulatory function, which ensure the proper spatiotemporal patterns of gene expression necessary for responses to development and environmental cues. Currently, the functional study of cis-regulatory elements in plants lags behind that of animals. However, relying on the improvement of genome annotation and open chromatin profiling methods in plants, great progress has been made in the research of plant cis-regulatory elements. This paper summarizes the latest research findings of plant cis-regulatory elements: active cis-regulatory elements correlate with chromatin activity, the interactions between transcription factors and cis-regulatory elements determine the level of gene transcription, the high-throughput sequencing technology provides omics data at different molecular levels to efficiently identify cis-regulatory elements, cis-regulatory elements derived from transposons regulate the transcription of agronomic trait genes. Accurate identification and in-depth functional analysis of cis-regulatory elements are important research directions in the future. The exploration and functional analysis of plant cis-regulatory elements are helpful to systematically elucidate the regulatory mechanism of important agronomic traits genes in crops, thereby better facilitating the cultivation of new varieties that are high-yield, high-quality, highly-resistance and high efficiency.

Key words: cis-regulatory element, open chromatin, transcription factor, chromatin activity

中图分类号:

张鑫, 刘鹏. 植物顺式调控元件研究进展[J]. 浙江农业学报, 2024, 36(8): 1945-1956.

ZHANG Xin, LIU Peng. Research progress of cis-regulatory elements in plants[J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1945-1956.

图/表 2

图1 不同功能CRM的染色质特征示意图 A,活性增强子。组蛋白乙酰化修饰在CRE富集。CRE与TF、辅助因子相互作用,从而靶向目标基因的启动子以激活其转录。B,抑制状态CRM。由于Polycomb Group蛋白和H3K27me3修饰的存在,局部染色质结构致密,CRE不能与TF结合,从而导致靶基因的转录沉默。C,平衡态CRM。CRE位于开放染色质区,具有低水平组蛋白乙酰化修饰,Polycomb Group蛋白和H3K27me3修饰仍然存在,因此只有少数的CRE能够和TF结合。Cofactor,辅助因子;TF,转录因子;CRE,顺式调控元件;P,启动子;CDS,基因编码序列;TSS,转录起始位点;Polycomb Group,多梳家族蛋白。

Fig.1 Schematic representation of chromatin features of CRMs in different states A, Active enhancer. Histone acetylation modifications are enriched around CREs. TFs as well as cofactors interact with CREs, which target the gene’s promoter to activate its transcription. B, Repressed CRM. Due to the occupation of Polycomb Group proteins and H3K27me3 modification at CREs, where local chromatin structure is dense, CREs aren’t able to bind to TFs, resulting in transcriptional silencing of the target gene. C, Poised CRM. Although CREs are located in the open chromatin region with low levels of histone acetylation modification, Polycomb Group proteins and H3K27me3 modification still exist, so only a few CREs can bind to TFs. Cofactor, Auxiliary factor; TF, Transcription factor; CRE, Cis-regulatory element; P, Promoter; CDS, Gene coding sequence; TSS; Transcription start site; Polycomb Group, Polycomb Group protein.

图2 CRM的高通量鉴定方法示意简图 ATAC-seq,转座酶可及性测序;DNase-seq,脱氧核糖核酸酶I超敏位点测序;FAIRE-seq,甲醛辅助分离调控元件测序;ChIP-seq,染色质免疫共沉淀测序;ChIA-PET,配对末端标签测序分析染色质相互作用;Hi-ChIP,基于染色质免疫共沉淀的原位Hi-C。

Fig.2 Schematic diagram of high-throughput identification method for CRM ATAC-seq, Assay for transposase accessible chromatin sequencing; DNase-seq, DNase I sequencing; FAIRE-seq, Formaldehyde assisted isolation of regulatory element sequencing; ChIP-seq, Chromatin immunoprecipitation sequencing; ChIA-PET, Chromatin interaction analysis by paired-end tag sequencing; Hi-ChIP, In situ Hi-C followed by chromatin immunoprecipitation.

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植物顺式调控元件研究进展

Research progress of cis-regulatory elements in plants

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