Research progress of cis-regulatory elements in plants

doi:10.3969/j.issn.1004-1524.20231144

Acta Agriculturae Zhejiangensis ›› 2024, Vol. 36 ›› Issue (8): 1945-1956.DOI: 10.3969/j.issn.1004-1524.20231144

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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

Abstract

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

CLC Number:

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

Figures/Tables 2

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.

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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