An expedient survey and characterization of the soybean JAGGED 1 (GmJAG1) transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts

Huang, Mingkun; Zhang, Ling; Zhou, Limeng; Wang, Mo‐Zhu; Yung, Wai‐Shing; Wang, Zhili; Duan, Shengwen; Xiao, Zhixia; Wang, Qianwen; Wang, Xin; Li, Man-Wah; Lam, Hon‐Ming

doi:10.1016/j.ygeno.2020.12.026

Cited by 7 publications

(4 citation statements)

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“…Furthermore, 22,333 enriched regions in the ATAC-seq were identified using the Genrich software (see method) and defined as OCRs ( Table S2 ). This number is similar to the number of OCRs identified in cultivated soybean leaves [ 17 ]. Furthermore, these OCRs were associated with 15,588 protein-coding genes in total ( Table S2 ).…”

Section: Resultssupporting

confidence: 70%

“…Currently, OCR profiling using ATAC-seq in plants has been reported, including in Arabidopsis [ 1 , 12 ], maize [ 15 , 16 , 31 ], and cultivated soybean [ 16 , 17 ], but less so in wild soybean [ 32 ]. In this study, the 22,333 OCRs we identified in wild soybean is similar to the OCR number previously reported in cultivated soybean [ 16 , 17 ]. Moreover, the association with histone marks as well as the distal enhancer-like feature of dOCRs are consistent with the published OCR profiles in other plants [ 16 ], suggesting that the genomic features of OCRs are conserved among plants.…”

Section: Discussionmentioning

confidence: 99%

“…The ATAC-seq library preparation was performed according to a previous study [ 17 ]. In brief, about 0.2 g of W05 trifoliate leaves was ground into powder in liquid N 2 .…”

Section: Methodsmentioning

confidence: 99%

“…According to the Encyclopedia of DNA Elements (ENCODE) project [ 11 ], ATAC-seq has been widely applied in mammalian genomic studies to identify more than tens of thousands of OCRs, which are essential for analyzing mammalian genome architecture. Due to the regulatory importance of OCRs, the application of ATAC-seq for mapping OCRs has been reported in the model plant Arabidopsis [ 1 , 8 , 12 ], maize [ 13 , 14 , 15 ], and other plants [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

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Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions

Huang

Zhang

Zhou

et al. 2021

Genes

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Transcription activation is tightly associated with the openness of chromatin, which allows direct contact between transcriptional regulators, such as transcription factors, and their targeted DNA for downstream gene activation. However, the annotation of open chromatin regions (OCRs) in the wild soybean (Glycine soja) genome is limited. We performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and successfully identified 22,333 OCRs in the leaf of W05 (a wild soybean accession). These OCRs were enriched in gene transcription start sites (TSS) and were positively correlated with downstream gene expression. Several known transcription factor (TF)-binding motifs were also enriched at the OCRs. A potential regulatory network was constructed using these transcription factors and the OCR-marked genes. Furthermore, by overlapping the OCR distribution with those of histone modifications from chromatin immunoprecipitation followed by sequencing (ChIP-seq), we found that the distribution of the activation histone mark, H3K4me3, but not that of the repressive H3K27me3 mark, was closely associated with OCRs for gene activation. Several putative enhancer-like distal OCRs were also found to overlap with LincRNA-encoding loci. Moreover, our data suggest that homologous OCRs could potentially influence homologous gene expression. Hence, the duplication of OCRs might be essential for plant genome architecture as well as for regulating gene expression.

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Section: Resultssupporting

confidence: 70%

Section: Discussionmentioning

confidence: 99%

“…The ATAC-seq library preparation was performed according to a previous study [ 17 ]. In brief, about 0.2 g of W05 trifoliate leaves was ground into powder in liquid N 2 .…”

Section: Methodsmentioning

confidence: 99%