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Dynamics of cis- regulatory sequences and transcriptional divergence of duplicated genes in soybean

文献类型： 外文期刊

作者： Fang, Chao 1 ; Yang, Mingyu 2 ; Tang, Yuecheng 2 ; Zhang, Ling 4 ; Zhao, Hainan 1 ; Ni, Hejia 3 ; Chen, Qingshan 3 ; Meng, Fanli 2 ; Ae, Jiming Jiang 1 ;

作者机构： 1.Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA

2.Chinese Acad Sci, Northeast Inst Geog & Agroecol, Key Lab Soybean Mol Design Breeding, Harbin 150081, Peoples R China

3.Northeast Agr Univ, Key Lab Soybean Biol, Chinese Minist Educ, Harbin 150030, Peoples R China

4.Jilin Acad Agr Sci, Agrobiotechnol Res Inst, Changchun 130033, Peoples R China

5.Michigan State Univ, Dept Hort, E Lansing, MI 48824 USA

6.Michigan State Univ, AgBioRes, E Lansing, MI 48824 USA

关键词： gene duplication; transcriptional divergence; accessible chromatin region; MNase hypersensitivity; CRISPR/Cas

期刊名称：PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA （ 影响因子：11.1； 五年影响因子：12.0 ）

ISSN： 0027-8424

年卷期： 2023 年 120 卷 44 期

页码：

收录情况： SCI

摘要： Transcriptional divergence of duplicated genes after whole genome duplication (WGD) has been described in many plant lineages and is often associated with subgenome dominance, a genome-wide mechanism. However, it is unknown what underlies the transcriptional divergence of duplicated genes in polyploid species that lack subgenome dominance. Soybean is a paleotetraploid with a WGD that occurred 5 to 13 Mya. Approximately 50% of the duplicated genes retained from this WGD exhibit transcriptional divergence. We developed accessible chromatin region (ACR) datasets from leaf, flower, and seed tissues using MNase- hypersensitivity sequencing. We validated enhancer function of several ACRs associated with known genes using CRISPR/Cas9- mediated genome editing. The ACR datasets were used to examine and correlate the transcriptional patterns of 17,111 pairs of duplicated genes in different tissues. We demonstrate that ACR dynamics are correlated with divergence of both expression level and tissue specificity of individual gene pairs. Gain or loss of flanking ACRs and mutation of cis- regulatory elements (CREs) within the ACRs can change the balance of the expression level and/ or tissue specificity of the duplicated genes. Analysis of DNA sequences associated with ACRs revealed that the extensive sequence rearrangement after the WGD reshaped the CRE landscape, which appears to play a key role in the transcriptional divergence of duplicated genes in soybean. This may represent a general mechanism for transcriptional divergence of duplicated genes in polyploids that lack subgenome dominance.

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