Identification of the accessible chromatin regions in six tissues in the soybean

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

doi:10.1016/j.ygeno.2022.110364

Cited by 11 publications

(7 citation statements)

References 42 publications

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“…Nearly 77% (75,581) of the MHSs were not covered by ATAC-seq peaks, which were referred to as “specific MHS” (sMHSs). Huang et al (2022) recently reported ATAC-seq datasets from six soybean tissues ( 34 ). The leaf, flower, and seed tissues used in the study were at the similar developmental stages as the same tissues used in our study.…”

Section: Resultsmentioning

confidence: 99%

“…MH-seq datasets and MHSs were deposited in NCBI Gene Expression Omnibus (GEO) under accession number GSE167578 ( 77 ). ATAC-seq data and respective RNA-seq data as well as H3 ChIP-seq data were downloaded from NCBI GEO under accession number GSE128434 ( 78 ) and BioProject accession number PRJNA751745 ( 79 ). RNA-seq data from tissues at similar stages with samples used for MH-seq were downloaded from NCBI SRA under the following accession numbers: SRR1174229 (leaf), SRR1174220 (flower), and SRR1174208 (seed) ( 80 ).…”

Section: Data Materials and Software Availabilitymentioning

confidence: 99%

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

Fang,

Yang,

Tang

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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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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Section: Resultsmentioning

confidence: 99%

Section: Data Materials and Software Availabilitymentioning

confidence: 99%

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

Fang,

Yang,

Tang

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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“…Huang et al showed that ACRs occupied about 3.3% of the entire soybean genome. 48 Wang et al found that nearly 25% of OCRs are distal intergenic OCRs in reproductive organs of rice. 49 The intergenic region of DNA is thought to regulate the expression of nearby genes.…”

Section: Discussionmentioning

confidence: 99%

Selective penetration of fullerenol through pea seed coats mitigates osmosis‐repressed germination via chromatin remodeling and transcriptional reprograming

Ning,

Sun,

Wang

et al. 2024

J Sci Food Agric

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BackgroundAlteration of chromatin accessibility plays an important role in plant responses to abiotic stress. Carbon‐based nanomaterials (CBNMs) have gained growing interest in agriculture due to their potential impact on crop productivity, showcasing effects on plant biological processes at transcriptional levels, yet their impacts chromatin accessibility remains unknown.ResultsIn this study, we found that fullerenol can penetrate seed coat of pea to mitigate the reduction of seed germination caused by osmotic stress. RNA‐seq revealed that the application of fullerenol resorted the high expression of genes related to oxidoreduction to the normal level. ATAC‐seq corroborated that fullerenol application reduced the overall levels of chromatin accessibility of numerous genes, including those related to environmental signaling, transcriptional regulation, and metabolism.ConclusionCollectively, our study suggests that fullerenol alleviates osmotic stress on various fronts, encompassing antioxidant, transcriptional, and epigenetic levels, which advances our understanding on the working mechanism of this nanomaterial within plant cells.This article is protected by copyright. All rights reserved.

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“…While current studies mostly reported the profiles of a single element of epigenetic mechanisms, integrating the information from different epigenetic layers would provide a better understanding of the different chromatin environments and their influences on the transcriptional status. In recent studies, the assay for transposase‐accessible chromatin using sequencing have been applied in analyzing accessible chromatin regions in legumes such as soybean and barrel clover, providing valuable information about cis ‐regulatory elements for constructing transcriptional networks (Huang et al., 2022; Lu et al., 2019; Maher et al., 2018). While the modules of stress‐inducible transcription factor were presented, future studies should validate the constructed networks using samples under stress treatment.…”

Section: Discussionmentioning

confidence: 99%

Changes in epigenetic features in legumes under abiotic stresses

Yung

Huang

et al. 2022

The Plant Genome

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Legume crops are rich in nutritional value for human and livestock consumption. With global climate change, developing stress‐resilient crops is crucial for ensuring global food security. Because of their nitrogen‐fixing ability, legumes are also important for sustainable agriculture. Various abiotic stresses, such as salt, drought, and elevated temperatures, are known to adversely affect legume production. The responses of plants to abiotic stresses involve complicated cellular processes including stress hormone signaling, metabolic adjustments, and transcriptional regulations. Epigenetic mechanisms play a key role in regulating gene expressions at both transcriptional and posttranscriptional levels. Increasing evidence suggests the importance of epigenetic regulations of abiotic stress responses in legumes, and recent investigations have extended the scope to the epigenomic level using next‐generation sequencing technologies. In this review, the current knowledge on the involvement of epigenetic features, including DNA methylation, histone modification, and noncoding RNAs, in abiotic stress responses in legumes is summarized and discussed. Since most of the available information focuses on a single aspect of these epigenetic features, integrative analyses involving omics data in multiple layers are needed for a better understanding of the dynamic chromatin statuses and their roles in transcriptional regulation. The inheritability of epigenetic modifications should also be assessed in future studies for their applications in improving stress tolerance in legumes through the stable epigenetic optimization of gene expressions.

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Identification of the accessible chromatin regions in six tissues in the soybean

Cited by 11 publications

References 42 publications

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

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

Selective penetration of fullerenol through pea seed coats mitigates osmosis‐repressed germination via chromatin remodeling and transcriptional reprograming

Changes in epigenetic features in legumes under abiotic stresses

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