Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq

Zhang, Aicen; Li, Xinxu; Zhao, Hainan; Jiang, Jiming; Zhang, Wenli

doi:10.1007/978-1-0716-2815-7_3

Cited by 2 publications

(2 citation statements)

References 31 publications

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“…To identify ACRs in the strawberry genome, we developed MH-seq libraries 54 using chromatin isolated from leaf tissue of octoploid strawberry cultivar ‘Royal Royce’ (RR). The MH-seq reads from two biological replicates were mapped to a high-quality RR reference genome 55 .…”

Section: Resultsmentioning

confidence: 99%

Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry

Fang,

Jiang,

Teresi

et al. 2024

Nat Commun

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Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.

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Section: Resultsmentioning

confidence: 99%

Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry

Fang,

Jiang,

Teresi

et al. 2024

Nat Commun

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“…We performed MH-seq ( 30 ) to detect ACRs in the soybean genome. We developed two MH-seq libraries from each of three tissues (leaves, flowers, and seeds) from soybean cultivar Williams 82.…”

Section: Resultsmentioning

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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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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Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq

Cited by 2 publications

References 31 publications

Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry

Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry

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

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