Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton

Song, Qingxin; Guan, Xueying; Chen, Z. Jeffrey

doi:10.1371/journal.pgen.1005724

Cited by 62 publications

(60 citation statements)

References 60 publications

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“…In some cases, demethylation was associated with gene down-regulation. Similar results have been reported in a number of plant species, including soybean (Song et al, 2013;Rambani et al, 2015), maize (Gent et al, 2013), rice (Secco et al, 2015), and cotton (Song et al, 2015). This may be linked to the properties of the DMRs including the presence of regulatory elements, active chromatin marks, and proximity to differentially methylated TEs.…”

Section: Discussionsupporting

confidence: 85%

Cyst Nematode Parasitism Induces Dynamic Changes in the Root Epigenome

et al. 2017

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A growing body of evidence indicates that epigenetic modifications can provide efficient, dynamic, and reversible cellular responses to a wide range of environmental stimuli. However, the significance of epigenetic modifications in plant-pathogen interactions remains largely unexplored. In this study, we provide a comprehensive analysis of epigenome changes during the compatible interaction between the beet cyst nematode Heterodera schachtii and Arabidopsis (Arabidopsis thaliana). Whole-genome bisulfite sequencing was conducted to assess the dynamic changes in the methylome of Arabidopsis roots in response to H. schachtii infection. H. schachtii induced widespread hypomethylation of protein-coding genes and transposable elements (TEs), preferentially those adjacent to protein-coding genes. The abundance of 24-nt siRNAs was associated with hypermethylation of TEs and gene promoters, with influence observed for methylation context and infection time points. mRNA sequencing revealed a significant enrichment for the differentially methylated genes among the differentially expressed genes, specifically those with functions corresponding to primary metabolic processes and responses to stimuli. The differentially methylated genes overlapped with more than one-fourth of the syncytium differentially expressed genes and are of functional significance. Together, our results provide intriguing insights into the potential regulatory role of differential DNA methylation in shaping the biological interplay between cyst nematodes and host plants.

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Section: Discussionsupporting

confidence: 85%

Cyst Nematode Parasitism Induces Dynamic Changes in the Root Epigenome

et al. 2017

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“…Few recent studies showed the importance of DNA methylation, histone methylation and small RNAs in the cotton fiber and root development. The DNA methylation is also responsible for the expression bias of homoeologous genes during ovule and fiber development in allotetraploid cotton (Song et al ., ). In another report, hypermethylated DNA governs the fiber differentiation by the H3K9me2‐dependent pathway in Gossypium barbadense (Wang et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Role of GhHDA5 in H3K9 deacetylation and fiber initiation in Gossypium hirsutum

Kumar

Singh

et al. 2018

The Plant Journal

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Cotton fibers are single-celled trichomes that initiate from the epidermal cells of the ovules at or before anthesis. Here, we identified that the histone deacetylase (HDAC) activity is essential for proper cotton fiber initiation. We further identified 15 HDACs homoeologs in each of the A- and D-subgenomes of Gossypium hirsutum. Few of these HDAC homoeologs expressed preferentially during the early stages of fiber development [-1, 0 and 6 days post-anthesis (DPA)]. Among them, GhHDA5 expressed significantly at the time of fiber initiation (-1 and 0 DPA). The in vitro assay for HDAC activity indicated that GhHDA5 primarily deacetylates H3K9 acetylation marks. Moreover, the reduced expression of GhHDA5 also suppresses fiber initiation and lint yield in the RNA interference (RNAi) lines. The 0 DPA ovules of GhHDA5RNAi lines also showed alterations in reactive oxygen species homeostasis and elevated autophagic cell death in the developing fibers. The differentially expressed genes (DEGs) identified through RNA-seq of RNAi line (DEP12) and their pathway analysis showed that GhHDA5 modulates expression of many stress and development-related genes involved in fiber development. The reduced expression of GhHDA5 in the RNAi lines also resulted in H3K9 hyper-acetylation on the promoter region of few DEGs assessed by chromatin immunoprecipitation assay. The positively co-expressed genes with GhHDA5 showed cumulative higher expression during fiber initiation, and gene ontology annotation suggests their involvement in fiber development. Furthermore, the predicted protein interaction network in the positively co-expressed genes indicates HDA5 modulates fiber initiation-specific gene expression through a complex involving reported repressors.

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“…Also, it has reported that DNA methylation could mediate gene and repeat element expression to enhance the transition from epidermal to fiber cells during ovule and seed development in cotton [34]. …”

Section: Discussionmentioning

confidence: 99%

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq

et al. 2017

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DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2. When comparing J1 against J2, there were 1222 down-methylated genes and 623 up-methylated genes. Methylated genes were significantly enriched in carbohydrate metabolism, biosynthesis of other secondary metabolites and amino acid metabolism pathways. The global DNA methylation level decreased from J1 to J2, especially in gene promoters, transcriptional termination regions and regions around CpG islands. We further investigated the expression patterns of 9 DNA methyltransferase-associated genes and 2 DNA demethyltransferase-associated genes from young to senescent cotyledons, which were down-regulated during cotyledon development. In this paper, we first reported that senescent cotton cotyledons exhibited lower DNA methylation levels, primarily due to decreased DNA methyltransferase activity and which also play important role in regulating secondary metabolite process.

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Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton

Cited by 62 publications

References 60 publications

Cyst Nematode Parasitism Induces Dynamic Changes in the Root Epigenome

Cyst Nematode Parasitism Induces Dynamic Changes in the Root Epigenome

Role of GhHDA5 in H3K9 deacetylation and fiber initiation in Gossypium hirsutum

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq

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