Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton
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PROVIDER: PRJNA325723 | ENA |
REPOSITORIES: ENA
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Project description:Histone modifications regulate gene expression in eukaryotes, but their roles in gene expression changes in interspecific hybrids or allotetraploids are poorly understood. Histone modifications can be mapped by immunostaining of metaphase chromosomes at the single cell level and/or by chromatin immunoprecipitation-sequencing (ChIP-seq) for individual genes. Here we examined H3K4me3 density and transcriptome maps in root-tip cells of allotetraploid cotton (Gossypium hirsutum L.). The overall H3K4me3 levels were relatively equal between A and D chromosomes, which were consistent with equal numbers of expressed genes between the two subgenomes. However, intensities per chromosomal area were nearly twice as high in the D homoeologs as in the A homoeologs. Consistent with the cytological observation, ChIP-seq analysis showed more D-homoeologs with biased H3K4me3 levels than A-homoeologs with biased modifications, which correlated with the greater number of genes with D-biased expression than that with A-biased expression in most homoeologous chromosome pairs. Two chromosomes displayed different expression levels compared with other chromosomes probably because of translocations, which may affect the local chromatin structure (hence expression levels) for the genes involved. This example of genome-wide histone modifications that determine expression bias of homoeologous genes in allopolyploids provides a molecular basis for the evolution and domestication of polyploid species including important crops.
2016-09-30 | GSE71418 | GEO
Project description:Histone modifications regulate gene expression in eukaryotes, but their roles in gene expression changes in interspecific hybrids or allotetraploids are poorly understood. Histone modifications can be mapped by immunostaining of metaphase chromosomes at the single cell level and/or by chromatin immunoprecipitation-sequencing (ChIP-seq) for individual genes. Here we examined H3K4me3 density and transcriptome maps in root-tip cells of allotetraploid cotton (Gossypium hirsutum L.). The overall H3K4me3 levels were relatively equal between A and D chromosomes, which were consistent with equal numbers of expressed genes between the two subgenomes. However, intensities per chromosomal area were nearly twice as high in the D homoeologs as in the A homoeologs. Consistent with the cytological observation, ChIP-seq analysis showed more D-homoeologs with biased H3K4me3 levels than A-homoeologs with biased modifications, which correlated with the greater number of genes with D-biased expression than that with A-biased expression in most homoeologous chromosome pairs. Two chromosomes displayed different expression levels compared with other chromosomes probably because of translocations, which may affect the local chromatin structure (hence expression levels) for the genes involved. This example of genome-wide histone modifications that determine expression bias of homoeologous genes in allopolyploids provides a molecular basis for the evolution and domestication of polyploid species including important crops.
2016-09-30 | GSE83372 | GEO
Project description:Histone modifications regulate gene expression in eukaryotes, but their roles in gene expression changes in interspecific hybrids or allotetraploids are poorly understood. Histone modifications can be mapped by immunostaining of metaphase chromosomes at the single cell level and/or by chromatin immunoprecipitation-sequencing (ChIP-seq) for individual genes. Here we examined H3K4me3 density and transcriptome maps in root-tip cells of allotetraploid cotton (Gossypium hirsutum L.). The overall H3K4me3 levels were relatively equal between A and D chromosomes, which were consistent with equal numbers of expressed genes between the two subgenomes. However, intensities per chromosomal area were nearly twice as high in the D homoeologs as in the A homoeologs. Consistent with the cytological observation, ChIP-seq analysis showed more D-homoeologs with biased H3K4me3 levels than A-homoeologs with biased modifications, which correlated with the greater number of genes with D-biased expression than that with A-biased expression in most homoeologous chromosome pairs. Two chromosomes displayed different expression levels compared with other chromosomes probably because of translocations, which may affect the local chromatin structure (hence expression levels) for the genes involved. This example of genome-wide histone modifications that determine expression bias of homoeologous genes in allopolyploids provides a molecular basis for the evolution and domestication of polyploid species including important crops.
2016-09-30 | GSE83371 | GEO
Project description:Five allotetraploid cotton species have adapted, through their transcriptional responses, to unique environments with distinct levels of inherent abiotic stresses. The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1). The microarray results identified 2721 and 2460 differentially expressed genes under salt stress that were significant in leaf and root tissue, respectively. Many of these genes were classified under gene ontology (GO) categories that suggest abiotic stress. These allotetraploid cottons shared transcriptional responses to salinity, but also showed responses that were species-specific. No consistent differences in transcriptional response among the previously estimated phylogenetic branches were found. Stomatal conductance, ion accumulation, and betaine, trigonelline, and trehalose contents also indicated salt stress. This global assessment of transcriptional and physiological responses to salt stress of these cotton species may identify possible gene targets for crop improvement and evolutionary studies of cotton. Keywords: CEGC Cotton oligo salt stress The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1).
2010-01-20 | E-GEOD-19966 | biostudies-arrayexpress
Project description:Five allotetraploid cotton species have adapted, through their transcriptional responses, to unique environments with distinct levels of inherent abiotic stresses. The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1). The microarray results identified 2721 and 2460 differentially expressed genes under salt stress that were significant in leaf and root tissue, respectively. Many of these genes were classified under gene ontology (GO) categories that suggest abiotic stress. These allotetraploid cottons shared transcriptional responses to salinity, but also showed responses that were species-specific. No consistent differences in transcriptional response among the previously estimated phylogenetic branches were found. Stomatal conductance, ion accumulation, and betaine, trigonelline, and trehalose contents also indicated salt stress. This global assessment of transcriptional and physiological responses to salt stress of these cotton species may identify possible gene targets for crop improvement and evolutionary studies of cotton. Keywords: CEGC Cotton oligo salt stress
2010-01-21 | GSE19966 | GEO
Project description:DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide bisulfite -, mRNA-, and small RNA-sequencing analyses reveal that CHH hypermethyaltion through RdDM in euchromatin is associated with expression changes of nearby genes in ovules. The ovule-derived fiber cells not only maintain euchromatic CHH hypermethylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM. Moreover, CHG and CHH methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. This epigenetic and expression dynamics of developmental regulation could provide a molecular basis for natural selection and domestication of plants and animals.
2016-01-21 | GSE61773 | GEO
Project description:DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide bisulfite -, mRNA-, and small RNA-sequencing analyses reveal that CHH hypermethyaltion through RdDM in euchromatin is associated with expression changes of nearby genes in ovules. The ovule-derived fiber cells not only maintain euchromatic CHH hypermethylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM. Moreover, CHG and CHH methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. This epigenetic and expression dynamics of developmental regulation could provide a molecular basis for natural selection and domestication of plants and animals.
2016-01-21 | GSE61761 | GEO
Project description:DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide bisulfite -, mRNA-, and small RNA-sequencing analyses reveal that CHH hypermethyaltion through RdDM in euchromatin is associated with expression changes of nearby genes in ovules. The ovule-derived fiber cells not only maintain euchromatic CHH hypermethylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM. Moreover, CHG and CHH methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. This epigenetic and expression dynamics of developmental regulation could provide a molecular basis for natural selection and domestication of plants and animals.
2016-01-21 | GSE61760 | GEO
Project description:Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton
| PRJNA291194 | ENA
Project description:Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton
| PRJNA325726 | ENA