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Histone H3 lysine 27 trimethylation (H3K27me3) modulates the fiber initiation in upland cotton

ABSTRACT: Histone H3 lysine 27 trimethylation (H3K27me3) modulates the fiber initiation in upland cotton

PROVIDER: PRJNA947208 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23932400_1.fastq.gz	Fastqsanger.gz
	SRR23932400_2.fastq.gz	Fastqsanger.gz
	SRR23932401_1.fastq.gz	Fastqsanger.gz
	SRR23932401_2.fastq.gz	Fastqsanger.gz
	SRR23932402_1.fastq.gz	Fastqsanger.gz

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Histone H3 lysine 27 trimethylation (H3K27me3) modulates the fiber initiation in upland cotton

Project description:Histone methylation is one of the most significant epigenetic modifications in plants because it is responsible for regulating and controlling the expression of many important functional genes. Although there have been many studies concerning histone methylation, its specific functions and mechanisms in cotton fiber initiation remain unclear. To determine if the H3K27me3 modification had regulated cotton fiber initiation in upland cotton (Gossypium hirsutum), we performed a comparative analysis on the cleavage under targets and tagmentation (CUT&Tag) between the wild-type cultivar Xu142 and its fibreless mutant Xu142 fl. This research was carried out three time points during the initiation period of cotton fibers, which were -1, 0 and 1 days post-anthesis (DPA). We also used the H3K27me3 antibody in Xu142 and Xu142 fl to examine the differential deposition of H3K27me3. Combing these results with RNA-seq analysis, we discovered a negative correlation between transcription and H3K27me3. We identified 336 genes with opposing trends in H3K27me3 deposition and expression. These genes are involved in various metabolic pathways, including fatty acid biosynthesis, galactose metabolism, plant hormone signal transduction, plant-pathogen interaction, glycolysis-/-gluconeogenesis, phenylpropanoid biosynthesis, and cutin, suberin and wax biosynthesis. Further physiological research revealed that in vitro ovule culture with an RDS 3434 inhibitor could alters the level of H3K27me3 in ovules, thus influencing the process of cotton fiber development. Taken together, these results indicate that H3K27me3 plays an important role in the fiber initiation process of cotton, and demonstrates the H3K27me3 network involved in fiber initiation in cotton ovules. The study also provides a foundation for the future study of genes involved in fiber development.

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Project description:Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. The 35nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and several kinds of contaminants from the 35nt tags. All clean tag sequences with copy numbers were then summarized into a fasta format file. Fiber samples from different seasons were used for small RNA sequencing and data processing.

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Comparison of cotton fiber to ovule at 9 DPA

Project description:RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule. RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule.

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Project description:To identify potential miRNAs involved in fiber development and elucidate their expression differences between G. barbadense and G. hirsutum, we constructed two small RNA libraries, Gb10 and Gh10, prepared from fibers of 3-79 (G. barbadense) and TM-1 (G. hirsutum) collected at 10 days post-anthesis (DPA). We identified 28 conserved miRNA families, including 24 that exactly match known plant miRNA families in miRBase. With MIREAP and newly developed software miRsearcher, 7 candidate-novel miRNAs were found. 5 candidate-novel miRNAs were expressed in both species, 2 candidate-novel miRNAs were expressed only in one species. Moreover, 4 miRNA families showed significant expression differences between sea-island cotton and upland cotton in 10 DPA fibers.

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Comparison of cotton fiber to ovule at 9 DPA

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cDNA expression profiles of wild-type and fl-mutant upland cotton ovules during fiber initiation peroid

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Histone H3 lysine 27 trimethylation of miRNA genes in HMEC and HMF

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Histone H3 lysine 4 trimethylation of miRNA genes in HMEC and HMF

Project description:Normal cell type specific histone H3 lysine 4 trimethylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including histone H3 lysine 4 trimethylation affect miRNA expression. Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-histone H3 trimethylated at lysine 4 (05-745, Upstate).

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