Differential accumulation of small RNAs and microRNAs during ovule and fiber development in allotetraploid cotton
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana Gossypium hirsutum
PROVIDER: GSE16986 | GEO | 2009/12/31
SECONDARY ACCESSION(S): PRJNA117331
REPOSITORIES: GEO
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Project description:To examine expression of miRNAs in cotton fiber development, we employed miRNA microarrays and compared miRNA accumulation level in cotton fibers, cotton leaves and mutant fibers. A total of 9 hybridization intensities in three biological replicates per miRNA were obtained.
2010-05-16 | E-GEOD-16986 | biostudies-arrayexpress
Project description:Cotton fibers are seed trichomes, and their development undergoes a series of rapid and dynamic changes from fiber cell initiation, elongation to primary and secondary wall biosynthesis and fiber maturation. Previous studies showed that cotton homologues encoding putative MYB transcription factors and phytohormone responsive factors were induced during early stages of ovule and fiber development. Many of these factors are targets of microRNAs (miRNAs). miRNAs are ~21 nucleotide (nt) RNA molecules derived from non-coding endogenous genes and mediate target regulation by mRNA degradation or translational repression. Here we show that among ~4-million reads of small RNAs derived from the fiber and non-fiber tissues, the 24-nt small RNAs were most abundant and were highly enriched in ovules and fiber-bearing ovules relative to leaves. A total of 28 putative miRNAs families, including 25 conserved and 3 novel miRNAs were identified in at least one of the cotton tissues examined. Thirty-two pre-miRNA hairpins representing 19 unique families were detected in Cotton Gene Indices version 9 (CGI9) using mirCheck. Sequencing, miRNA microarray, and small RNA blot analyses showed that many of these miRNAs differentially accumulated during ovule and fiber development. The cotton miRNAs examined triggered target cleavage in the same predicted sites of the cotton targets in ovules and fibers as that of the orthologous target genes in Arabidopsis. Targets of the potential new cotton miRNAs matched the previously characterized ESTs derived from cotton ovules and fibers. The miRNA targets including those encoding auxin response factors were differentially expressed during fiber development. We suggest that both conserved and new miRNAs play an important role in the rapid and dynamic process of fiber and ovule development in cotton.
2009-11-12 | GSE16332 | GEO
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.
2010-07-01 | E-GEOD-4642 | biostudies-arrayexpress
Project description:RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule. Keywords: tissue comparison
2006-04-12 | GSE4642 | 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 via distinct pathways. Cotton is an allotetraploid consisting of two progenitor genomes. Each cotton fiber is a rapidly-elongating cell derived from the ovule epidermis, but the molecular basis for this developmental transition is unknown. Here we analyzed methylome, transcriptome, and small RNAome and revealed distinct changes in CHH methylation during ovule and fiber development. In ovules, CHH hypermethylation in promoters correlated positively with siRNAs, inducing RNA-dependent DNA methylation (RdDM), and up-regulation of ovule-preferred genes. In fibers, the ovule-derived cells generated additional heterochromatic CHH hypermethylation independent of RdDM, which repressed transposable elements (TEs) and nearby genes including fiber-related genes. Furthermore, CHG and CHH methylation in genic regions contributed to homoeolog expression bias in ovules and fibers. Inhibiting DNA methylation using 5-aza-2'-deoxycytidine in cultured ovules has reduced fiber cell number and length, suggesting a potential role for DNA methylation in fiber development. Thus, RdDM-dependent methylation in promoters and RdDM-independent methylation in TEs and nearby genes could act as a double-lock feedback mechanism to mediate gene and TE expression, potentiating the transition from epidermal to fiber cells during ovule and seed development.
2016-01-21 | GSE61774 | GEO
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. two examples including 3-79 and TM-1 10 DPA fibers
2010-12-03 | E-GEOD-25773 | biostudies-arrayexpress
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.
2010-12-03 | GSE25773 | 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 | GSE61760 | 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