Dataset Information

Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing.

ABSTRACT: Plant microRNAs (miRNAs) have been shown to play essential roles in the regulation of gene expression. In this study, small RNA deep sequencing was applied to explore novel miRNAs expressed in elongating cotton fibers. A total of 46 novel and 96 known miRNAs, primarily derived from the corresponding specific loci in genome of Gossypium arboreum, were identified. 64 miRNAs were shown to be differentially expressed during the fiber elongation process; 16 were predicted to be novel miRNAs while the remaining 48 belong to known miRNA families. Furthermore, RLM-5' RACE (RNA ligase-mediated rapid amplification of 5'-cDNA ends) experiments identified the targets of eight important miRNAs, and the expression levels of these target genes were confirmed to be negatively correlated with the expression patterns of their corresponding miRNAs. We propose a potential functional network mediated through these eight miRNAs to illustrate their important functions in fiber elongation. Our study provides novel insights into the dynamic profiles of these miRNAs and a basis for investigating the regulatory mechanisms involved in the elongation of cotton fibers.

SUBMITTER: Wang Y

PROVIDER: S-EPMC5112280 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing.

Wang Yanmei Y Ding Yan Y Liu Jin-Yuan JY

Frontiers in plant science 20161117

Plant microRNAs (miRNAs) have been shown to play essential roles in the regulation of gene expression. In this study, small RNA deep sequencing was applied to explore novel miRNAs expressed in elongating cotton fibers. A total of 46 novel and 96 known miRNAs, primarily derived from the corresponding specific loci in genome of <i>Gossypium arboreum</i>, were identified. 64 miRNAs were shown to be differentially expressed during the fiber elongation process; 16 were predicted to be novel miRNAs wh ...[more]

PMID: 27909445

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Project description:BackgroundMicroRNAs (miRNAs) are one of the functional non-coding small RNAs involved in the epigenetic control of the plant genome. Although plants contain both evolutionary conserved miRNAs and species-specific miRNAs within their genomes, computational methods often only identify evolutionary conserved miRNAs. The recent sequencing of the Brassica rapa genome enables us to identify miRNAs and their putative target genes. In this study, we sought to provide a more comprehensive prediction of B. rapa miRNAs based on high throughput small RNA deep sequencing.ResultsWe sequenced small RNAs from five types of tissue: seedlings, roots, petioles, leaves, and flowers. By analyzing 2.75 million unique reads that mapped to the B. rapa genome, we identified 216 novel and 196 conserved miRNAs that were predicted to target approximately 20% of the genome's protein coding genes. Quantitative analysis of miRNAs from the five types of tissue revealed that novel miRNAs were expressed in diverse tissues but their expression levels were lower than those of the conserved miRNAs. Comparative analysis of the miRNAs between the B. rapa and Arabidopsis thaliana genomes demonstrated that redundant copies of conserved miRNAs in the B. rapa genome may have been deleted after whole genome triplication. Novel miRNA members seemed to have spontaneously arisen from the B. rapa and A. thaliana genomes, suggesting the species-specific expansion of miRNAs. We have made this data publicly available in a miRNA database of B. rapa called BraMRs. The database allows the user to retrieve miRNA sequences, their expression profiles, and a description of their target genes from the five tissue types investigated here.ConclusionsThis is the first report to identify novel miRNAs from Brassica crops using genome-wide high throughput techniques. The combination of computational methods and small RNA deep sequencing provides robust predictions of miRNAs in the genome. The finding of numerous novel miRNAs, many with few target genes and low expression levels, suggests the rapid evolution of miRNA genes. The development of a miRNA database, BraMRs, enables us to integrate miRNA identification, target prediction, and functional annotation of target genes. BraMRs will represent a valuable public resource with which to study the epigenetic control of B. rapa and other closely related Brassica species. The database is available at the following link: http://bramrs.rna.kr [1].

Project description:BackgroundHypoxia is a critical aspect of the glioma microenvironment and has been associated with poor prognosis and resistance to various therapies. However, the mechanisms responsible for hypoxic survival of glioma cells remain unclear. Recent studies strongly suggest that microRNAs act as critical mediators of the hypoxic response. We thus hypothesized their prominent role in hypoxia resistance in glioblastoma (GBM) and aimed to identify those.ResultsWith this study, we present the first detailed analysis of small RNA transcriptome of cell line U87MG, a grade IV glioma cell line, and its alteration under hypoxic condition. Based on deep sequencing and microarray data, we identify a set of hypoxia regulated microRNAs, with the miR-210-3p and its isomiRs showing highest induction in GBM cell lines U87MG and U251MG. We show miR-210-3p, miR-1275, miR-376c-3p, miR-23b-3p, miR-193a-3p and miR-145-5p to be up-regulated, while miR-92b-3p, miR-20a-5p, miR-10b-5p, miR-181a-2-3p and miR-185-5p are down-regulated by hypoxia. Interestingly, certain hypoxia-induced miRNAs are also known to be over-expressed in GBM tumors, suggesting that hypoxia may be one of the factors involved in establishing the miRNA signature of GBM. Transcription factor binding sites for Hypoxia inducible factor 1 A (HIF1A) were identified in the promoter region (5 kb upstream) of 30 hypoxia-induced miRNAs. HIF-1A over-expression and silencing studies show regulation of specific miRNAs, including miR-210-3p, to be HIF1A dependent. On the other hand, miR-210-3p leads to an increase in transcriptional activity of HIF and its target genes vascular endothelial growth factor (VEGF) and carbonic anhydrase 9 (CA9). MiR-210-3p levels were found to be high in GBM patient samples and showed good correlation with the known hypoxia markers CA9 and VEGF. We show that miR-210-3p promotes hypoxic survival and chemoresistance in GBM cells and targets a negative regulator of hypoxic response, HIF3A. Additionally, a total of 139 novel miRNAs were discovered by the analysis of deep sequencing data and three of these were found to be differentially expressed under hypoxia.ConclusionsOverall, our study reveals a novel miRNA signature of hypoxia in GBM and suggests miR-210-3p to be an oncogenic player and a novel potential intrinsic marker of hypoxia in glioblastoma.

Project description:Cotton (Gossypium) fiber is the most prevalent natural product used in the textile industry. The two major cultivated species, G. hirsutum (Gh) and G. barbadense (Gb), are allotetraploids with contrasting fiber quality properties. To better understand the molecular basis for their fiber differences, EST pyrosequencing was used to document the fiber transcriptomes at two key development stages, 10 days post anthesis (dpa), representing the peak of fiber elongation, and 22 dpa, representing the transition to secondary cell wall synthesis. The 617,000 high quality reads (89% of the total 692,000 reads) from 4 libraries were assembled into 46,072 unigenes, comprising 38,297 contigs and 7,775 singletons. Functional annotation of the unigenes together with comparative digital gene expression (DGE) revealed a diverse set of functions and processes that were partly linked to specific fiber stages. Globally, 2,770 contigs (7%) showed differential expression (>2-fold) between 10 and 22 dpa (irrespective of genotype), with 70% more highly expressed at 10 dpa, while 2,248 (6%) were differentially expressed between the genotypes (irrespective of stage). The most significant genes with differential DGE at 10 dpa included expansins and lipid transfer proteins (higher in Gb), while at 22 dpa tubulins, cellulose, and sucrose synthases showed higher expression in Gb. DGE was compared with expression data of 10 dpa-old fibers from Affymetrix microarrays. Among 543 contigs showing differential expression on both platforms, 74% were consistent in being either over-expressed in Gh (242 genes) or in Gb (161 genes). Furthermore, the unigene set served to identify 339 new SSRs and close to 21,000 inter-genotypic SNPs. Subsets of 88 SSRs and 48 SNPs were validated through mapping and added 65 new loci to a RIL genetic map. The new set of fiber ESTs and the gene-based markers complement existing available resources useful in basic and applied research for crop improvement in cotton.

Project description:BackgroundmicroRNAs (miRNAs) in fish have not been as extensively studied as those in mammals. The fish species Takifugu rubripes is an intensively studied model organism whose genome has been sequenced. The T. rubripes genome is approximately eight times smaller than the human genome, but has a similar repertoire of protein-coding genes. Therefore, it is useful for identifying non-coding genes, including miRNA genes. To identify miRNA expression patterns in different organs of T. rubripes and give fundamental information to aid understanding of miRNA populations in this species, we extracted small RNAs from tissues and performed deep sequencing analysis to profile T. rubripes miRNAs. These data will be of assistance in functional studies of miRNAs in T. rubripes.ResultsAfter analyzing a total of 139 million reads, we found miRNA species in nine tissues (fast and slow muscles, heart, eye, brain, intestine, liver, ovaries, and testes). We identified 1420 known miRNAs, many of which were strongly expressed in certain tissues with expression patterns similar to those described for other animals in previous reports. Most miRNAs were expressed in tissues other than the ovaries or testes. However, some miRNA families were highly abundant in the gonads, but expressed only at low levels in somatic tissue, suggesting specific function in germ cells. The most abundant isomiRs (miRNA variants) of many miRNAs had identical sequences in the 5' region. However, isomiRs of some miRNAs, including fru-miR-462-5p, varied in the 5' region in some tissues, suggesting that they may target different mRNA transcripts. Longer small RNAs (26-31 nt), which were abundant in the gonads, may be putative piRNAs because of their length and their origin from repetitive elements. Additionally, our data include possible novel classes of small RNAs.ConclusionsWe elucidated miRNA expression patterns in various organs of T. rubripes. Most miRNA sequences are conserved in vertebrates, indicating that the basic functions of vertebrate miRNAs share a common evolution. Some miRNA species exhibit different distributions of isomiRs between tissues, suggesting that they have a broad range of functions.

Dataset Information

Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing.

Publications

Identification and Profiling of microRNAs Expressed in Elongating Cotton Fibers Using Small RNA Deep Sequencing.

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