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High-throughput pyrosequencing of endogenous small RNAs in O. Europaea

ABSTRACT: Small RNAs of 20 to 25 nucleotides in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the small RNA component of more than 40 plant species. Here, use deep sequencing and molecular methods to report the first inventory of small RNAs in olive (Olea europaea). Small RNAs of 24 nts dominate the small RNA transcriptome and atypically accumulate to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. By contrast, small RNAs of 20 to 22 nts were poorly represented in the population at levels lower than those found in most plant species tested. A total of 14 known miRNA families were identified in two libraries prepared from growing and dormant lateral buds. We found that some known miRNAs showed tissue- and/or developmental-specific expression. Also, seven novel, olive-specific miRNA candidates were found in our sequenced set of which 1 were supported by their star strands. Potential precursors for these miRNA candidates with intramolecular folding capacities were found in the olive EST database. Target mRNAs of conserved miRNAs and new olive-specific miRNA were computationally predicted among the olive EST collection and experimentally validated through endonucleolytic cleavage assays.

ORGANISM(S): Olea europaea

PROVIDER: GSE27093 | GEO | 2011/03/31

SECONDARY ACCESSION(S): PRJNA137457

REPOSITORIES: GEO

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High-throughput pyrosequencing of endogenous small RNAs in O. Europaea

Project description:Small RNAs of 20 to 25 nucleotides in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the small RNA component of more than 40 plant species. Here, use deep sequencing and molecular methods to report the first inventory of small RNAs in olive (Olea europaea). Small RNAs of 24 nts dominate the small RNA transcriptome and atypically accumulate to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. By contrast, small RNAs of 20 to 22 nts were poorly represented in the population at levels lower than those found in most plant species tested. A total of 14 known miRNA families were identified in two libraries prepared from growing and dormant lateral buds. We found that some known miRNAs showed tissue- and/or developmental-specific expression. Also, seven novel, olive-specific miRNA candidates were found in our sequenced set of which 1 were supported by their star strands. Potential precursors for these miRNA candidates with intramolecular folding capacities were found in the olive EST database. Target mRNAs of conserved miRNAs and new olive-specific miRNA were computationally predicted among the olive EST collection and experimentally validated through endonucleolytic cleavage assays. Two samples analyzed: growing (juvenile) and dormant (adult) lateral buds from the progeny of a genetic cross between the Picual and Arbequina olive varieties

2011-03-31 | E-GEOD-27093 | biostudies-arrayexpress

Global analysis of non-coding small RNAs in Arabidopsis in response to jasmonate treatment by deep sequencing technology

Project description:In plants, non-coding small RNAs play a vital role for plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate (JA) pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. 30 new miRNAs and 27 new miRNA candidates were identified through a bioinformatics approach. 49 known miRNAs (belonging to 24 families), 15 new miRNAs and new miRNA candidates (belonging to 11 families) and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs (belonging to 9 families) were repressed by JA.

2014-12-16 | GSE34497 | GEO

Global analysis of non-coding small RNAs in Arabidopsis in response to jasmonate treatment by deep sequencing technology

2014-12-16 | E-GEOD-34497 | biostudies-arrayexpress

miRNAs target conserved motifs of diverse genes encoding NB-LRRs to trigger trans-acting siRNAs in legumes.

Project description:Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide 'phased' intervals. TasiRNAs have not been extensively described in many plant species. We identified dozens of new miRNAs in Medicago and soybean and confirmed 119 Medicago targets. A search for phased tasiRNA-like small RNAs ('phasiRNAs') found at least 114 Medicago loci, the majority of which were NB-LRR encoding genes. Notably, conserved domains in NB-LRR-encoding RNAs are targeted by several 22-nt miRNA families to trigger phasiRNA production. DCL2 and SGS3 transcripts were also cleaved by these 22-nt miRNAs, generating phased small RNAs, suggesting synchronization between silencing and pathogen defense pathways. A second example of 'two-hit' phasiRNA processing was identified, utilizing miR156-miR172 sites. Our data illustrate a complex tasiRNA-mediated regulatory circuit that potentially modulates plant-microbe interactions. A few miRNA triggers regulate an extremely large gene family by targeting highly conserved protein motif-encoding sequences, representing a new paradigm for miRNA function.

2011-10-24 | GSE31061 | GEO

miRNAs target conserved motifs of diverse genes encoding NB-LRRs to trigger trans-acting siRNAs in legumes.

2011-10-24 | E-GEOD-31061 | biostudies-arrayexpress

Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C

Project description:Small, non-coding RNAs control gene expression post-transcriptionally and play important roles in virus-host interactions. Within the liver, the microRNA (miRNA) miR-122 is essential for replication of hepatitis C virus (HCV), while repression of miR-148a by hepatitis B virus (HBV) may enhance tumorigenesis. Despite their importance to the outcome of these infections, few previous studies have described unbiased profiling of small RNAs in the liver during chronic viral hepatitis. Here, we sequenced small (14-40 nts) RNAs in liver from subjects with chronic hepatitis B and C. We found that small RNAs derived from tRNAs, specifically 5’ tRNA-halves (“5’ tRHs”, ~31-34 nts), are abundant in liver and significantly increased during chronic viral infection in humans and also chimpanzees. In most infected livers, 5’ tRH abundance exceeded that of miRNAs. In contrast, in hepatocellular carcinoma (HCC) tissue from these subjects, tRH abundance was reduced concomitant with decreased expression of the tRNA-cleaving ribonuclease, angiogenin. Although tRHs have been identified in mice, our results show they are abundantly expressed in human tissue, increased in chronic viral infection, and decreased in liver cancer. Our findings highlight the potential biological and clinical relevance of these small non-coding RNAs.

2014-12-18 | GSE57381 | GEO

Identification of miRNA-like RNAs in a plant pathogen fungus Sclerotinia sclerotiorum by High-throughput sequencing

Project description:This study provides a first large-scale cloning and characterization of Sclerotinia sclerotiorum milRNAs and milRNAs candidates. Two microRNA-like RNAs (milRNAs) and 42 milRNA candidates were identified by sequence analysis. These milRNAs and candidates provide new insights into the functional roles of small RNAs and adds new resources for the study of plant pathogenic fungi. We constructed a small RNA library from Sclerotinia sclerotiorum.

2012-05-17 | E-GEOD-28730 | biostudies-arrayexpress

Identification of miRNA-like RNAs in a plant pathogen fungus Sclerotinia sclerotiorum by High-throughput sequencing

2012-05-18 | GSE28730 | GEO

Identification the target genes of microRNA in Ammopiptanthus mongolicus

Project description:Ammopiptanthus mongolicus is an ecologically important desert plant. miRNA are endogenous 20-22 nt small RNAs that play important roles in regulating gene expression in plants. To identify to the target genes of miRNA in Ammopiptanthus mongolicus, degradome sequencing was performed and a batch of transcripts were found to be targeted by miRNA. The result is helpful in understanding the roles on miRNA in plant development and environmental stress response.

2017-02-19 | GSE66095 | GEO

Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart

Project description:As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases, a highly regulated transition known as cardiac maturation. Small noncoding RNAs, such as microRNAs (miRNAs), contribute to the establishment and control of tissue-specific transcriptional programs. However, small RNA expression dynamics and genome wide miRNA regulatory networks controlling maturation of the human fetal heart remain poorly understood. Transcriptome profiling of small RNAs revealed the temporal expression patterns of miRNA, piRNA, circRNA, snoRNA, snRNA and tRNA in the developing human heart between 8 and 19 weeks of gestation. Our analysis revealed that miRNAs were the most dynamically expressed small RNA species throughout mid-gestation. Cross-referencing differentially expressed miRNAs and mRNAs predicted 6,200 mRNA targets, 2134 of which were upregulated and 4066 downregulated as gestation progresses. Moreover, we found that downregulated targets of upregulated miRNAs predominantly control cell cycle progression, while upregulated targets of downregulated miRNAs are linked to energy sensing and oxidative metabolism. Furthermore, integration of miRNA and mRNA profiles with proteomes and reporter metabolites revealed that proteins encoded in mRNA targets, and their associated metabolites, mediate fatty acid oxidation and are enriched as the heart develops.This study revealed the small RNAome of the maturing human fetal heart. Furthermore, our findings suggest that coordinated activation and repression of miRNA expression throughout mid-gestation is essential to establish a dynamic miRNA-mRNA-protein network that decreases cardiomyocyte proliferation potential while increasing the oxidative capacity of the maturing human fetal heart.

2024-01-26 | PXD044936 | Pride

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