Unknown,Transcriptomics,Genomics,Proteomics

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Profling of the Drosophila melanogaster neuronal microRNA transcriptome by small RNA deep sequencing

ABSTRACT: microRNAs (miRNAs) are a class of small non-coding RNAs involved in the coordination and/or fine-tuning of gene expression. As such, miRNAs are thought to be critical cis-acting regulatory factors that control a wide range of physiological processes in the brain. The datasets presented here represent the miRNA transcriptome of the adult and larval Drosophila melanogaster CNS as determined by small RNA deep sequencing (RNA-Seq). They were derived from adult and larval samples explanted from the animal that contain minimal extraneous (non-neuronal) tissues. Here we present a concise summary of our profiling results as well as the original sequencing data. We identify many miRNAs that are expressed at equal levels in both tissues and several that are significantly enriched in the larval and adult brain. Some of these belong to miRNA families with conserved members in mammals. These datasets should provide a good starting point for others interested in characterizing miRNAs with putative functions in Drosophila neurons. The datasets presented here represent the miRNA transcriptome of the adult and larval Drosophila melanogaster CNS as determined by small RNA deep sequencing (RNA-Seq).

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Scott Barbee

PROVIDER: E-GEOD-57687 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:MicroRNA (miRNA) is a class of functional non-coding small RNA with 19-25 nucleotides in length. Amur grape (Vitis amurensis Rupr.) is an important wild fruit crop with the strongest cold resistance in the Vitis genus and is used as an excellent breeding parent for grapevine, and with growing interest in terms of wine production. To date, there is a relatively large number of grapevine miRNAs (vv-miRNAs) from cultivated grapevine varieties such as Vitis vinifera L. and hybrids of V. vinifera and V. labrusca, but there is no report on miRNAs from Vitis amurensis Rupr, a wild grapevine species. In this study, a small RNA library from Amur grapes was constructed and Solexa technology used to perform deep sequencing of the library followed by subsequent bioinformatics analysis to identify new miRNAs. In total, 126 conserved miRNA belonging to 27 miRNA families were identified, and 34 known but non-conserved miRNAs were also found. Significantly, 72 new potential Amur grapevine-specific miRNAs were discovered. The sequences of these new potential va-miRNAs were further validated through miR-RACE, accumulation of 18 new va-miRNAs in seven tissues of grapevines were also confirmed by real time RT-PCR (qRT-PCR) analysis, and expression levels of va-miRNAs in flowers and berries were basically consistent in identity to those from deep sequenced sRNAs libraries of independent corresponding tissues. We also describe the conservation and variation of va-miRNAs using miR-SNPs and miR-LDs during plant evolution based on comparison of orthologous sequences, and revealed the number and sites of miR-SNP of diverse miRNA families exhibited distinct divergence. Finally, 346 target genes for the new miRNAs were predicted and they include a number of Amur grapevine stress tolerance genes and many genes regulating anthocyanin systhesis and sugar metabolism. Deep sequencing of short RNAs from Amur grapes flowers and fruits identified 72 new potential miRNAs and 34 known but non-conserved miRNAs, indicating that specific miRNAs exist in Amur grapes. These results show that a number of regulatory miRNAs exist in Amur grapes and play an important role in Amur grape growth, development, and response to abiotic or biotic stress. High throughput sequencing was employed to identify miRNAs in Amur grapevine and try to describe their functions in Amur grapevine growth and development.

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Profling of the Drosophila melanogaster neuronal microRNA transcriptome by small RNA deep sequencing

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