Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR159616.fastq.gz | Fastqsanger.gz | |||
| ERR159617.fastq.gz | Fastqsanger.gz | |||
| ERR159618.fastq.gz | Fastqsanger.gz | |||
| ERR159619.fastq.gz | Fastqsanger.gz | |||
| ERR159620.fastq.gz | Fastqsanger.gz |
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Project description:The present study is expected to reveal regulatory network of small RNAs under drought in Sorghum (Sorghum bicolor (L.) Moench). Sorghum genotype drought tolerant (DT) and drought susceptible (DS) were grown at 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80 degrees C, and used for generation of a small RNA library. Total RNA was isolated from the leaves using the TRIzol reagent (Invitrogen, USA). Small RNA sequencing libraries were prepared using Illumina Truseq small RNA Library preparation kit following manufacturer's protocol and these libraries were sequenced on GAIIx platform (Illumina Inc., USA). Small RNA reads contaminated with poor-quality and adaptor sequences were trimmed by using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/). Then, all unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/) to predict novel miRNAs from high-throughput small RNA sequencing data.
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Project description:Arabidopsis thaliana (Arabidopsis) encodes five DOUBLE-STRANDED RNA BINDING (DRB) proteins, DRB1 to DRB5, that predominantly act as non-catalytic cofactors for DICER-LIKE (DCL) proteins in the double-stranded RNA (dsRNA) processing stages of small RNA (sRNA) production pathways. In the nucleus, DRB1 is required for microRNA (miRNAs) processing from imperfectly dsRNA precursors by DCL1. Similarly, DRB4 is required by DCL4 for small-interfering RNAs (siRNAs) production from endogenous or exogenous perfectly dsRNA templates. DRB2 has been recently demonstrated to be required for miRNA and siRNA production in developmentally-important tissues of Arabidopsis while the requirement of either DRB3 or DRB5 in sRNA production remains unclear. Here, we analyse in parallel, the contribution of all five DRB protein family members to the global sRNA landscape of Arabidopsis floral tissues. In depth bioinformatic analysis of sRNA sequencing datasets generated from floral tissues of DRB knockout mutant (drb) plant lines, drb1, drb2, drb4, drb12, drb14, drb24, and drb35 and their comparison to the floral sRNA profile of wild-type Arabidopsis, has enabled confident assignment of the requirement of DRB1, DRB2 and DRB4 for the production of specific miRNA and siRNA subclasses in this tissue. Our analyses have additionally identified novel and/or expanded roles for DRB2 in miRNA, trans-acting siRNAs (tasiRNAs) and natural antisense transcript siRNAs (natsiRNAs) production.
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Project description:We performed Illumina sequencing of sRNA libraries prepared from 10-day-old seedlings in Arabidopsis. SE is a key component in miRNA processing and pre-mRNA splicing, whereas ATXR5/6 is engaged in epigenetic silencing. Genome-wide sRNA sequencing revealed that ATXR5/6 did not participate in SE-mediated miRNA biogenesis.
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Project description:This experiment was designed to improve the proportion of miRNA mapping reads from sRNA library sequencing, by reducing the amount of particularly abundant rRNA fragments.
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Project description:Small RNAs (sRNAs) play important roles in plants encountering stress environments. However, limited research has been conducted on the sRNAs involved in plant wound responses. To identify potential roles for the wounding-related sRNAs, sRNA deep sequencing was used. After leaves were wounded for 0.5 hour, total RNAs from unwounded and wounded leaves were isolated for sRNA library construction. The Illumina platform was used to sequence sRNA libraries. About 12 million sequence reads were obtained for each sample.
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Project description:The overall goal of this study is to determine the small non-coding RNA expression profile in developing mouse nephron progenitors and whole kidney. Using a limited digestion and negative selection approach, an enriched fraction of nephron progenitors were isolated from E15.5 whole kidney samples followed by small RNA-Sequencing (sRNA-Seq). A total of 3 biological replicates of mouse nephron progenitors and whole kidney samples were used for the sRNA-Seq. The NEBNext Multiplex Small RNA Library Prep Kit allowed us to prepare sequencing libraries from as little as 100ng total RNA. Multiplex sequencing was performed using the Illumina NextSeq 550 system with 50bp single reads, resulting in approximately 18 million reads per sample. Reads were aligned to the mm10 genome using Bowtie2, and the miRDeep2 software package was used to identify and quantify known and novel micro RNA (miRNA) within our sRNA-seq libraries. Differential expression analysis of miRNA expression between nephron progenitor and whole kidney samples identified 162 differentially expressed miRNAs (padj <= 0.05).
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Project description:Many evolutionarily conserved miRNAs in plants regulate transcription factors with key functions in plant development. Hence, mutations in core components of the miRNA biogenesis machinery causes strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from an arm of the fold-back precursor. Defects in the selection of the correct miRNA sequence will ultimately affect miRNA target specificity, plant development and other processes controlled by these small RNAs. Intriguingly, plant miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized genomic approaches to detect processing intermediates during miRNA biogenesis. We identified and characterized an endogenous miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes suggesting intrinsic differences between miRNA biogenesis pathways. Despite the various potential structural determinants present in a single a miRNA precursor, we found that DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, genomic studies of miRNA processing intermediates in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative or cryptic processing determinants in miRNA precursors. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.
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