Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Identification of small non-coding RNAs in zebrafish

ABSTRACT: MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. Their small size, low abundance and high instability complicated early identification; however, cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish (Danio rerio). For this, a series of cDNA libraries were prepared from small non-coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Small RNA libraries were prepared from different zebrafish developmental stages, namely, 24 hours post-fertilization (hpf), 72 hpf, 96 hpf, 5 days post-fertilization (dpf), 45 dpf, young adult and from adult brain, eyes, gills, heart, skin and fins.

ORGANISM(S): Danio rerio

SUBMITTER: Ana Soares

PROVIDER: E-GEOD-66718 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in the process of plant development. To date, extensive studies of miRNAs have been performed in a few model plants, but few efforts have focused on small RNAs in conifers because of the lack of reference sequences for these enormous genomes. In this study, Solexa sequencing of three small RNA libraries obtained from dormant, reactivating, and active vascular cambium in Chinese ﬁr samples identified 76 known miRNAs from 27 miRNA families and 18 new potential miRNAs, of which 15 novel miRNA precursors were validated by RT-PCR and sequencing. More than half of these novel miRNAs displayed stage-specific expression patterns in the vascular cambium. Furthermore, analyzing the 103 miRNAs and their predicted targets indicated that 30% of miRNAs appeared to negatively regulate their targets, of which 4 target genes involved in the regulation of cambial cell division were validated via RNA ligase-mediated rapid amplification of 5’ cDNA ends (RLM 5’-RACE). Interestingly, miRNA156 and miRNA172 may regulate the phase transition in vascular cambium from dormancy to active growth. These results provide new insights into the important regulatory functions of miRNAs in vascular cambium development and wood formation in conifers. The aim of this study is to investigate the small RNA transcriptome in different stages of vascular cambium development in Cunninghamia lanceolata. We herein conducted our comprehensive analysis of a plant sRNAome during development of the vascular cambium in Chinese fir using cryosectioning to isolate cambial meristem, which allowed a higher cellular resolution for defining small RNA profiles and overcomed the limitations resulting from the mixed samples in many previous investigations. Total RNAs of dormant, reactivating, and active cambial meristem, respectively were isolated using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA, USA), and were then treated with RNase-free DNase I (Promega, Madison, WI, USA). Twenty micrograms of total RNAs were used and 16 to 30-nt sRNAs were purified using Novex 15% TBE-¬Urea gel (Invitrogen). Two adaptors were sequentially ligated to the 5' and 3' ends of purified sRNAs. The ligation products were further purified from Novex 10% TBE-Urea gel. Reverse transcriptase SuperScript II (Invitrogen) and high-fidelity DNA polymerase Phusion (New England Biolabs, Ipswich, MA, USA) were used in the following RT-PCR reaction. The amplification products were cut from Novex 6% TBE-Urea gel. The purified DNA fragments were used for sequencing on an Illumina 2G Genome Analyzer at the Beijing Genomics Institute, Shenzhen, China.

Dataset Information

Identification of small non-coding RNAs in zebrafish

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure