Dataset Information

Ribosome RNA Profiling to Quantify Ovarian Development and Identify Sex in Fish.

ABSTRACT: Terminologies of ovary development, by somewhat subjective describing and naming main changes of oocytes, have been criticized for confusing and inconsistency of terms and classifications, and the incurred consequences impede communication among researchers. In the present work, we developed regression between ovary development and three ribosome RNA (rRNA) indexes, namely 5S rRNA percent, 18S rRNA percent, and 5S-18S rRNA ratio, using close relationship between volume percent of primary growth stage oocytes or gonadosomatic index and rRNA content, demonstrating species-specific quantification of ovary development can be established in species with either synchronous and asynchronous oogenesis. This approach may be extended to any species with primary growth oocytes, e.g. anurans and reptiles, to predict maturity stages in females. We further confirmed that 5S rRNA percent and 5S/18S rRNA ratio can serve as markers to distinguish sexes unambiguously. A micro-invasive sampling method may be invented for non-lethal prediction of ovary development and sex because only a small amount of ovary sample (<50?mg) is needed for the approach established in the current work. Researchers who work with ovary RNA-seq in these taxa should realize that insufficient depletion of rRNA will probably lead to incorrect quantification of gene expression and inaccurate conclusions.

SUBMITTER: Shen ZG

PROVIDER: S-EPMC5482860 | biostudies-other | 2017 Jun

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Ribosome RNA Profiling to Quantify Ovarian Development and Identify Sex in Fish.

Shen Zhi-Gang ZG Yao Hong H Guo Liang L Li Xiao-Xia XX Wang Han-Ping HP

Scientific reports 20170623 1

Terminologies of ovary development, by somewhat subjective describing and naming main changes of oocytes, have been criticized for confusing and inconsistency of terms and classifications, and the incurred consequences impede communication among researchers. In the present work, we developed regression between ovary development and three ribosome RNA (rRNA) indexes, namely 5S rRNA percent, 18S rRNA percent, and 5S-18S rRNA ratio, using close relationship between volume percent of primary growth ...[more]

PMID: 28646175

Similar Datasets

Project description:UnlabelledThe more than 200 closely spaced annotated open reading frames, extensive transcriptional read-through, and numerous unpredicted RNA start sites have made the analysis of vaccinia virus gene expression challenging. Genome-wide ribosome profiling provided an unprecedented assessment of poxvirus gene expression. By 4 h after infection, approximately 80% of the ribosome-associated mRNA was viral. Ribosome-associated mRNAs were detected for most annotated early genes at 2 h and for most intermediate and late genes at 4 and 8 h. Cluster analysis identified a subset of early mRNAs that continued to be translated at the later times. At 2 h, there was excellent correlation between the abundance of individual mRNAs and the numbers of associated ribosomes, indicating that expression was primarily transcriptionally regulated. However, extensive transcriptional read-through invalidated similar correlations at later times. The mRNAs with the highest density of ribosomes had host response, DNA replication, and transcription roles at early times and were virion components at late times. Translation inhibitors were used to map initiation sites at single-nucleotide resolution at the start of most annotated open reading frames although in some cases a downstream methionine was used instead. Additional putative translational initiation sites with AUG or alternative codons occurred mostly within open reading frames, and fewer occurred in untranslated leader sequences, antisense strands, and intergenic regions. However, most open reading frames associated with these additional translation initiation sites were short, raising questions regarding their biological roles. The data were used to construct a high-resolution genome-wide map of the vaccinia virus translatome.ImportanceThis report contains the first genome-wide, high-resolution analysis of poxvirus gene expression at both transcriptional and translational levels. The study was made possible by recent methodological advances allowing examination of the translated regions of mRNAs including start sites at single-nucleotide resolution. Vaccinia virus ribosome-associated mRNA sequences were detected for most annotated early genes at 2 h and for most intermediate and late genes at 4 and 8 h after infection. The ribosome profiling approach was particularly valuable for poxviruses because of the close spacing of approximately 200 open reading frames and extensive transcriptional read-through resulting in overlapping mRNAs. The expression of intermediate and late genes, in particular, was visualized with unprecedented clarity and quantitation. We also identified novel putative translation initiation sites that were mostly associated with short protein coding sequences. The results provide a framework for further studies of poxvirus gene expression.

Project description:Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global "snap-shot" of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal frameshift site. To our knowledge this is the first application of ribosome profiling to an RNA virus.

Dataset Information

Ribosome RNA Profiling to Quantify Ovarian Development and Identify Sex in Fish.

Publications

Ribosome RNA Profiling to Quantify Ovarian Development and Identify Sex in Fish.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure