• Communications for Statistical Applications and Methods
• /
• v.22 no.2
• /
• pp.181-199
• /
• 2015

In a short history, RNA-seq data have established a revolutionary tool to directly decode various scenarios occurring on whole genome-wide expression profiles in regards with differential expression at gene, transcript, isoform, and exon specific quantification, genetic and genomic mutations, and etc. RNA-seq technique has been rapidly replacing arrays with seq-based platform experimental settings by revealing a couple of advantages such as identification of alternative splicing and allelic specific expression. The remarkable characteristics of high-throughput large-scale expression profile in RNA-seq are lied on expression levels of read counts, structure of correlated samples and genes, larger number of genes compared to sample size, different sampling rates, inevitable systematic RNA-seq biases, and etc. In this study, we will comprehensively review how robust Bayesian and non-parametric methods have a better performance than classical statistical approaches by explicitly incorporating such intrinsic RNA-seq specific features with flexible and more appropriate assumptions and distributions in practice.

• Journal of fish pathology
• /
• v.23 no.3
• /
• pp.273-280
• /
• 2010

To determine whether rock bream Oplegnathus fasciatus can be protected from rock bream iridovirus (RBIV) infection by intramuscular injection of long double-stranded RNAs (dsRNAs), we compared protective effect of virus-specific dsRNAs corresponding to major capsid protein (MCP), ORF 084, ORF 086 genes, and virus non-specific green fluorescent protein (GFP) gene. Furthermore, to determine whether the non-specific type I interferon (IFN) response was associated with protective effect, we estimated the activation of type I IFN response in fish using expression level of IFN inducible Mx gene as a marker. As a result, mortality of fish injected with dsRNAs and challenged with RBIV was delayed for a few days when comparing with PBS injected control group. However, virus-specific dsRNA injected groups exhibited no significant differences in survival period when compared to the GFP dsRNA injected group. Semi-quantitative analysis indicated that the degree of antiviral response via type I IFN response is supposedly equal among dsRNA injected fish. These results suggest that type I IFN response rather than sequence-specific RNA interference might involve in the lengthened survival period of fish injected with virus-specific dsRNAs.

• Molecules and Cells
• /
• v.27 no.6
• /
• pp.689-695
• /
• 2009

Chemically synthesized small interfering RNAs (siRNAs) can specifically knock-down expression of target genes via RNA interference (RNAi) pathway. To date, the length of synthetic siRNA duplex has been strictly maintained less than 30 bp, because an early study suggested that double-stranded RNAs (dsRNAs) longer than 30 bp could not trigger specific gene silencing due to the induction of non-specific antiviral interferon responses. Contrary to the current belief, here we show that synthetic dsRNA as long as 38 bp can result in specific target gene silencing without non-specific antiviral responses. Using this longer duplex structure, we have generated dsRNAs, which can simultaneously knock-down expression of two target genes (termed as dual-target siRNAs or dsiRNAs). Our results thus demonstrate the structural flexibility of gene silencing siRNAs, and provide a starting point to construct multifunctional RNA structures. The dsiRNAs could be utilized to develop a novel therapeutic gene silencing strategy against diseases with multiple gene alternations such as viral infection and cancer.

• Molecules and Cells
• /
• v.42 no.5
• /
• pp.379-385
• /
• 2019

Non-coding RNAs (ncRNAs) comprise various RNA species, including small ncRNAs and long ncRNAs (lncRNAs). ncRNAs regulate various cellular processes, including transcription and translation of target messenger RNAs. Recent studies also indicate that ncRNAs affect organismal aging and conversely aging influences ncRNA levels. In this review, we discuss our current understanding of the roles of ncRNAs in aging and longevity, focusing on recent advances using the roundworm Caenorhabditis elegans. Expression of various ncRNAs, including microRNA (miRNA), tRNA-derived small RNA (tsRNA), ribosomal RNA (rRNA), PIWI-interacting RNA (piRNA), circular RNA (circRNA), and lncRNA, is altered during aging in C. elegans. Genetic modulation of specific ncRNAs affects longevity and aging rates by modulating established aging-regulating protein factors. Because many aging-regulating mechanisms in C. elegans are evolutionarily conserved, these studies will provide key information regarding how ncRNAs modulate aging and lifespan in complex organisms, including mammals.

• Asian-Australasian Journal of Animal Sciences
• /
• v.32 no.7
• /
• pp.1044-1051
• /
• 2019

Objective: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of long non-coding RNA (lncRNA) annotation database has increased the importance and proportion of mapped reads accordingly. Methods: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue. We employed two quantification pipeline: mRNA annotation only and mRNA+lncRNA annotation. Results: As a result, the tissue-specific sexually dimorphic genes are affected by the addition of lncRNA annotation at a non-negligible level. In addition, many lncRNAs are expressed in a more tissue-specific fashion and with greater variation between tissues compared to protein-coding genes. Due to the genic region lncRNAs, the differentially expressed gene list changes, which results in certain sexually biased genes to become ambiguous across the tissues. Conclusion: In a past study, it has been reported that tissue-specific patterns can be seen throughout the differentially expressed genes between sexes in cattle. Using the same dataset, this study used a more recent reference, and the addition of conjugate lncRNA information, which revealed alterations of differentially expressed gene lists that result in an apparent distinction in the downstream analysis and interpretation. We firmly believe such misquantification of genic lncRNAs can be vital in both future and past studies.

• Molecules and Cells
• /
• v.39 no.5
• /
• pp.375-381
• /
• 2016

MicroRNAs (miRNAs) are small non-coding RNAs (~22 nucleotides) regulating gene expression at the post-transcriptional level. By directing the RNA-induced silencing complex (RISC) to bind specific target mRNAs, miRNA can repress target genes and affect various biological phenotypes. Functional miRNA target recognition is known to majorly attribute specificity to consecutive pairing with seed region (position 2-8) of miRNA. Recent advances in a transcriptome-wide method of mapping miRNA binding sites (Ago HITS-CLIP) elucidated that a large portion of miRNA-target interactions in vivo are mediated not only through the canonical "seed sites" but also via non-canonical sites (~15-80%), setting the stage to expand and determine their properties. Here we focus on recent findings from transcriptome-wide non-canonical miRNA-target interactions, specifically regarding "nucleation bulges" and "seed-like motifs". We also discuss insights from Ago HITS-CLIP data alongside structural and biochemical studies, which highlight putative mechanisms of miRNA target recognition, and the biological significance of these non-canonical sites mediating marginal repression.

• Molecules and Cells
• /
• v.42 no.6
• /
• pp.495-500
• /
• 2019

Brain cytoplasmic 200 RNA (BC200 RNA), originally identified as a neuron-specific non-coding RNA, is also observed in various cancer cells that originate from non-neural cells. Studies have revealed diverse functions of BC200 RNA in cancer cells. Accordingly, we hypothesized that BC200 RNA might be modified in cancer cells to generate cancerous BC200 RNA responsible for its cancer-specific functions. Here, we report that BC200 RNA sequences are highly heterogeneous in cancer cells by virtue of multiple adenine nucleotide insertions in the internal A-rich region. The insertion of adenine nucleotides enhances BC200 RNA-mediated translation inhibition, possibly by increasing the binding affinity of BC200 RNA for eIF4A (eukaryotic translation initiation factor 4A).

• BMB Reports
• /
• v.50 no.4
• /
• pp.158-159
• /
• 2017

MicroRNAs (miRNAs) regulate gene expression by guiding the Argonaute (Ago)-containing RNA-induced silencing complex (RISC) to specific target mRNA molecules. It is well established that miRNAs are stabilized by Ago proteins, but the molecular features that trigger miRNA destabilization from Ago proteins remain largely unknown. To explore the molecular mechanisms of how targets affect the stability of miRNAs in human Ago (hAgo) proteins, we employed an in vitro system that consisted of a minimal hAgo2-RISC in HEK293T cell lysates. Surprisingly, we found that miRNAs are drastically destabilized by binding to seedless, non-canonical targets. We showed that miRNAs are destabilized at their 3' ends during this process, which is largely attributed to the conformational flexibility of the L1-PAZ domain. Based on these results, we propose that non-canonical targets may play an important regulatory role in controlling the stability of miRNAs, instead of being regulated by miRNAs.

• Korean Journal of Microbiology
• /
• v.30 no.3
• /
• pp.177-180
• /
• 1992

Among 120 U. maydis strains isolated in Korea 14 different strains containing specific viral dsRNA segments were analyzed for the distribution of dsRNA and the production of toxin protein. Several distinctive dsRNA patterns were identified, 9 cases of P type with typical H, M and L ds RNA and one case of non-P-type, the frequency of a specific isolate was decreased with increasing number of dsRNA segments. The presence of dsRNA had no effect on the cultural or morphological phenotype of the host. Two isolates containing P type dsRNA segments appeared to produce toxin protein (killer strains) which inhibited the growth of 4 isolates (sensitive strain) with different susceptibility. Two killer strains contain unique M dsRNA segment which may code for toxin protein. However, the presence of toxin-sensitive strains among dsRNA-free isolates was similar to that of ds RNA containing strains.

• Tuberculosis and Respiratory Diseases
• /
• v.56 no.4
• /
• pp.393-404
• /
• 2004

Background : Nucleic acid hybridization has become an essential technique in the development of our understanding of gene structure and function. The quantitative analysis of hybridization has been used in the measurement of genome complexity and gene copy number. The filter hybridization assay is rapid, sensitive and can be used to measure RNAs complementary to any cloned DNA sequence. Methods : The authors assessed the accuracy, linearity, correlation coefficient and specificity of the hybridization depending on the added dose(0, 1, 5, and $10{\mu}g$) of non-specific rat spleen RNA to hybridization of surfactant protein A mRNA. Filter hybridization assays were used to obtain the equation of standard curve and thereby to quantitate the mRNA quantitation. Results : 1. Standard curve equation of filter hybridization assay between counts per minute (X) and spleen RNA input (Y) was Y=0.13X-19.35. Correlation coefficient was 0.98. 2. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) was Y=0.00066X-0.046. Correlation coefficient was 0.99. 3. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $1{\mu}g$ spleen RNA was Y=0.00056X-0.051. Correlation coefficient was 0.99. 4. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $5{\mu}g$ spleen RNA was Y=0.00065X-0.088. Correlation coefficient was 0.99. 5. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $10{\mu}g$ spleen RNA was Y=0.00051X-0.10. Correlation coefficient was 0.99. Conclusions : Comparison of cpm/filter in a linear range allowed accurate and reproducible estimation of surfactant protein A mRNA copy number irrespective of the addition dosage of non-specific rat spleen RNA over the range $0-10{\mu}g$.