• BMB Reports
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• v.50 no.4
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• pp.226-231
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• 2017

At the post-transcriptional and translational levels, microRNA (miRNA) represses protein-coding genes via seed pairing to the 3' untranslated regions (UTRs) of mRNA. Although working models of miRNA-mediated gene silencing are successfully established using miRNA transfections and knockouts, the regulatory interaction between miRNA and long non-coding RNA (lncRNA) remain unknown. In particular, how the mRNA-resembling lncRNAs with 5' cap, 3' poly(A)-tail, or coding features, are regulated by miRNA is yet to be examined. We therefore investigated the functional interaction between miRNAs and lncRNAs with/without those features, in miRNA-transfected early zebrafish embryos. We observed that the greatest determinants of the miRNA-mediated silencing of lncRNAs were the 5' cap and 3' poly(A)-tails in lncRNAs, at both the post-transcriptional and translational levels. The lncRNAs confirmed to contain 5' cap, 3' poly(A)-tail, and the canonical miRNA target sites, were observed to be repressed in the level of both RNA and ribosome-protected fragment, while those with the miRNA target sites and without 5' cap and 3' poly(A)-tail, were not robustly repressed by miRNA introduction, thus suggesting a role as a miRNA-decoy.

• Korean Journal of Microbiology
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• v.26 no.2
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• pp.106-112
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• 1988

We have examined the structures and cellular distributions of the SV40 late RNAs present in monkey cells at late times after infection. One particular RNA species, spliced at residue 373(373-RNA), was found to be as abundant as the major late 16S RNAs. This result was unexpected since previous reports showed that the molecular ratio of the 373-spliced 19S RNA to 16S RNA is approximately 0.1 among either cytoplasmic polyadenylated or polysomal viral RNAs. Both sedimentation and electrophoretic analysis indicated that the 373-RNA was approximately 16S to 19S in size. Therefore, it was not a splicing intermediate or the product of premature termination of transcription within the late leader region. Whereas most SV40 late 16S RNA is polyadenylated and located in the cytoplasm, the majority of 373-RNA was found to lack poly A, and be located in the nucleus.

• Korean Journal of Microbiology
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• v.27 no.1
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• pp.1-9
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• 1989

The locations of 5' ends as well as the splicing pattern of viral poly A(-) 19S RNA from monkey cells infected with SV40 were determined by a modification of primer extension method. The 5' end of this RNA mapped at the major cap site at nucleotide residue 325, used most frequently by SV40 late RNAs. The intron from nt.373 to nt.558 was removed as the ordinary cytoplasmic poly A(+) 19S RNA. The 3'end of this RNA was very heterogeneous and distributed over 1 kb upstream of polyadenylation site, as determined by S1 nuclease mapping. The reason for this normally initiated and spliced RNA to accumulate in the nucleus was investigated. In order to test whether the presence of unused 3' splice region on this RNA caused such subcellular distribution, cells were transfected with SV40 mutant KNA containing deletion around 3' splice site. The RNA deleted of 3' splice region accumulated mainly in the cytoplasm. This accumulation did not result from the increased stability of the RNA due to the deletion, since the wild type and mutant RNAs exhibited similar half lives after chase with actinomycin D. Therefore it is likely that the 19S spliced RNA is hindered from being transported into the cytoplasm due to some pre-splicing complexes formed at the unused 3' splice site.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.77-85
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• 2004

A significant portion (about 8% in human genome) of mammalian mRNA sequences contains AU(Adenine and Uracil) rich elements or AREs at their 3' untranslated regions (UTR). These mRNA sequences are usually stable. ARE motifs are assorted into three classes. The importance of AREs in biology is that they make certain mRNA unstable. We analyzed the occurrences of AREs and Alu, and propose a possible mechanism on how human mRNA could acquire and keep A REs at its 3' UTR originated from Alu repeats. Interspersed in the human genome, Alu repeats occupy 5% of the 3' UTR of mRNA sequences. Alu has poly-adenine (poly-A) regions at the end that lead to poly -thymine (poly-T) regions at the end of its complementary Alu. It has been discovered that AREs are present at the poly -T regions. In the all ARE's classes, 27-40% of ARE repeats were found in the poly -T region of Alu with mismatch allowed within 10% of ARE's length from the 3' UTRs of the NCBI's reference m RNA sequence database. We report that Alu, which has been reported as a junk DNA element, is a source of AREs. We found that one third of AREs were derived from the poly -T regions of the complementary Alu.

• Journal of Life Science
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• v.6 no.4
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• pp.234-240
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• 1996

A double-stranded RNA binding factor (RBF), characterized as an inhibitor of PKR kinase in our previous study, was evaluated for its RNA binding specificities by RNA gel electrophoretic mobility shift analysis and membrane filter binding assay, RBF displayed affinities for a broad range of RNAs including viral RNAs and synthetic RNAs consiting of stem and loop structures. GC-rich RNA stem helices as short as 11 bp are suggested to represent the minimal binding motif for RBF. RBF binding to all the natural RNAs tested was reversible by poly(I): poly(C) addition, but E. coli 5S RNA was inefficient.

• Molecules and Cells
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• v.25 no.4
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• pp.545-552
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• 2008

A hepadnaviruses replicates its DNA genome via reverse transcription of an RNA template (pregenomic RNA or pgRNA), which has a cap structure at the 5' end and a poly(A) tail at the 3' end. We have previously shown that the 5' cap is indispensable for encapsidation of the pgRNA. A speculative extension of the above finding is that the cap contributes to encapsidation via its interaction with the poly(A) tail, possibly involving eIF4E-eIF4G-PABP interaction. To test this hypothesis, poly(A)-less pgRNAs were generated via cleavage by a cis-acting hepatitis delta virus ribozyme sequence. We found that accumulation of the poly(A)-less pgRNA was markedly diminished, mostly likely due to its reduced stability. Importantly, however, the remaining poly(A)-less pgRNAs were nonetheless encapsidated and reverse transcribed normally when the reduced stability was taken account. Our finding clearly contradicts the notion that the poly(A) tail has any function in encapsidation and viral reverse transcription.

• Journal of Life Science
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• v.8 no.2
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• pp.119-125
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• 1998

Column-purified double-stranded RNA binding factor (RBF) protein was tested for its binding affinity for the different forms of nucleic acids structure such as single-stranded(ss) and double-stranded(ds)RNA and ss- and dsDNA. The RBF protein was incubated with each of these nucleic acid structures in separate reactions and its comparative binding affnity was visualized by SDS-polyacrylamide gel electrophoresis. The RBF protein bound to the dsRNA molecule to form a tight RNA:protein complex in agreement with previous studies, but not to the other nucleic acid molecules confirming its distinctive affinity for the dsRNA structure. In phosphorylation assay in vito, the purified RBF protein significantly inhibited the autophosphorylation of the PKR derived from not only human but mouse source in the presence of poly(I):poly(C). It is suggesting that PKR vs. RBF is similarly under a competitive interaction among different eukaryotic organisms during protein synthesis.

• Journal of Microbiology and Biotechnology
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• v.1 no.4
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• pp.232-239
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• 1991

Caboxymethyl cellulase (CMCase) I was purified from the induced culture filtrate of Penicllium verruculosum F-3 by ammonium sulfate precipitation, DEAE-Sephadex A-50 chromatography and Bio-gel P-150 filtration. The purified enzyme was assumed to be a glycoprotein consisting of 8.5% carbohydrate and having a molecular weight of 70.000 in SDS-polycrylamide gel electrophoresis (SDS-PAGE). The purified enzyme-specific anti-CMCase I IgG was obtained by rabbit immunization and protein A-sepharose CL-4B chromatography. The fungal poly($A^+$) RNA was isolated from the total RNA of the mycelium grown under cellulase induction conditions by oligo(dT)-cellulosse chromatography. The translation products in vitro were prepared by translating the isolated poly ($A^+$) RNA in rabbit reticulocyte lysate and analyzed by SDS-PAGE and fluorography. Of the translation products, CMCase I was identified by the immunoprecipitation against anti-CMCase I IgG.

• Molecules and Cells
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• v.27 no.1
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• pp.47-54
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• 2009

A cDNA clone for a transcript preferentially expressed during an early phase of flooding was isolated from Nicotiana tabacum. Nucleotide sequencing of the cDNA clone identified an open reading frame that has high homology to the previously reported glycine-rich RNA-binding proteins. The open reading frame consists of 157 amino acids with an N-terminal RNA-recognition motif and a C-terminal glycine-rich domain, and thus the cDNA clone was designated as Nicotiana tabaccum glycine-rich RNA-binding protein-1 (NtGRP1). Expression of NtGRP1 was upregulated under flooding stress and also increased, but at much lower levels, under conditions of cold, drought, heat, high salt content, and abscisic acid treatment. RNA homopolymer-binding assay showed that NtGRP1 binds to all the RNA homopolymers tested with a higher affinity to poly r(G) and poly r(A) than to poly r(U) and poly r(C). Nucleic acid-binding assays showed that NtGRP1 binds to ssDNA, dsDNA, and mRNA. NtGRP1 suppressed expression of the fire luciferase gene in vitro, and the suppression of luciferase gene expression could be rescued by addition of oligonucleotides. Collectively, the data suggest NtGRP1 as a negative modulator of gene expression by binding to DNA or RNA in bulk that could be advantageous for plants in a stress condition like flooding.

• Journal of Microbiology and Biotechnology
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• v.29 no.1
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• pp.127-140
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• 2019

Since 1990, many nucleic acid expression platforms consisting of DNA or RNA have been developed. However, although RNA expression platforms have been relatively neglected, several such platforms capped at the 5' end of RNA by an anti-reverse cap analog have now been developed. At the same time, the capping reaction is a bottleneck in the production of such platforms, with high cost and low efficiency. Here, we investigated several viral and eukaryotic internal ribosome entry sites (IRESs) to develop an optimal RNA expression platform, because IRES-dependent translation does not require a capping step. RNA expression platforms constructed with IRESs from the 5' untranslated regions of the encephalomyocarditis virus (EMCV) and the intergenic region of the cricket paralysis virus (CrPV) showed sufficient expression efficiency compared with cap-dependent RNA expression platforms. However, eukaryotic IRESs exhibited a lower viral IRES expression efficiency. Interestingly, the addition of a poly(A) sequence to the 5' end of the coxsackievirus B3 (CVB3) IRES (pMA-CVB3) increased the expression level compared with the CVB3 IRES without poly(A) (pCVB3). Therefore, we developed two multiexpression platforms (termed pMA-CVB3-EMCV and pCrPV-EMCV) by combining the IRESs of CVB3, CrPV, and EMCV in a single-RNA backbone. The pMA-CVB3-EMCV-derived RNA platform showed the highest expression level. Moreover, it clearly exhibited expression in mouse muscles in vivo. These RNA expression platforms prepared using viral IRESs will be useful in developing potential RNA-based prophylactic or therapeutic vaccines, because they have better expression efficiency and do not need a capping step.