• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2004.11a
• /
• pp.150-157
• /
• 2004

microRNA (miRNA)는 21-25 nucleotide (nt)의 single-stranded RNA 분자로서 mRNA의 3' untranslated region (3' UTR)에 상보적으로 결합하여 유전자 발현을 제어하는 새로운 조절물질이다. 지금까지 실험을 통해 수백 개의 miRNA가 알려져 있으나, miRNA에 의해 조절되는 target 유전자는 실험상의 어려움으로 아직까지 거의 알려지지 않았다. miRNA는 서열의 길이가 짧고 target과 느슨한 상보적 결합을 하기 때문에 기존의 서열 비교 방법으로 miRNA의 target을 찾는 것은 쉬운 일이 아니다. 본 논문은 신경망을 이용하여 Caenorhabditis elegans mRNA의 3' UTR에서 miRNA가 결합하는 영역을 예측하였다. 신경망은 복잡한 비선형 데이터를 잘 분리해내고 불완전하고 잡음이 많은 입력에 강하기 때문에 miRNA target 예측에 적합하다. miRNA와 mRNA의 결합 영역을 다양하게 분석하였고 민감도 0.59, 특수도 0.99의 성능을 갖는 신경망을 구현하였다. 신경망 입력 값을 달리하여 각각의 특성이 결과에 미치는 영향을 분석하였고 기존 예측 방법에 의한 결과와 비교하여 성능을 평가하였다.

• Molecules and Cells
• /
• v.20 no.2
• /
• pp.167-172
• /
• 2005

Ceruloplasmin (Cp) is a copper protein with important functions in iron homeostasis and in inflammation. Cp mRNA expression is induced by interferon (IFN)-${\gamma}$ in U937 monocytic cells, but synthesis of Cp protein is halted after about 12 h by transcript-specific translational silencing. The silencing mechanism requires binding of a 4-component cytosolic inhibitor complex, IFN-gamma-activated inhibitor of translation (GAIT), to a defined structural element (GAIT element) in the Cp 3'-UTR. Translational silencing of Cp mRNA requires the essential proteins of mRNA circularization, suggesting that the translational inhibition requires end-to-end mRNA closure. These studies describe a new mechanism of translational control, and may shed light on the role that macrophage-derived Cp plays at the intersection of iron homeostasis and inflammation.

• BMB Reports
• /
• v.49 no.1
• /
• pp.3-10
• /
• 2016

microRNAs (miRNAs) are key regulators of cell state transition and retention during stem cell proliferation and differentiation by post-transcriptionally downregulating hundreds of conserved target genes via seed-pairing in their 3' untranslated region. In embryonic and adult stem cells, dozens of miRNAs that elaborately control stem cell processes by modulating the transcriptomic context therein have been identified. Some miRNAs accelerate the change of cell state into progenitor cell lineages—such as myoblast, myeloid or lymphoid progenitors, and neuro precursor stem cells—and other miRNAs decelerate the change but induce proliferative activity, resulting in cell state retention. This cell state choice can be controlled by endogenously or exogenously changing miRNA levels or by including or excluding target sites. This control of miRNA-mediated gene regulation could improve our understanding of stem cell biology and facilitate their development as therapeutic tools. [BMB Reports 2016; 49(1): 3-10]

• Korean Journal Plant Pathology
• /
• v.10 no.3
• /
• pp.235-239
• /
• 1994

Viral RNA was extracted from purified Chinese cabbage strain of turnip mosaic virus (TuMV-Ca) from infected leaves of turnip. Polyadenylated genomic viral RNA was recovered by oligo (dT) cellulose column chromatography and used as a template for the synthesis of complementary DNA (cDNA). Recombinant plasmids contained cDNA ranged from about 900 bp to 2, 450 bp were synthesized. Among the selected 41 transformants, pTUCA31 and pTUCA35 had over 2 Kbp cDNA insert. Restriction endonuclease patterns of the clones examined were very similar among them. Clones pTUCA23 and pTUCA31 were overlapped with pTUA35. The longest clone pTUCA35, encoding 3'-end, showed that it contained two sites for EcoRI, and one site for BamHI, ClaI, HincII, SacI and XbaI, respectively. The restriction mapping indicated that the clone pTUCA35 contained partial nuclear inclusion body gene, complete coding region of the coat protein and 3' untranslated region of TuMV-Ca genomic RNA.

• BMB Reports
• /
• v.43 no.10
• /
• pp.677-682
• /
• 2010

Kv4.2, a pore-forming $\alpha$-subunit of voltage-gated A-type potassium channels, is expressed abundantly in the soma and dendrites of hippocampal neurons, and is responsible for somatodendritic $I_A$ current. Recent studies have suggested that changes in the surface levels of Kv4.2 potassium channels might be relevant to synaptic plasticity. Although the function and expression of Kv4.2 protein have been extensively studied, the dendritic localization of Kv4.2 mRNA is not well described. In this study, Kv4.2 mRNAs were shown to be localized in the dendrites near postsynaptic regions. The dendritic transport of Kv4.2 mRNAs were mediated by microtubule-based movement. The 500 nucleotides of specific regions within the 3'-untranslated region of Kv4.2 mRNA were found to be necessary and sufficient for its dendritic localization. Collectively, these results suggest that the dendritic localization of Kv4.2 mRNAs might regulate the dendritic surface level of Kv4.2 channels and synaptic plasticity.

• Journal of the Korean Magnetic Resonance Society
• /
• v.19 no.3
• /
• pp.143-148
• /
• 2015

In some pathogenic bacteria, there are RNA thermometers, which regulate the production of virulence associated factors or heat shock proteins depending on temperature changes. Like a riboswitches, RNA thermometers are located in the 5'-untranslated region and involved translational gene regulatory mechanism. RNA thermometers block the ribosome-binding site and start codon area under the $37^{\circ}C$ within their secondary structure. After bacterial infection, increased the temperature in the host causes conformations changes of RNA, and the ribosome-binding site is exposed for translational initiation. Because structural differences between open and closed forms of RNA thermometers are mainly mediated by base pairing changes, NMR spectroscopy is a very useful method to study these thermodynamically changing RNA structure. In this review, we briefly provide a fundamental function of RNA thermometers, and also suggest a proper NMR experiments for studying RNA thermometers.

• Journal of Life Science
• /
• v.11 no.5
• /
• pp.423-431
• /
• 2001

Genomic and cDNA clones containing the RAT3 gene involving in Agobacterium-mediated plant transformation were identified using plant DNA flanking the righ border of a T-DNA rescued from the rat3 mutant as hy-bridization probe. Two highly homologous cDNA clones were identified; one (RAT3-1) weakly hybridized with the probe whereas another (RAT3-2) strongly hybridized with the probe. Both Rat3-1 and Rat3-2 proteins contain a putative signal peptide for secretion. The deduced molecular weights of encoded proteins are 15 kDa. The results of genomic DNA blot analysis and DNA sequencing indicated that RAT3-1 and RAT3-2 exist as single copy genes and they were arranged side by side with just 600 bp distance between them. RAT3-1 was disrupted by the integration of T-DNA into the 3 untranslated region in rat3 mutant. A BLAST search showed that both RAT3-1 and RAT3-2 proteins have homology with only the C-terminal region of $\beta$-1,3-glucanase homologues from Triticum aestivum and Arabidopsis thaliana. Thses $\beta$-1,3-glucanase homologues contain an unusually long C-terminal region with no sig-nificant homology to other $\beta$-1,3-glucanase.

• Journal of Life Science
• /
• v.26 no.11
• /
• pp.1232-1236
• /
• 2016

Mitochondrial calcium uptake 1 (MICU1) including two canonical EF hands, located in the mitochondrial inner membrane, is known to play a crucial role in the calcium uptake in mitochondria. Mitochondrial calcium uptake in muscular cells is related to post mortem shortening by calcium release from muscles. Therefore, the porcine MICU1 gene has been estimated as a genetic candidate for meat quality traits. In this study, variations on the exonic regions of the porcine MICU1 gene were investigated by sequencing cDNAs and tested for their association with meat quality traits. A total of 667 Berkshire heads (347 sows and 320 castrated boars) were used for this association test. Three SNPs were detected on the 3' untranslated region (UTR) of the porcine MICU1 gene. SNP1 (c.*136G>A) was associated with drip loss (p=0.017) and intramuscular fat content (p=0.039). In addition, SNP2 (c.*222G>A) and SNP3 (c.*485G>A) were associated with drip loss (p=0.018) and intramuscular fat content (p<0.001), respectively. In conclusion, it was verified that three variations on the 3' UTR of the porcine MICU1 gene were significantly associated with meat quality traits. It was also suggested that molecular biological analyses are needed to validate the function of variations on the 3 UTR of the porcine MICU1 gene.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.19
• /
• pp.8319-8324
• /
• 2014

Although genetic markers identifying women at an increased risk of developing breast cancer exist, the majority of inherited risk factors remain elusive. Mutations in the BRCA1/BRCA2 gene confer a substantial increase in breast cancer risk, yet routine clinical genetic screening is limited to the coding regions and intronexon boundaries, precluding the identification of mutations in noncoding and untranslated regions. Because 3' untranslated region (3'UTR) polymorphisms disrupting microRNA (miRNA) binding can be functional and can act as genetic markers of cancer risk, we aimed to determine genetic variation in the 3'UTR of BRCA1/BRCA2 in familial and early-onset breast cancer patients with and without mutations in the coding regions of BRCA1/BRCA2 and to identify specific 3'UTR variants that may be risk factors for cancer development. The 3'UTRs of the BRCA1 and BRCA2 genes were screened by heteroduplex analysis and DNA sequencing in 100 patients from 46 BRCA1/2 families, 54 non-BRCA1/2 families, and 47 geographically matched controls. Two polymorphisms were identified. SNPs $c.^*1287C$ >T (rs12516) (BRCA1) and $c.^*105A$ >C (rs15869) (BRCA2) were identified in 27% and 24% of patients, respectively. These 2 variants were also identified in controls with no family history of cancer (23.4% and 23.4%, respectively). In comparison to variations in the 3'UTR region of the BRCA1/2 genes and the BRCA1/2 mutational status in patients, there was a statistically significant relationship between the BRCA1 gene polymorphism $c.^*1287C$ >T (rs12516) and BRCA1 mutations (p=0.035) by Fisher's Exact Test. SNP $c.^*1287C$ >T (rs12516) of the BRCA1 gene may have potential use as a genetic marker of an increased risk of developing breast cancer and likely represents a non-coding sequence variation in BRCA1 that impacts BRCA1 function and leads to increased early-onset and/or familial breast cancer risk in the Turkish population.

• Journal of Plant Biotechnology
• /
• v.37 no.1
• /
• pp.89-95
• /
• 2010

Dihydroflavonol 4-reductase (DFR) is a key enzyme of the flavonoid biosynthesis pathway which catalyses the NADPH-dependent reduction of 2R,3R-trans-dihydroflavonols to leucoanthocyanidins. In this study we describe cloning and expression of the genes encoding the flavonoid-biosynthetic enzyme DFR in Gypsophila paniculata L. Inspection of the 1279 bp long sequence revealed an open reading frame 1063 bp, including a 36 bp 5' leader region and 181 bp 3' untranslated region. Comparison of the coding region of this DFR cDNA sequence including the sequences of Arabidopsis thaliana, Citrus sinensis, Dianthus caryophyllus, Ipomoea batatas, Matthiola incana, Nierembergia sp, Petunia hybrida, Solanum tuberosum, Vitis vinifera reveals an identity higher than 69% at the nucleotide level. The function of this nucleotide sequences was verified by comparison with amino acid sequences of the amino-terminus and tryptic peptides from purified plant enzyme, by northern blotting with mRNA from wild type and mutant plants, by in vitro expression yielding and enzymatically active reductase, as indicated by the small leucopelargonidin peak. Genomic southern blot analysis showed the presence of only one gene for DFR in Gypsophila paniculata.