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

• Development and Reproduction
• /
• v.27 no.1
• /
• pp.39-46
• /
• 2023

Pumilio (Pum) is an RNA-binding protein and translational repressor important to diverse biological processes. In the Drosophila ovary, Pum is expressed in female germline stem cells (GSCs), wherein it acts as an intrinsic stem cell maintenance factor via repressing target mRNAs that are as yet mostly unknown. Pum recognizes the Pum binding sequence (PBS) in the mRNA 3'UTR through its C-terminus Puf domain. Translational repression is mediated through its N-terminal domain, but the molecular mechanism remains largely unknown. We previously showed that Bag-of-marbles, a critical differentiation-promoting factor of female GSCs, physically interacts with the N-terminus of Pum. We further showed that this interaction is critical to Bam inhibition of Pum repressive action in cultured cells, but the physiological relevance was not addressed. Here we design an in vivo GFP translational reporter bearing the PBS in its 3'UTR and show that GFP expression is reduced in cells wherein Pum is known to be active. Furthermore, we demonstrate in pum mutant ovary that this GFP repression requires Pum, and also that the sensor faithfully monitors Pum activity. Finally, we show that forced expression of Bam inhibits Pum-mediated repression, validating that Bam inhibits Pum activity in vivo.

• 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.

• 한국생물공학회:학술대회논문집
• /
• 2005.04a
• /
• pp.402-406
• /
• 2005

Lipomyces starkeyi produces a novel glucanhydrolase containing endo-dextranase and ${\alpha}-amylase$ activities. A cDNA from L. starkeyi encoding a dextranase was isolated and characterized. The 2,052 kb cDNA fragment (lsd1) carrying dextranase gene showed one open reading frame (ORF) composed of 1,824 bp flanked by a 41 bp 5'-UTR and a 184 bp 3'-UTR including a poly(A) tail of 27 bp. The ORF encodes for a 608 amino acid with a predicted molecular mass of 67.6 kDa. There was 77% deduced amino acid sequence identity between the LSD1 dextranase and the dextranase from Penicillium minioluteum. The primary structure of the dextranase from L. starkeyi has distant similarity with enzymes belonging to glycosyl hydrolase family 49. The lsd1 protein was expressed in the Saccharmyces cerevisiae under control of GAL1 promoter and active dextranase was produced.

• Journal of Veterinary Clinics
• /
• v.27 no.3
• /
• pp.220-224
• /
• 2010

Bovine viral diarrhea virus (BVDV) is an important worldwide disease in the livestock industry. To characterize BVDV circulating in Gyeongbuk province in the Republic of Korea which has the highest cattle population density, 365 rectal swabs from clinically BVDV Korean indigenous calves were collected. Fifty cases were identified as positive for BVDV. A phylogenetic analysis of 5'- untranslated regions (UTR) revealed that most of our cases belonged to BVDV-2a (n = 48), while only two cases were classified as BVDV-1a (n = 1) and 1b (n = 1), respectively. These results indicated that BVDV-2a is the most prevalent subgroup in Korean indigenous calves of Gyeongbuk province.

• The Korean Journal of Mycology
• /
• v.25 no.1 s.80
• /
• pp.1-5
• /
• 1997

The cDNA encoding ${\beta}-tubulin$ of Pleurotus sajor-caju was isolated using an internal gene segment probe amplified by polymerase chain reaction (PCR) of genomic DNA and by cDNA library screening. The cDNA was consisted of 1560 nucleotides(nt), including a 5'-untranslation region (UTR) of 27nt, an open reading frame (ORF) of 1341nt, and a 3'-UTR of 191nt. The ORF encoded a protein of 446 amino acids(aa), which shows over 80% homology with ${\beta}-tubulins$ of other filamentous fungi. Southern hybridization analysis showed that there were two isotypes of ${\beta}-tubulin$ genes in P. sajor-caju. Through sequence analysis we found that ${\beta}-tubulin$ had a unusual $Cys^{165}$ residue, which might be a significant factor for the insensitivity of fungi to fungicide benomyl.

• The Korean Journal of Physiology and Pharmacology
• /
• v.27 no.3
• /
• pp.277-287
• /
• 2023

Actin dynamics play an essential role in myogenesis through multiple mechanisms, such as mechanotransduction, cell proliferation, and myogenic differentiation. Twinfilin-1 (TWF1), an actin-depolymerizing protein, is known to be required for the myogenic differentiation of progenitor cells. However, the mechanisms by which they epigenetically regulate TWF1 by microRNAs under muscle wasting conditions related to obesity are almost unknown. Here, we investigated the role of miR-103-3p in TWF1 expression, actin filament modulation, proliferation, and myogenic differentiation of progenitor cells. Palmitic acid, the most abundant saturated fatty acid (SFA) in the diet, reduced TWF1 expression and impeded myogenic differentiation of C2C12 myoblasts, while elevating miR-103-3p levels in myoblasts. Interestingly, miR-103-3p inhibited TWF1 expression by directly targeting its 3'UTR. Furthermore, ectopic expression of miR-103-3p reduced the expression of myogenic factors, i.e., MyoD and MyoG, and subsequently impaired myoblast differentiation. We demonstrated that miR-103-3p induction increased filamentous actin (F-actin) and facilitated the nuclear translocation of Yes-associated protein 1 (YAP1), thereby stimulating cell cycle progression and cell proliferation. Hence, this study suggests that epigenetic suppression of TWF1 by SFA-inducible miR-103-3p impairs myogenesis by enhancing the cell proliferation triggered by F-actin/YAP1.

• Molecules and Cells
• /
• v.39 no.8
• /
• pp.611-618
• /
• 2016

Fibroblast-like synoviocytes (FLS) with aberrant expression of microRNA (miRNA) are critical pathogenic regulators in rheumatoid arthritis (RA). Previous studies have found that overexpression or silencing of miRNA can contribute to the development of miRNA-based therapeutics in arthritis models. In this study, we explored the effects of miR-27a on cell migration and invasion in cultured FLS from RA patients. We found that miR-27a was markedly downregulated in the serum, synovial tissue, and FLS of RA patients. Meanwhile, the expression of follistatin-like protein 1 (FSTL1) was upregulated, which suggests that FSTL1 plays a key role in RA development. The results of a Transwell assay showed that miR-27a inhibited FLS migration and invasion. However, miR-27a inhibition promoted the migration and invasion of FLS. In addition, the down-regulated expression of matrix metalloproteinases (MMP2, MMP9, and MMP13) and Rho family proteins (Rac1, Cdc42, and RhoA) was detected after treatment with miR-27a in RA-FLS by quantitative reverse transcription-PCR and western blot analysis. Then, a luciferase reporter assay validated that miR-27a targeted the 3-untranslated region (3'-UTR) of FSTL1. Moreover, miR-27a caused a significant decrease of FSTL1. In addition, the expression of TLR4 and $NF{\kappa}B$ was inhibited by miR-27a but increased by FSTL1 overexpression. In conclusion, we found that miR-27a inhibited cell migration and invasion of RA-FLS by targeting FSTL1 and restraining the $TLR4/NF{\kappa}B$ pathway.

• International Journal of Oral Biology
• /
• v.40 no.4
• /
• pp.197-204
• /
• 2015

MicroRNA (miRNA, miR) is essential in regulating cell differentiation either by inhibiting mRNA translation or by inducing its degradation. However, the role of miRNA in odontoblastic cell differentiation is still unclear. In this study, we examined the molecular mechanism of miR-27-mediated regulation of odontoblast differentiation in MDPC-23 mouse odontoblastic cells derived from mouse dental papilla cells. The results of the present study demonstrated that the miR-27 expression increases significantly during MDPC-23 odontoblastic cell differentiation. Furthermore, miR-27 up-regulation promotes the differentiation of MDPC-23 cells and accelerates mineralization without cell proliferation. The over-expression of miR-27 significantly increased the expression levels of Wnt1 mRNA and protein. In addition, the results of target gene prediction revealed that Wnt1 mRNA has an miR-27 binding site in its 3'UTR, and is increased by miR-27. These results suggested that miR-27 promotes MDPC-23 odontoblastic cell differentiation by targeting Wnt1 signaling. Therefore, miR-27 is a critical odontoblastic differentiation molecular target for the development of miRNA based therapeutic agents in dental medicine.

• The Plant Pathology Journal
• /
• v.27 no.1
• /
• pp.33-36
• /
• 2011

The genome of a potyvirus isolate associated with chlorotic spots and vein banding symptoms on Spathiphyllum spp., in Andhra Pradesh state, India was amplified by RT-PCR using degenerate potyvirus primers, amplicons cloned, and sequence (1.6 kb) analyzed. This virus isolate shared maximum identity of 74.8% and 80.2% at coat protein (CP) gene nucleotide (906 nucleotides) and amino acid (302 amino acids) levels, respectively with Dasheen mosaic virus (DsMV)-M13 isolate reported from China. But its 3'-UTR (258 nucleotides) had maximum identity of 62.5% with DsMV-Vietnam isolate. The deduced molecular weight of CP is 33.57 kDa and it contained DAG triplet in its N-terminal region. In CP amino acid based phylogenetic analysis, this virus isolate represented a separate branch but closer to DsMV isolates cluster. Based on the molecular criteria set for the discrimination of species and genus in the Potyviridae family, the present virus isolate was identified as a distinct virus species in the genus Potyvirus and proposed the name Spathiphyllum chlorotic vein banding virus (SCVbV).