• Title/Summary/Keyword: tissue-specific transcription

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The Biological Functions of Plant Long Noncoding RNAs (식물의 긴비암호화 RNA들의 생물학적 기능)

  • Kim, Jee Hye;Heo, Jae Bok
    • Journal of Life Science
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    • v.26 no.9
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    • pp.1097-1104
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    • 2016
  • With the development of next generation sequencing (NGS), large numbers of transcriptional molecules have been discovered. Most transcripts are non -coding RNAs (ncRNAs). Among them, long non-coding RNAs (lncRNAs) with more than 200 nucleotides represent functional RNA molecule that will not be translated into protein. In plants, lncRNAs are transcribed by RNA polymerase II (Pol II) or Pol III, Pol VI and Pol V. After transcription of these lncRNAs, more RNA processing mechanisms such as splicing and polyadenylation occurs. The expression of plant lncRNAs is very low and is tissue specific. However, these lncRNAs are strongly induced by specific external stimuli. Because different external stimuli including environmental stresses induce a large number of plant lncRNAs, these lncRNAs have been gradually considered as new regulatory factors of various biological and development processes such as epigenetic repression, chromatin modification, target mimicry, photomorphogenesis, protein relocalization, environmental stress response, pathogen infection in plants. Moreover, some lncRNAs act as precursor of short RNAs. Although a large number of lncRNAs have been predicted and identified in plants, our current understanding of the biological function of these lncRNAs is still limited and their detailed regulatory mechanisms should be elucidated continuously. Here, we reviewed the biogenesis and regulation mechanisms of lncRNAs and summarized the molecular functions unraveled in plants.

Amino Acid Biosynthesis and Gene Regulation in Seed (종자내 아미노산 합성 조절 유전자에 관한 연구)

  • ;;;;;Fumio Takaiwa
    • Proceedings of the Botanical Society of Korea Conference
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    • 1996.07a
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    • pp.61-74
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    • 1996
  • Human and monogastric animals can not synthesize 10 out of the 20 amino asids and therefor need to obtain these from their diet. The plant seed is a major source of dietary protein. It is particular important in their study to increase nutritional quality of the seed storage proteins. The low contents of lysine, asparagine and threonenein various cereal seeds and of cystein and methionine. In legume seeds is due to the low proportions of these amino acids in the major storage proteins, we have tried to apply the three strategies; (1) mutagenesis and selection of specific amino acid analogue resistance, (2) cloning and expression study of lysine biosynthesis related gene, (3) transfomation of lysine rich soybean glycinin gene. The 5-methyltryptophan (5MT) resistant cell lines, SAR1, SAR2 and SAR3 were selected from anther derived callus of rice (Oryza sativa L. "Sasanishiki"). Among these selected cell lines, two (SAR1 and SAR3) were able to grow stably at 200 mg/L of 5MT. Analysis of the freed amino acids in callus shows that 5MT resistant cells (SAR3) accumulated free tryptophan at least up to 50 times higher than those that of the higher than of SAS. These results indicated that the 5MT resistant cell lines are useful in studies of amino acid biosynthesis. Tr75, a rice (Oryza sativa L., var. Sasanishiki) mutant resistant to 5MT was segregated from the progenies of its initial mutant line, TR1. The 5MT resistant of TR75 was inherited in the M8 generations as a single dominant nuclear gene. The content of free amino acids in the TR75 homozygous seeds increased approximately 1.5 to 2.0 fold compared to wild-type seeds. Especially, the contents of tryptophan, phenylalanine and aspartic acid were 5.0, 5.3 and 2.7 times higher than those of wild-type seeds, respectively. The content of lysine is significantly low in rice. The lysine is synthesized by a complex pathway that is predominantly regulated by feedback inhibition of several enzymes including asparginase, aspatate kinase, dihydrodipicolinat synthase, etc. For understanding the regulation mechanism of lysine synthesis in rice, we try to clone the lysine biosynthetic metabolism related gene, DHPS and asparaginase, from rice. We have isolated a rice DHPS genomic clone which contains an ORF of 1044 nucleotides (347 amino acids, Mr. 38, 381 daltons), an intron of 587 nucleotides and 5'and 3'-flanking regions by screening of rice genomic DNA library. Deduced amino acid sequence of mature peptide domain of GDHPS clone is highly conserved in monocot and dicot plants whereas that of transit peptide domain is extremely different depending on plant specie. Southern blot analysis indicated that GDHPS is located two copy gene in rice genome. The transcripts of a rice GDHPS were expressed in leaves and roots but not detected in callus tissues. The transcription level of GDHPS is much higher in leaves indicating enormous chloroplast development than roots. Genomic DNA clones for asparaginase genes were screened from the rice genomic library by using plaque hybridization technique. Twelve different genomic clones were isolated from first and second screening, and 8 of 12 clones were analyzed by restriction patterns and identified by Southern Blotting, Restriction enzyme digestion patterns and Southern blot analysis of 8 clones show the different pattern for asparaginase gene. Genomic Southern blot analysis from rice were done. It is estimated that rice has at least 2-3 copy of asparaginase gene. One of 8 positive clones was subcloned into the pBluescript SK(+) vector, and was constructed the physical map. For transformation of lysine rich storage protein into tobacco, soybean glycinin genes are transformed into tobacco. To examine whether glycinin could be stably accumulated in endosperm tissue, the glycinin cDNA was transcriptionally fused to an endosperm-specific promotor of the rice storage protein glutelin gene and then introduced into tobacco genomic via Agrobacterium-mediated transformation. Consequently the glycinin gene was expressed in a seed-and developmentally-specific manner in transgenic tobacco seeds. Glycinin were targeted to vacuole-derived protein bodies in the endosperm tissue and highly accumulated in the matrix region of many transgenic plant (1-4% of total seed proteins). Synthesized glycinin was processed into mature form, and assembled into a hexamer in a similar manner as the glycinin in soybean seed. Modified glycinin, in which 4 contiguous methionine residues were inserted at the variable regions corresponding to the C - teminal regions of the acidic and basic polypeptides, were also found to be accumulated similarly as in the normal glycinin. There was no apparent difference in the expression level, processing and targeting to protein bodies, or accumulation level between normal and modified glycinin. glycinin.

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Relationship between the Expression of Forkhead box M1 (FoxM1) and $p27^{kip1}$ in Non-Small Cell Lung Cancers

  • Lee, Kyung-Eun;Hong, Young-Seoub;Choi, Phil-Jo;Um, Soo-Jung;Son, Choon-Hee;Roh, Mee-Sook
    • Biomedical Science Letters
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    • v.14 no.4
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    • pp.243-248
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    • 2008
  • The Forkhead box M1 (FoxM1) has been shown to regulate transcription of cell cycle genes essential for $G_1$-S and $G_2$-M progression, including $p27^{kip1}$. The $p27^{kip1}$ gene is a member of the universal cyclin-dependent kinase inhibitor family. Immunohistochemical studies for FoxM1 and $p27^{kip1}$ were performed in 154 lung cancers (69 squamous cell carcinomas (SCC) and 85 adenocarcinomas (ADC)). Immunoreactivity for FoxM1 and $p27^{kip1}$ were found in 79 (51.3%) and 49 (31.8%) out of 154 cases, respectively. Forty-six (58.2%) of the 79 cases with a positive FoxM1 immunoreactivity showed a negative $p27^{kip1}$ expression in 154 lung cancers. According to histologic type, 22 (53.7%) of the 41 SCC cases with a positive FoxM1 immunoreactivity showed a negative $p27^{kip1}$ expression and 24 (63.2%) of the 38 ADC cases with a positive FoxM1 immunoreactivity showed a negative $p27^{kip1}$ expression. The expression of $p27^{kip1}$ was significantly higher in the SCC than in the ADC (P=0.050). There were no significant associations between the FoxM1 and $p27^{kip1}$ expressions and other clinicopathologic factors. These findings suggest that FoxM1 overexpression may diminish the expression of $p27^{kip1}$ protein in lung cancers. Further studies are needed to define the relation between FoxM1 and $p27^{kip1}$ for examining the mechanisms of tissue-specific FoxM1 expression.

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Isolation and Characterization of ACC Synthase Gene Family in Mung Bean (Vigna radiata L.): Differential Expression of the Three ACC Synthase enes in Response to Auxin and Brassinosteroid

  • Sunjoo Joo;Kim, Woo-Taek
    • Journal of Plant Biotechnology
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    • v.2 no.2
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    • pp.61-71
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    • 2000
  • By screening a cDNA library of auxin-treated mung bean (Vigna radiata L.) hypocotyls, we have isolated two full-length cDNA clones, pVR-ACS6 and pVR-ACS7, for 1-aminocyclopropane-1-carboxylate (ACC) synthase, the rate-limiting enzyme in the ethylene biosynthetic pathway. While PVR-ACS6 corresponds to the previously identified PCR fragment pMBA1, pVR-ACS7 is a new cDNA clone. A comparison of deduced amino acid sequences among auxin-induced ACC synthases reveal that these enzymes share a high degree of homology (65-75%) to VR-ACS6 and VR-ACS7 polypeptides, but only about 50% to VR-ACS1 polypeptide. ACS6 and ACS7 are specifically induced by auxin, while ACS1 is induced by cycloheximide, and to lesser extent by excision and auxin treatment. Results from nuclear run-on transcription assay and RNA gel blot studies revealed that all three genes were transcriptionally active displaying unique patterns of induction by IAA and various hormones in etiolated hypocotyls. Particularly, 24-epibrassinolide (BR), an active brassinosteroid, specifically enhanced the expression of VR-ACS7 by distinct temporal induction mechanism compared to that of IAA. In addition, BR synergistically increased the IAA-induced VR-ACS6 and VR-ACS7 transcript levels, while it effectively abolished both the IAA- and kinetin-induced accumulation of VR-ACS1 mRNA. In light-grown plants, VR-ACS1 was induced by IAA in roots, whereas W-ACS6 in epicotyls. IAA- and BR-treatments were not able to increase the VR-ACS7 transcript in the light-grown tissues. These results indicate that the expression of ACC synthase multigene family is regulated by complex hormonal and developmental networks in a gene- and tissue-specific manner in mung bean plants. The VR-ACS7 gene was isolated, and chimeric fusion between the 2.4 kb 5'-upstream region and the $\beta$-glucuronidase (GUS) reporter gene was constructed and introduced into Nicotiana tobacum. Analysis of transgenic tobacco plants revealed the VR-ACS7 promoter-driven GUS activity at a highly localized region of the hypocotyl-root junction of control seedlings, while a marked induction of GUS activity was detected only in the hypocotyl region of the IAA-treated transgenic seedlings where rapid cell elongation occurs. Although there was a modest synergistic effect of BR on the IAA-induced GUS activity, BR alone failed to increase the GUS activity, suggesting that induction of VR-ACS7 occurs via separate signaling pathways in response to IAA and BR.

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Isolation of human mesenchymal stem cells from the skin and their neurogenic differentiation in vitro

  • Byun, Jun-Ho;Kang, Eun-Ju;Park, Seong-Cheol;Kang, Dong-Ho;Choi, Mun-Jeong;Rho, Gyu-Jin;Park, Bong-Wook
    • Journal of the Korean Association of Oral and Maxillofacial Surgeons
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    • v.38 no.6
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    • pp.343-353
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    • 2012
  • Objectives: This aim of this study was to effectively isolate mesenchymal stem cells (hSMSCs) from human submandibular skin tissues (termed hSMSCs) and evaluate their characteristics. These hSMSCs were then chemically induced to the neuronal lineage and analyzed for their neurogenic characteristics in vitro. Materials and Methods: Submandibular skin tissues were harvested from four adult patients and cultured in stem cell media. Isolated hSMSCs were evaluated for their multipotency and other stem cell characteristics. These cells were differentiated into neuronal cells with a chemical induction protocol. During the neuronal induction of hSMSCs, morphological changes and the expression of neuron-specific proteins (by fluorescence-activated cell sorting [FACS]) were evaluated. Results: The hSMSCs showed plate-adherence, fibroblast-like growth, expression of the stem-cell transcription factors Oct 4 and Nanog, and positive staining for mesenchymal stem cell (MSC) marker proteins (CD29, CD44, CD90, CD105, and vimentin) and a neural precursor marker (nestin). Moreover, the hSMSCs in this study were successfully differentiated into multiple mesenchymal lineages, including osteocytes, adipocytes, and chondrocytes. Neuron-like cell morphology and various neural markers were highly visible six hours after the neuronal induction of hSMSCs, but their neuron-like characteristics disappeared over time (24-48 hrs). Interestingly, when the chemical induction medium was changed to Dulbecco's Modified Eagle Medium (DMEM) supplemented with fetal bovine serum (FBS), the differentiated cells returned to their hSMSC morphology, and their cell number increased. These results indicate that chemically induced neuron-like cells should not be considered true nerve cells. Conclusion: Isolated hSMSCs have MSC characteristics and express a neural precursor marker, suggesting that human skin is a source of stem cells. However, the in vitro chemical neuronal induction of hSMSC does not produce long-lasting nerve cells and more studies are required before their use in nerve-tissue transplants.

Effect of Enamel Matrix Drivatives application on the expression of PDLs17, PDLs22 of cultured human periodontal ligament cells in vitro (Enamel Matrix Derivatives가 사람 치주인대 세포의 특이유전자인 PDLs17, PDLs22의 발현에 끼치는 효과)

  • Han, Geun-A;Jang, Hyun-seon;Kok, Jung-Ki;Park, Ju-Chol;Kim, Heoung-Jung;Kim, Jung-Gwan;Kim, Byung-Ock
    • Journal of Periodontal and Implant Science
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    • v.34 no.2
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    • pp.333-344
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    • 2004
  • The enamel matrix derivative (EMD) has been recently used in the periodontal regenerative techniques. The present study was established to investigate the influence of EMD on human periodontal ligament cells using expression of mRNA of periodontal ligament specific gene (PDLs)17, PDLs22, type I collagen when EMD applied to periodontal ligament cells. Periodontal ligament cells were obtained from a healthy periodontium and cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% fetal bovine serum and ${\beta}-glycerophosphate$ with ascorbic acid. Test groups were two; One adds EMD in culture media and another added EMD and Dexamethasone (DEX) in culture media. Positive control group added DEX in culture media, and negative control group adds niether of EMD nor DEX. $Emdogain^{(R)}$ (Biora, Sweden, 30 mg/ml) was diluted by 75 ${\mu}g/ml$ concentration to culture media. For reverse transcription-polymerase chain reaction (RT-PCR), total RNA isolated on days 0, 7, 14 and 21. mRNA of PDLs17 was expressed on days 14 and 21 in EMD or DEX group, and expressed on days 7, 14 and 21 in EMD plus DEX group, the other side, expressed on days 21 in negative control group. mRNA of PDLs22 expressed on days 7, 14 and 21 in EMD group, and expressed on days 14 and 21 in DEX group, and expressed on days 7, 14 and 21 in EMD plus DEX group. Negative control group expressed on days 14 and 21. Type I collagen was expressed on all days and all groups. These results indicate that EMD promotes differentiation of periodontal ligament cells, and this is considered to offer basis that can apply EMD to periodontal tissue regeneration technique.

Isolation and Identification of Respiratory Cells from Human Amniotic Fluid (사람 양수에서 호흡기세포의 분리)

  • Kim, Eun-Jung;Park, Yong-Won;Kim, Young-Han;Kim, Yu-Seun;Oh, Jung-Tak
    • Advances in pediatric surgery
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    • v.15 no.1
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    • pp.1-10
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    • 2009
  • Recently, amniotic fluid has gained attention as one of the potential sources for cell therapy and tissue engineering because it has characteristics of multipotent stem cells. However, current knowledge about what types of cells are naturally found in amniotic fluid is still limited. In this study, we aimed to investigate whether human amniotic fluid contains cells that have characteristics of respiratory cells. Samples of human amniotic fluid (5 mL per sample) obtained from amniocenteses were cultured with small airway growth medium (SAGM). Cells were grown until the third passage and the presence of type II alveolar cells were characterized by inverted microscopy, immunofluorescence, and reverse transcription polymerase chain reaction (RT-PCR). On inverted microscopy, cultured cells showed typical polygonal and cobblestone-like epithelial morphology. The morphology of cells was not changed after selection and passing. Immunofluorescence analysis demonstrated that the isolated cells stained positive for surfactant protein C (SPC), specific marker for type II alveolar cells. Cells also stained positive for TTF-1 protein but negative for CD 31 and vimentin. RT-PCR analysis of cells showed expression of SPC mRNA. This study has demonstrated that respiratory cells can be isolated and identified from human amniotic fluid cultured in SAGM medium. Our results may provide the basis for further investigations of amniotic fluid.

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Histone H3 Lysine Methylation in Adipogenesis (Adipogenesis에서 히스톤 H3 lysine methylation)

  • Jang, Younghoon
    • Journal of Life Science
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    • v.30 no.8
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    • pp.713-721
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    • 2020
  • Adipogenesis as a model system is needed to understand the molecular mechanisms of human adipocyte biology and the pathogenesis of obesity, diabetes, and other metabolic syndromes. Many relevant studies have been conducted with a focus on gene expression regulation and intracellular signaling relating to Peroxisome proliferator-activated receptor gamma (PPARγ) and CCAAT/enhancer-binding protein alpha (C/EBPα), which are master adipogenic transcription factors. However, epigenome regulation of adipogenesis by epigenomic modifiers or histone mutations is not fully understood. Histone methylation is one of the major epigenetic modifications on gene expression in mammals, and histone H3 lysine methylation (H3Kme) in particular implicates cell differentiation during various tissue and organ development. During adipogenesis, cell type-specific enhancers are marked by histone H3K4me1 with the active enhancer mark H3K27ac. Mixed-lineage leukemia 4 (MLL4) is a major H3K4 mono-methyltransferase on the adipogenic enhancers of PPARγ and C/EBPα loci. Thus, MLL4 is an important epigenomic modifier for adipogenesis. The repressive mark H3K27me3 is mediated by the enzymatic subunit Enhancer zeste homolog 2 (EZH2) of the polycomb repressive complex 2. EZH2-mediated H3K27 tri-methylation on the Wnt gene increases adipogenesis because WNT signaling is a negative regulator of adipogenesis. This review summarizes current knowledge about the epigenomic regulation of adipogenesis by histone H3 lysine methylation which fundamentally regulates gene expression.

Expression of Antisense Mouse Obese Gene in Transgenic Mice (형질전환 생쥐에서 Antisense 비만유전자의 발현)

  • Kwon, B.S.;Hong, K.H.;Jahng, J.W.;Lee, H.T.;Chung, K.S.
    • Korean Journal of Animal Reproduction
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    • v.24 no.4
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    • pp.419-428
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    • 2000
  • Leptin, the product of obese (ob) gene, is an adipocyte-derived satiety factor that plays a major role in the regulation of food intake, energy homeostasis, body weight, reproductive physiology and neuropeptide secretion. The present study was designed to generate transgenic mice expressing antisense mouse ob (mob) gene. Total RNA was extracted from the adipose tissues of mouse, then reverse transcription was performed. The 303 and 635 bp fragments of anti I and II cDNAs were amplified from mob cDNAs by PCR. The two mob cDNAs were reversely ligated into between adipose tissue specific aP2 promote and SV40 poly(A) site. Transgenic mice carrying two different kinds of antisense mob transgenes were generated by DNA microinjection into pronucleus. Total 14 transgenic mice were born, and the 4 and 5 founder lines of the transgenic mice with anti I and II transgenes were respectively established. Antisense mRNA expression was detected in transgenic F$_1$ mice by RT-PCR analysis. This result suggests that the transgenic mice expressing antisense mob mRNA may be useful as an animal disease model to be obesity caused by decreased amount of leptin secretion.

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Effects of Estrogen on the Transcriptional Activities of Catecholamine Biosynthesizing Enzymes in the Brain and Adrenal Gland of Ovariectomized Rats (난소 절제 흰쥐의 뇌와 부신에서의 Catecholamine Biosynthesizing Enzyme들의 전사에 미치는 Estrogen의 효과)

  • 유경신;이종화;최돈찬;이성호
    • Development and Reproduction
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    • v.6 no.2
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    • pp.117-122
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    • 2002
  • Dopamine(DA), norepinephrine(NE), and epinephrine(E) belong to a class of neurotransmitters known as catecholamine (CA) which are synthesized and secreted by mammalian brain and adrenal medulla. CA regulate several behavior patterns connected with breeding, and regulate GnRH-gonadotropin hormone axis' vitality between hypothalamus-pituitary gland linking with reproduction freeze. The present study examined effects of sex steroid hormone on the transcriptional activities of CA biosynthesis enzymes, tyrosine hydroxylase(TH), dopamine $\beta$ -hydroxylase(DBH), and phenylethaolamine-N-methyl transferase(PNMT). Mature female rats were ovariectomized(OVX) and implanted with 17 $\beta$-estradiol(E$_2$: 500 $\mu\textrm{g}$/ml) or sesame oil. Forty-eight hours after implantation all the animals were sacrificed. Total RNAs were extracted immediately and were applied to semi-quantitative reverse transcription-polymerase chain reaction(RT-PCR). The expression level of TH was appeared by hypothalamus > SNc> adrenal medulla orders in OVX+Oil group, and by SNc > hypothalamus) adrenal medulla orders in OVX+E$_2$ group. Treatment with E$_2$ significantly increased TH expression in SNc and adrenal medulla but in hypothalamus, the reduced TH expression was observed. The expression level of DBH was appeared by adrenal medulla > SNc > hypothalamus orders in OVX+Oil group and in OVX+E$_2$ group. Administration of E$_2$ significantly reduced DBH expression in SNc, and increased in adrenal medulla. Two cDNA products, large(PNMT1) and small(PMNTs) species of 110bp difference, were amplified in SNc and hypothalamus, but only PNMTs was observed in adenal medulla. The PNMTs expression level was in the order of adrenal medulla > hypothalamus > SNc in both OVX+Oil and OVX+E$_2$ group. The PNMTs expression in SNc and adrenal medulla was significantly increased byE$_2$. The present report demonstrated that estrogen effects on transcriptional activities for CA biosynthethic enzymes were tissue specific in adrenal medulla as well as different region of brain. These results suggest that it might be crucial relationship between the type of estrogen receptor and CA enzyme gene expression.

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