Kinds Of mRNAs Research Articles

Analysis of maternal effect genes from maternal mRNA in eggs of Sogatella furcifera

To understand how many kinds of mRNAs in female adults can be transferred into the eggs and the molecular basis of embryonic axis specification in Sogatella furcifera, we performed de novo transcriptome sequencing of six cDNA libraries of female adults and unfertilized eggs. Total 60,306 unigenes were obtained, with an average length of 1114.51 bp and N50 length of 2112 bp. Total 2900 differentially expressed genes with 496 upregulated and 2404 downregulated were found in unfertilized egg compared to female adult. Most of mRNAs in female adult could be passed into its eggs. Total 65 maternal effect genes were identified, including many homologous genes involved in embryonic axis specialization of D. melanogaster. This study provide transcriptome resources to elucidate the functions of maternal effect genes and the molecular basis of embryonic axis specification in S. furcifera in the future.

Combination of mRNA of Repair-related Genes in Rat Skeletal Muscles for Wound Age Estimation.

Objective To investigate the estimation of early and mid-term wound age by a combination of four mRNAs, the DNA polymerase delta-interacting protein 3 （POLDIP3） mRNA, regulator of chromosome condensation 1 like （RCC1L） mRNA, proline-rich 5 （PRR5） mRNA, and ribonucleic acid export 1 （RAE1） mRNA in rats skeletal muscles. Methods The model of rat skeletal muscle contusion was established, and then contusion area muscle tissue was extracted 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44 and 48 h after injury. Histomorphological changes during the repair process after rat skeletal muscle contusion were observed. The relative expressions of Poldip3, Rcc1l, Prr5 and Rae1 mRNAs were detected by reverse transcription real-time quantitative polymerase chain reaction （RT-qPCR）. Different stages of wound age were classified by using the expression patterns of four genes at various time points after injury. The accuracy of the results was verified by Fisher discriminant analysis. Results Histomorphological results showed that the repair process after skeletal muscle contusion occurred with the prolonging of time. Through combination of the expression trends of the four kinds of mRNAs, the 48 h after injury could be divided into three periods, 4-12 h, 16-28 h and 32-48 h. The Fisher discrimination method showed that the classification accuracy rates of the three periods were 83.3%, 75.0% and 73.3%, respectively. Conclusion The classification discrimination based on the relative expression of every gene has a higher accuracy, and the accuracy of wound age estimation with combination of mRNA relative expressions is higher than that with a single indicator. By combining with Fisher discrimination method, this method can be used for early and mid-term wound age estimation.

Naked eye detection of multiple tumor-related mRNAs from patients with photonic-crystal micropattern supported dual-modal upconversion bioprobes.

Development of a portable device for the detection of multiple mRNAs is a significant need in the early diagnosis of cancer. We have designed a biochip-based mRNA detection device by combining a hydrophilic-hydrophobic micropattern with upconversion luminescence (UCL) probes. The device achieves highly sensitive detection, using the naked eye, of multiple mRNAs among patient samples. The high sensitivity is attributed to enrichment of the target concentration and a fluorescence enhancement effect. In addition, since the photonic crystal (PC) dot biochip is functionalized with dual-wavelength excitation UCL probes, two kinds of mRNAs in the heterogeneous biological samples are detected simultaneously, and the corresponding luminescence signals are captured using an unmodified camera phone. The biochip-based mRNA detection device reported here demonstrates that multiple mRNAs extracted from patient samples can be simultaneously and sensitively detected in a visual way without sophisticated instrumentation. Therefore, this device is promising for real-time detection of multiple biomarkers in patient samples, and it is anticipated that it will provide a powerful tool for convenient early diagnosis of cancer.

Differential Genes Expression between Fertile and Infertile Spermatozoa Revealed by Transcriptome Analysis.

BackgroundIt was believed earlier that spermatozoa have no traces of RNA because of loss of most of the cytoplasm. Recent studies have revealed the presence of about 3000 different kinds of mRNAs in ejaculated spermatozoa. However, the correlation of transcriptome profile with infertility remains obscure.MethodsTotal RNA from sperm (after exclusion of somatic cells) of 60 men consisting of individuals with known fertility (n=20), idiopathic infertility (normozoospermic patients, n=20), and asthenozoospermia (n=20) was isolated. After RNA quality check on Bioanalyzer, AffymetrixGeneChip Human Gene 1.0 ST Array was used for expression profiling, which consisted of >30,000 coding transcripts and >11,000 long intergenic non-coding transcripts.ResultsComparison between all three groups revealed that two thousand and eighty one transcripts were differentially expressed. Analysis of these transcripts showed that some transcripts [ribosomal proteins (RPS25, RPS11, RPS13, RPL30, RPL34, RPL27, RPS5), HINT1, HSP90AB1, SRSF9, EIF4G2, ILF2] were up-regulated in the normozoospermic group, but down-regulated in the asthenozoospermic group in comparison to the control group. Some transcripts were specific to the normozoospermic group (up-regulated: CAPNS1, FAM153C, ARF1, CFL1, RPL19, USP22; down-regulated: ZNF90, SMNDC1, c14orf126, HNRNPK), while some were specific to the asthenozoospermic group (up-regulated: RPL24, HNRNPM, RPL4, PRPF8, HTN3, RPL11, RPL28, RPS16, SLC25A3, C2orf24, RHOA, GDI2, NONO, PARK7; down-regulated: HNRNPC, SMARCAD1, RPS24, RPS24, RPS27A, KIFAP3). A number of differentially expressed transcripts in spermatozoa were related to reproduction (n = 58) and development (n= 210). Some of these transcripts were related to heat shock proteins (DNAJB4, DNAJB14), testis specific genes (TCP11, TESK1, TSPYL1, ADAD1), and Y-chromosome genes (DAZ1, TSPYL1).ConclusionA complex RNA population in spermatozoa consisted of coding and non-coding RNAs. A number of transcripts that participate in a host of cellular processes, including reproduction and development were differentially expressed between fertile and infertile individuals. Differences between comparison groups suggest that sperm RNA has strong potential of acting as markers for fertility evaluation.

Over-expression of transglutaminase in the Drosophila eye imaginal disc induces a rough eye phenotype

Transglutaminases (TGs) catalyze the cross-linking of proteins and are involved in various biological processes in mammals. In invertebrates, except for the involvement in the hemolymph clotting, the functions of TG have not been revealed. Drosophila has a single TG gene (CG7356), from which two kinds of mRNAs (dTG-RA and dTG-RB) are formed. RT-PCR analyses indicated that both dTGs-RA and -RB are synthesized in all the developmental stages tested. To reveal the roles of dTG during the development, we examined a phenotype induced through the ectopic expression of dTG by using a GAL4-UAS targeted expression system. Over-expression of dTG-A in the eye imaginal disc of larva induced a rough eye phenotype in adult compound eyes. Co-expression of P35, an inhibitor of apoptosis, suppressed the rough eye phenotype, suggesting that the rough eye phenotype induced by the over-expression of dTG-A in the eye imaginal disc is due to the occurrence of apoptosis. The rough eye phenotype induced by the over-expression of dTG-A was suppressed by the crossing with mutant fly lines lacking Drosophila JNK gene basket (bsk) or Drosophila JNKK gene hemipterous. FLP-out experiments using an enhancer trap line showed that the over-expression of dTG-A in the eye imaginal disc increased the puckered enhancer activity, a reporter of Bsk activity. These results suggested that the rough eye phenotype induced by the over-expression of dTG-A is related to an enhancement of JNK signaling pathway.

Heme oxygenase-1 induction in the brain during lipopolysaccharide-induced acute inflammation

Delirium occurs in 23% of sepsis patients, in which pro-inflammatory cytokines and nitric oxide are suggested to be involved. However, in animal experiments, even a subseptic dose of lipopolysaccharide (LPS) injection induces both pro-inflammatory cytokines and inducible nitric oxide synthase in the brain, suggesting that the brain oxidative reaction can be induced in the subseptic condition. Then, we evaluated the changes of heme oxygenase-1 (HO-1), a sensitive oxidative marker, as well as interleukin (IL)-1beta, IL-6, and inductible nitric oxide synthase (iNOS) mRNA in the hypothalamus and hippocampus of rats using real-time PCR after peripheral injection of LPS (2.0 mg/kg). As a result, these four kinds of mRNAs were induced significantly in both areas after LPS injection. These results suggest that peripheral inflammation induces an oxidative reaction in the brain, even if the inflammation is not lethal. It is also considered that several pathways are involved in brain HO-1 induction.

324 EFFECT OF AGING ON AMOUNTS OF DNA METHYLTRANSFERASE mRNA IN MOUSE SPERMATOZOA

The spermatozoon is a specially differentiated cell designed to carry a haploid male genome into an oocyte at fertilization. It recently was reported that a matured spermatozoon contains several kinds of mRNAs and these are delivered into the oocyte at fertilization (Ostermeier et al. 2004 Nature 429, 154). The physiological role of paternally derived mRNAs is not clear; however, there is a report that the DNA methyltransferase (Dnmt) mRNA level in spermatozoa from male rats exposed to ethanol was significantly reduced (Bielawski et al. 2002 Alcohl. Clin. Res. 26, 347–351). The reduction of mRNA levels of Dnmt in spermatozoa would lead to altered epigenetic modification of the genome. Because factors such as age may affect spermatozoa mRNA levels, this study evaluated the effect of individual aging on the expression levels of Dnmts during spermatogenesis. This was accomplished by determining expression levels of Dnmts in the whole testis and in spermatozoa from young and aged mice by quantitative reverse-transcription-PCR. Seven- (young) and 68- (aged) week-old C57BL/6N male mice (n = 3/group) were sacrificed by cervical dislocation and whole testes and matured spermatozoa were collected. Total RNA was extracted and purified from each sample. In this study, 5 Dnmts (Dnmt1s, Dnmt1p, Dnmt3a, Dnmt3b, and Dnmt3l) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a reference gene, were examined for expression levels in whole testis and spermatozoa using SYBR Premix Ex Taq (Takara Bio, Inc., Otsu, Shiga, Japan) and the 7300 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA). Real-Time PCR runs for each Dnmt and GAPDH were repeated 3 times using different RNA batches from different individuals. The GAPDH expression level was used to normalize the expression levels of each Dnmt. Data were analyzed by Student's t-test. Relative expression levels of each Dnmt in testis from aged males compared to that of young males were 0.94, 1.15, 0.91, 1.15, and 1.14 (Dnmt1s, Dnmt1p, Dnmt3a, Dnmt3b, and Dnmt3l, respectively). There was no difference in the expression levels of the 5 Dnmts examined between testes from aged and young males. On the other hand, the relative amounts of each Dnmt mRNA in spermatozoa from aged males compared to that of young males were 0.87, 0.01, 0.54, 1.07, and 1.75 (Dnmt1s, Dnmt1p, Dnmt3a, Dnmt3b, and Dnmt3l, respectively). There was a significant reduction (P < 0.05) in the amount of Dnmt1p mRNA. The reason why the amount of Dnmt1p mRNA in spermatozoa from aged male mice showed such reduction is not clear. There was no difference in the relative expression levels of Dnmt1p in testis irrespective of male age. Dnmt1p is only translated in the spermatocyte during the pachytene stage in meiosis and its physiological role is not clear. To elucidate this male, age-related reduction of the amount of Dnmt1p mRNA in spermatozoa would clarify part of physiological role of Dnmt1p. This work was supported by Wakayama Prefecture Collaboration of Regional Entities for the Advanced of Technological Excellence, Japan, and by a Grant-in-Aid for the 21st Century Center of Excellence Program of the MEXT, Japan.

Partial iodide organification defect caused by a novel mutation of the thyroid peroxidase gene in three siblings.

Three siblings with goitre and latent to mild hypothyroidism were suspected of having thyroid peroxidase (TPO) abnormality. Direct sequencing of their genomic DNAs showed two novel mutations of the TPO gene, one of which was G1687T (Gly533Cys; exon 9) and the other 1808-13del (Asp574/Leu575del; exon 10). The two mutations were compound heterozygous, as the former was found in their father's DNA as heterozygous, and the latter was found in DNA from their mother, also as heterozygous. As Gly533 and Asp574/Leu575 were well-conserved amino acids in the peroxidase superfamily, Gly533Cys- and Asp574/Leu575del-TPOs were thought to be affected structurally or functionally. In expression studies using CHO-Kl cells and mRNAs introduced with individual mutations, both mutated TPO proteins were expressed at the same molecular size as wild-type TPO and had enzyme activity, although Gly533Cys-TPO was slightly lower in efficiency of expression and more degenerative than wild-type TPO. We examined the localization of both mutated TPOs. Gly533Cys-TPO was located on the endoplasmic reticulum (ER) and nuclear envelope but not on the plasma membrane, whereas Asp574/Leu575del-TPO was located not only on the ER and nuclear envelope but also on the plasma membrane, as wild-type TPO. Nevertheless, only one point differed between Asp574/Leu575del- and wild-type TPOs: the mutated TPO was expressed on the plasma membrane surface at less than half the rate of wild-type TPO. Gly533Cys-TPO synthesized almost no thyroid hormone because of its defective localization on the apical membrane surface of thyrocytes, whereas Asp574/Leu575del-TPO performed thyroid hormone synthesis at a rate of less half that of wild-type TPO. In cotransfection experiments using three combinations of wild-type and G1687T-mRNAs, wild-type and 1808-13del-mRNAs, and G1687T-, 1808-13del-mRNAs, the three kinds of mRNAs were considered to have no influence on cell surface TPO expression of another mRNA when a 50%-maximal amount of each mRNA was transfected. When a larger amount of each mRNA was transfected, the former two combinations showed the level of cell surface TPO expression obtained from the saturating amount of wild-type mRNA, whereas the last combination of mutated mRNAs covered only about half of the expression level. Defective thyroid hormone production resulting from the abnormal TPOs was at a level that caused latent hypothyroidism when the patients were born. With their growth, thyroid hormone volume gradually became inadequate and their thyroid gland enlarged compensatorily.

Tissue responses around polymethylmethacrylate particles implanted into bone: analysis of expression of bone matrix protein mRNAs by in situ hybridization.

Tissue responses around implanted polymethylmethacrylate (PMMA) particles were analyzed by in situ hybridization with digoxigenin-labeled procollagen alpha1(I) (COL), osteonectin, osteocalcin, and osteopontin (OPN) mRNA probes. PMMA particles (150-300 microm in diameter) were implanted into rat tibiae, and specimens were collected at 3, 5, 7, and 10 days after operation. New bone was formed centripetally, and bone-forming osteoblasts expressed all four kinds of mRNAs. A COL signal was expressed most strongly and widely. In the early stage, COL-positive cells were detected on and among particles sporadically. A COL signal was rarely detected in cells on the surfaces of the particles, suggesting that PMMA particles may suppress osteoblast differentiation. Osteonectin and osteocalcin mRNAs were expressed in bone-forming osteoblasts in a similar pattern by day 7. By contrast, an OPN signal was detected mainly on the particles, not only in COL-positive osteoblasts but also in COL-negative round cells. The latter cells had acid phosphatase activity, suggesting that they might be macrophages responding to a foreign body. At day 10, an OPN signal was detected continuously in multinucleated cells on PMMA particles, whereas new bone was formed away from particles. Our approach helped us to understand the initial cellular reaction to materials, which may determine their biocompatibility.

Cloning of rabbit TR4 and its bone cell-specific activity to suppress estrogen receptor-mediated transactivation.

To clone a new nuclear receptor, we screened a rabbit heart complementary DNA (cDNA) library with degenerate oligonucleotide probes corresponding to the DNA-binding domain of nuclear receptors, which is highly conserved among receptors. One of the cDNA clones, clone 23, encodes a novel protein of 596 amino acids, and predicted molecular mass is 66 kDa. Homology search analysis identified this protein as rabbit TR4 (TR4-0). We also cloned the cDNA encoding a rabbit TR4 isoform (TR4-1), which lacks the putative C-terminal ligand-binding domain (350 amino acids) caused by a 23-bp exon deletion, which probably occurred during messenger RNA (mRNA) splicing. Northern blot analysis showed that TR4s are expressed with two kinds of mRNAs (9.0 kb and 2.8 kb), both of which are relatively abundant in brain, testis, and bone. RT-PCR analysis, using pairs of primers specific for each TR4, showed that both types of receptor express in various tissues. Furthermore, both are present in primary osteoblasts and bone marrow cells, though the mRNA levels of TR4-0 were much higher than those of TR4-1. A functional study, using a transient transfection assay, showed that both receptors suppressed retinoid X receptor (RXR)-retinoid acid receptor, RXR-TR, and RXR-VDR-mediated transactivation significantly in COS-1 and osteosarcoma cells (UMR-106, ROS17/2.8) and that TR4-0 was much more effective than TR4-1. Unexpectedly, we found that the TR4s effectively suppressed estrogen receptor-mediated transactivation in bone cells, but neither in kidney (COS-1) nor breast cancer cells (MCF-7, one of the major target cells of the estrogen action). Thus, the present study shows a novel property of the TR4 orphan receptor, acting as a bone cell-specific repressor in the estrogen receptor-mediated signaling pathway.

Dynamic Aspects in the Expression of the Goat Insulin-like Growth Factor-I (IGF-I) Gene: Diversity in Transcription and Post-transcription

Goat IGF-I (gIGF-I) cDNA was cloned using the reverse transcriptase-polymerase chain reaction (RT-PCR). The cDNA, which was homologous to rat class 1 IGF-I cDNA, was 969 bp long. From the open reading frame found in it, we predicted a 154 amino acid protein consisting of a 49 amino acid signal peptide, a 70 amino acid mature IGF-I peptide, and a 35 amino acid E domain (the COOH-terminal peptide). From the gIGF-I gene, we isolated and sequenced some segments containing four exons that encompassed the entire gIGF-I cDNA sequence. Goat liver RNA was analyzed by RT-PCR, and the nucleotides of the RT-PCR products were sequenced and checked with the nucleotide sequences of the segments from the gIGF-I gene. The gene had three leader exons (1W, 1, and 2, from upstream to downstream) and was transcribed into three kinds of mRNAs (classes 1W, 1, and 2). Another RNA species was detected by RT-PCR analysis of exon 1W. We sequenced it and found that in this transcript, the 3'-portion of exon 1 was inserted between exons 1W and 3, resulting in class 1W-1 del. mRNA. That is to say, the gIGF-I gene had three leader exons and four kinds of mature mRNA.

Tissue- and development-specific expression of goat insulin-like growth factor-I (IGF-I) mRNAs.

We cloned four kinds of goat insulin-like growth factor-I (IGF-I) cDNAs. Each of them encodes the same mature IGF-I and different signal peptides. In this study, we analyzed expression of the four kinds of mRNAs in tissues in various developmental stages by a reverse transcriptase-polymerase chain reaction assay. The results suggest that their expression may be controlled by different promoters, the activities of which are tissue- and development-specific.

Cloning and structural analysis of cDNA and the gene for mouse transcription factor UBF

The gene and protein structure of the mouse UBF (mUBF), a transcription factor for mouse ribosomal RNA gene, have been determined by cDNA and genomic clones. The unique mUBF gene consists of 21 exons spanning over 13 kb. Two mRNAs coding for mUBF1 and mUBF2 having 765 a.a. and 728 a.a., respectively, are produced by an alternative splicing of exon 8. It specifies 37 amino acids constituting a part of the regions homologous to high mobility group proteins (HMG box 2). A human UBF (hUBF) cDNA obtained by polymerase chain reaction also indicates the presence of two kinds of mRNAs, the shorter form lacking the same region as mUBF2. Comparison of the cDNAs from hUBF and mUBF revealed an unusual conservation of nucleotide sequence in the 3'-terminal non-coding region. We examined the relative amounts of expression of mUBF1 and mUBF2. The eight tissues studied contained both molecular species, although mUBF2 was the predominant form of UBF. The mRNA of mUBF1 was expressed one half of the mUBF2 in quiescent mouse fibroblasts but reached the same amount in growing state.

Regulation of flower organogenesis: Phytohormone control of mRNA populations during sexual differentiation inMercurialis annua L.

Some general data on the genetic control and the possibilities of regulation of developmental paths inDrosophila are furnished. The insights to be gained from this insect will surely have implications that extend far beyond the fruit-fly. For example, in plants, developmental programs for floral organs, implying specific proteins are known. Developmental mutants in which mutate alleles control developmental programs for flowering were also selected in several species (Zea, Pisum, Sorghum, Cucumis, Mercurialis). Chemicals, especially phytohormones interfering with these programs are discussed. The case of sexual differentiation ofMercurialis is discussed in more detail. In this species, sex organs are controlled by sex determination genes and by auxins (male) and cytokinins (female). Flowers of each sex can be characterized by specific mRNA populations. They were evidenced by translationin vitro in a cell-free system of the various kinds of mRNAs [poly(A), non poly(A), polysomes]. The feminisation of genetic males by cytokinins induces the mRNA population of female type. Evidence concerning the implications of cytokinins in protein synthesis before translation level is presented. This is also probably true for auxins, although direct evidence is lacking.

Translation of capped virus mRNA in encephalomyocarditis virus-infected cells.

The pattern of protein synthesis in HeLa cells simultaneously infected with encephalomyocarditis virus (EMCV) and Semliki Forest virus (SFV) has been analysed throughout the time course of the infection. The ratio of the picornavirus protein gamma versus the togavirus late protein C increased when the m.o.i. of EMCV was raised, and the ratio of C/gamma increased with higher multiplicities of SFV. Under some conditions, the co-infected cells simultaneously synthesized the picornavirus and togavirus proteins, and the cells exclusively translated the capped 26S mRNA from SFV at the end of the co-infection experiment. The influence of the time of addition of the second virus on the relative translation of the capped and uncapped mRNAs was also studied. When HeLa cells were co-infected with 5 p.f.u./cell of EMCV and 200 p.f.u./cell of SFV, only the synthesis of SFV proteins was apparent, whereas if SFV was added 1 to 3 h later during the course of EMCV infection the cells synthesized picornavirus and togavirus proteins. If the cells were superinfected with SFV 1 h after EMCV addition, host protein synthesis was drastically inhibited after 3 h of EMCV infection. By 5 h post-infection both kinds of virus proteins were synthesized and at 7 h post-infection the cells preferentially translated the capped 26S mRNA from SFV. If cells were first infected with SFV (10 p.f.u./cell) and co-infected or superinfected at 1 h with EMCV (50 p.f.u./cell), shut-off of host protein synthesis occurred 3 h after infection and the cells synthesized both kinds of virus proteins. However, 9 h after infection the cells synthesized SFV proteins only. When double-infected HeLa cells were placed in a hypotonic medium, they mainly synthesized the togavirus late proteins, whereas under hypertonic conditions, they translated the picornavirus RNA exclusively. These results suggest that the two kinds of mRNAs (SFV 26S mRNA and EMCV 35S mRNA) are present in the infected cells and that the relative translation of each of them depends on the external ionic conditions.