Intronless Gene Research Articles

Identification of seven polyamine oxidase genes in tomato (Solanum lycopersicum L.) and their expression profiles under physiological and various stress conditions

Polyamines (PAs) are implicated in developmental processes and stress responses of plants. Polyamine oxidases (PAOs), flavin adenine dinucleotide-dependent enzymes that function in PA catabolism, play a critical role. Even though PAO gene families of Arabidopsis and rice have been intensely characterized and their expression in response to developmental and environmental changes has been investigated, little is known about PAOs in tomato (Solanum lycopersicum). We found seven PAO genes in S. lycopersicum and named them SlPAO1∼7. Plant PAOs form four clades in phylogenetic analysis, of which SlPAO1 belongs to clade-I, SlPAO6 and SlPAO7 to clade-III, and the residual four (SlPAO2∼5) to clade-IV, while none belongs to clade-II. All the clade-IV members in tomato also retain the putative peroxisomal-targeting signals in their carboxy termini, suggesting their peroxisome localization. SlPAO1 to SlPAO5 genes consist of 10 exons and 9 introns, while SlPAO6 and SlPAO7 are intronless genes. To address the individual roles of SlPAOs, we analyzed their expression in various tissues and during flowering and fruit development. The expression of SlPAO2∼4 was constitutively high, while that of the other SlPAO members was relatively lower. We further analyzed the expressional changes of SlPAOs upon abiotic stresses, oxidative stresses, phytohormone application, and PA application. Based on the data obtained, we discuss the distinctive roles of SlPAOs.

Molecular Characterization, Evolution, and Expression Profiling of the Dirigent (DIR) Family Genes in Chinese White Pear (Pyrus bretschneideri).

Stone cells content and size are the key factors determining the internal quality of the pear fruit. Synthesis of lignin and thickening of secondary cell wall are the keys to the development of stone cells. The polymerization of monolignols and secondary cell wall formation requires the participation of dirigent proteins (DIRs). In recent years, DIR family have been studied in higher plants, but lack of comprehensive study in the pear DIR (PbDIR) family. This study focuses on the identification and analysis of PbDIR family for the first time. We identified 35 PbDIRs from the pear genome, 89% of which are intronless genes. Phylogenetic tree and chromosome localization analysis showed that 35 PbDIRs were divided into four subfamilies (DIR-a, -b/d, -e, and -g) and irregularly distributed among 10 chromosomes. In addition, we identified 29, 26, and 14 DIRs from the other three Rosids (peach, Mei, and grape), respectively. Interspecies microsynteny analysis revealed the collinear gene pairs between pear and peach are the most. Temporal expression analysis showed that the expression changes of seven PbDIRs (DIR-a subfamily: PbDIR4 and PbDIR5; DIR-b/d subfamily: PbDIR11; DIR-g subfamily: PbDIR19; DIR-e subfamily: PbDIR23, 25 and 26) in fruits were consistent with the changes of fruit lignin and stone cells contents. In addition, the subfamily of PbDIRs in fruits showed significant responses after treatment with ABA, SA, and MeJA. According to the protein tertiary structure, key amino acid residues and expression patterns analysis found that PbDIR4 might be involved in the metabolism of lignin and related to stone cells contents in pear fruits. In this study, we systematically analyzed the structure, evolution, function and expression of PbDIR family, which not only confirmed the characteristics of PbDIR family, but also laid the foundation for revealing the role of DIR in pear stone cell development and lignin polymerization.

Epstein-Barr Virus Protein EB2 Stimulates Translation Initiation of mRNAs through Direct Interactions with both Poly(A)-Binding Protein and Eukaryotic Initiation Factor 4G.

Epstein-Barr virus (EBV) expresses several mRNAs produced from intronless genes that could potentially be unfavorably translated compared to cellular spliced mRNAs. To overcome this situation, the virus encodes an RNA-binding protein (RBP) called EB2, which was previously found to both facilitate the export of nuclear mRNAs and increase their translational yield. Here, we show that EB2 binds both nuclear and cytoplasmic cap-binding complexes (CBC and eukaryotic initiation factor 4F [eIF4F], respectively) as well as the poly(A)-binding protein (PABP) to enhance translation initiation of a given messenger ribonucleoparticle (mRNP). Interestingly, such an effect can be obtained only if EB2 is initially bound to the native mRNPs in the nucleus. We also demonstrate that the EB2-eIF4F-PABP association renders translation of these mRNPs less sensitive to translation initiation inhibitors. Taken together, our data suggest that EB2 binds and stabilizes cap-binding complexes in order to increase mRNP translation and furthermore demonstrate the importance of the mRNP assembly process in the nucleus to promote protein synthesis in the cytoplasm.IMPORTANCE Most herpesvirus early and late genes are devoid of introns. However, it is now well documented that mRNA splicing facilitates recruitment on the mRNAs of cellular factors involved in nuclear mRNA export and translation efficiency. To overcome the absence of splicing of herpesvirus mRNAs, a viral protein, EB2 in the case of Epstein-Barr virus, is produced to facilitate the cytoplasmic accumulation of viral mRNAs. Although we previously showed that EB2 also specifically enhances translation of its target mRNAs, the mechanism was unknown. Here, we show that EB2 first is recruited to the mRNA cap structure in the nucleus and then interacts with the proteins eIF4G and PABP to enhance the initiation step of translation.

The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation

We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron-containing genes, R-loops are bounded between the transcription start site and the first exon-intron junction. In intronless genes, the 3' boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation.

Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability

Transcription is a source of genetic instability that can notably result from the formation of genotoxic DNA:RNA hybrids, or R-loops, between the nascent mRNA and its template. Here we report an unexpected function for introns in counteracting R-loop accumulation in eukaryotic genomes. Deletion of endogenous introns increases R-loop formation, while insertion of an intron into an intronless gene suppresses R-loop accumulation and its deleterious impact on transcription and recombination in yeast. Recruitment of the spliceosome onto the mRNA, but not splicing per se, is shown to be critical to attenuate R-loop formation and transcription-associated genetic instability. Genome-wide analyses in a number of distant species differing in their intron content, including human, further revealed that intron-containing genes and the intron-richest genomes are best protected against R-loop accumulation and subsequent genetic instability. Our results thereby provide a possible rationale for the conservation of introns throughout the eukaryotic lineage.

Coordinated Regulation of Anthocyanin Biosynthesis Genes Confers Varied Phenotypic and Spatial-Temporal Anthocyanin Accumulation in Radish (Raphanus sativus L.).

Anthocyanins are natural pigments that have important functions in plant growth and development. Radish taproots are rich in anthocyanins which confer different taproot colors and are potentially beneficial to human health. The crop differentially accumulates anthocyanin during various stages of growth, yet molecular mechanisms underlying this differential anthocyanin accumulation remains unknown. In the present study, transcriptome analysis was used to concisely identify putative genes involved in anthocyanin biosynthesis in radish. Spatial-temporal transcript expressions were then profiled in four color variant radish cultivars. From the total transcript sequences obtained through illumina sequencing, 102 assembled unigenes, and 20 candidate genes were identified to be involved in anthocyanin biosynthesis. Fifteen genomic sequences were isolated and sequenced from radish taproot. The length of these sequences was between 900 and 1,579 bp, and the unigene coverage to all of the corresponding cloned sequences was more than 93%. Gene structure analysis revealed that RsF3′H is intronless and anthocyanin biosynthesis genes (ABGs) bear asymmetrical exons, except RsSAM. Anthocyanin accumulation showed a gradual increase in the leaf of the red radish and the taproot of colored cultivars during development, with a rapid increase at 30 days after sowing (DAS), and the highest content at maturity. Spatial-temporal transcriptional analysis of 14 genes revealed detectable expressions of 12 ABGs in various tissues at different growth levels. The investigation of anthocyanin accumulation and gene expression in four color variant radish cultivars, at different stages of development, indicated that total anthocyanin correlated with transcript levels of ABGs, particularly RsUFGT, RsF3H, RsANS, RsCHS3 and RsF3′H1. Our results suggest that these candidate genes play key roles in phenotypic and spatial-temporal anthocyanin accumulation in radish through coordinated regulation and the major control point in anthocyanin biosynthesis in radish is RsUFGT. The present findings lend invaluable insights into anthocyanin biosynthesis and may facilitate genetic manipulation for enhanced anthocyanin content in radish.

Genome-wide analysis and evolution of the bZIP transcription factor gene family in six Fragaria species

Basic leucine zipper (bZIP) transcription factor gene family is one of the largest and most conserved plant-specific gene families and plays key roles in regulating diverse biological processes. The recent completion of genome sequences of the woodland strawberry (F. vesca), cultivated strawberry (F. × ananassa), and its four wild relatives (F. iinumae, F. nipponica, F. nubicola, and F. orientalis) provides the opportunity to study the micro-evolution of bZIP genes among six Fragaria genomes. In this study, we presented the first genome-wide identification and characterization of bZIP genes in six Fragaria genomes using bioinformatics. The total of 51, 36, 34, 33, 26, and 50 bZIP genes were detected in the genomes of F. × ananassa, F. iinumae, F. nipponica, F. nubicola, F. orientalis, and F. vesca, respectively, which were divided into eight sub-families according to the phylogenetic relationship with those in Arabidopsis thaliana. Diverse gene structures were found in Fragaria bZIPs, including eight major motif patterns. Interestingly, two sub-families consisted intron-less genes only, except FvbZIP19 and FnibZIP28. Paralogs had greater Ks values than those of orthologs, which indicated that the most duplication events of Fragaria bZIP genes occurred prior to the divergence of the six Fragaria species plant. In addition, orthologs are subject to weaker functional constraints and faster evolutionary processes than paralogs based on the Ka/Ks values. The great variation was also detected in the promoter region. This study provided insight into the micro-evolution of bZIP gene family within genus Fragaria.

CRISPR/Cas9 Genome Editing Reveals That the Intron Is Not Essential for var2csa Gene Activation or Silencing in Plasmodium falciparum.

ABSTRACTPlasmodium falciparum relies on monoallelic expression of 1 of 60 var virulence genes for antigenic variation and host immune evasion. Each var gene contains a conserved intron which has been implicated in previous studies in both activation and repression of transcription via several epigenetic mechanisms, including interaction with the var promoter, production of long noncoding RNAs (lncRNAs), and localization to repressive perinuclear sites. However, functional studies have relied primarily on artificial expression constructs. Using the recently developed P. falciparum clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, we directly deleted the var2csa P. falciparum 3D7_1200600 (Pf3D7_1200600) endogenous intron, resulting in an intronless var gene in a natural, marker-free chromosomal context. Deletion of the var2csa intron resulted in an upregulation of transcription of the var2csa gene in ring-stage parasites and subsequent expression of the PfEMP1 protein in late-stage parasites. Intron deletion did not affect the normal temporal regulation and subsequent transcriptional silencing of the var gene in trophozoites but did result in increased rates of var gene switching in some mutant clones. Transcriptional repression of the intronless var2csa gene could be achieved via long-term culture or panning with the CD36 receptor, after which reactivation was possible with chondroitin sulfate A (CSA) panning. These data suggest that the var2csa intron is not required for silencing or activation in ring-stage parasites but point to a subtle role in regulation of switching within the var gene family.

Splicing stimulates siRNA formation at Drosophila DNA double-strand breaks.

DNA double-strand breaks trigger the production of locus-derived siRNAs in fruit flies, human cells and plants. At least in flies, their biogenesis depends on active transcription running towards the break. Since siRNAs derive from a double-stranded RNA precursor, a major question is how broken DNA ends can generate matching sense and antisense transcripts. We performed a genome-wide RNAi-screen in cultured Drosophila cells, which revealed that in addition to DNA repair factors, many spliceosome components are required for efficient siRNA generation. We validated this observation through site-specific DNA cleavage with CRISPR-cas9 followed by deep sequencing of small RNAs. DNA breaks in intron-less genes or upstream of a gene’s first intron did not efficiently trigger siRNA production. When DNA double-strand breaks were induced downstream of an intron, however, this led to robust siRNA generation. Furthermore, a downstream break slowed down splicing of the upstream intron and a detailed analysis of siRNA coverage at the targeted locus revealed that unspliced pre-mRNA contributes the sense strand to the siRNA precursor. Since splicing factors are stimulating the response but unspliced transcripts are entering the siRNA biogenesis, the spliceosome is apparently stalled in a pre-catalytic state and serves as a signaling hub. We conclude that convergent transcription at DNA breaks is stimulated by a splicing dependent control process. The resulting double-stranded RNA is converted into siRNAs that instruct the degradation of cognate mRNAs. In addition to a potential role in DNA repair, the break-induced transcription may thus be a means to cull improper RNAs from the transcriptome of Drosophila melanogaster. Since the splicing factors identified in our screen also stimulated siRNA production from high copy transgenes, it is possible that this surveillance mechanism serves in genome defense beyond DNA double-strand breaks.

참굴(Crassostrea gigas)의 BTG1 유전자의 특성

BTG 1 (B-cell translocation gene 1) gene was first identified as a translocation gene in a case of B-cell chronic lympocytic leukemia. BTG1 is a member of the BTG/TOB family with sharing a conserved N-terminal region, which shows anti-proliferation properties and is able to stimulate cell differentiation. In this study, we identified and characterized the pacific oyster Crassostrea gigas BTG1 (cg-BTG1) gene from the gill cDNA library by an Expressed Sequence Tag (EST) analysis and its nucleotide sequence was determined. The cg-BTG1 gene encodes a predicted protein of 182 amino acids with 57% 56% identities to its zebrafish and human counterparts, and is an intron-less gene, which was confirmed by PCR analysis of genomic DNA. Maximal homologies were shown in conserved Box A and B. The deduced amino acid sequence shares high identity with other BTG1 genes of human, rat, mouse and zebrafish. The phylogenic analysis and sequence comparison of cg-BTG1 with other BTG1 were found to be closely related to the BTG1 gene structure. In addition, the predicted promoter region and the different transcription-factor binding site like an activator protein-1 (AP-1) response element involved in negative regulation and serum response element (SRE) were able to be identified by the genomic DNA walking experiment. The quantitative real-time PCR analysis showed that the mRNA of cg-BTG1 gene was expressed in gill, heart, digestive gland, intestine, stomach and mantle. The cg-BTG1 gene was expressed mainly in heart and mantle.

Overexpression of a Plasma Membrane-Localized SbSRP-Like Protein Enhances Salinity and Osmotic Stress Tolerance in Transgenic Tobacco.

An obligate halophyte, Salicornia brachiata grows in salt marshes and is considered to be a potential resource of salt- and drought-responsive genes. It is important to develop an understanding of the mechanisms behind enhanced salt tolerance. To increase this understanding, a novel SbSRP gene was cloned, characterized, over-expressed, and functionally validated in the model plant Nicotiana tabacum. The genome of the halophyte S. brachiata contains two homologs of an intronless SbSRP gene of 1,262 bp in length that encodes for a stress-related protein. An in vivo localization study confirmed that SbSRP is localized on the plasma membrane. Transgenic tobacco plants (T1) that constitutively over-express the SbSRP gene showed improved salinity and osmotic stress tolerance. In comparison to Wild Type (WT) and Vector Control (VC) plants, transgenic lines showed elevated relative water and chlorophyll content, lower malondialdehyde content, lower electrolyte leakage and higher accumulation of proline, free amino acids, sugars, polyphenols, and starch under abiotic stress treatments. Furthermore, a lower build-up of H2O2 content and superoxide-radicals was found in transgenic lines compared to WT and VC plants under stress conditions. Transcript expression of Nt-APX (ascorbate peroxidase), Nt-CAT (catalase), Nt-SOD (superoxide dismutase), Nt-DREB (dehydration responsive element binding factor), and Nt-AP2 (apetala2) genes was higher in transgenic lines under stress compared to WT and VC plants. The results suggested that overexpression of membrane-localized SbSRP mitigates salt and osmotic stress in the transgenic tobacco plant. It was hypothesized that SbSRP can be a transporter protein to transmit the environmental stimuli downward through the plasma membrane. However, a detailed study is required to ascertain its exact role in the abiotic stress tolerance mechanism. Overall, SbSRP is a potential candidate to be used for engineering salt and osmotic tolerance in crops.

Frequent GU wobble pairings reduce translation efficiency in Plasmodium falciparum

Plasmodium falciparum genome has 81% A+T content. This nucleotide bias leads to extreme codon usage bias and culminates in frequent insertion of asparagine homorepeats in the proteome. Using recodonized GFP sequences, we show that codons decoded via G:U wobble pairing are suboptimal codons that are negatively associated to protein translation efficiency. Despite this, one third of all codons in the genome are GU wobble codons, suggesting that codon usage in P. falciparum has not been driven to maximize translation efficiency, but may have evolved as translational regulatory mechanism. Particularly, asparagine homorepeats are generally encoded by locally clustered GU wobble AAT codons, we demonstrated that this GU wobble-rich codon context is the determining factor that causes reduction of protein level. Moreover, insertion of clustered AAT codons also causes destabilization of the transcripts. Interestingly, more frequent asparagine homorepeats insertion is seen in single-exon genes, suggesting transcripts of these genes may have been programmed for rapid mRNA decay to compensate for the inefficiency of mRNA surveillance regulation on intronless genes. To our knowledge, this is the first study that addresses P. falciparum codon usage in vitro and provides new insights on translational regulation and genome evolution of this parasite.

P01.37 Impact of C/EBPβ isoforms on brain tumor initiating cells

BACKGROUND: The transcription factor C/EBPβ has been identified as a master regulator of the mesenchymal phenotype in malignant glioma. It is transcribed from an intronless gene, but can be translated into three isoforms (LAP, LAP*, LIP). C/EBPβ has been shown to be upregulated in mesenchymal GBMs and its expression correlates to a worse prognosis in patients. Downregulation of C/EBPβ reduces proliferation and migration in vitro and diminishes tumor growth in vivo. In addition, C/EBPβ protein levels are increased in hypoxic and necrotic areas in human GBM tissue samples. However, expression levels and impact of the different isoforms in glioma are unknown. Crosstalk of C/EBPβ and TFGβ has been shown to influence metastatic behavior of breast carcinoma cells. The aim of this project is therefore to investigate the impact of C/EBPβ isoforms LAP and LIP on phenotype, proliferation and migration of brain tumor initiating cells (BTICs) and their possible interaction with transforming growth factor beta (TGFβ). Methods: LAP and LIP isoforms were stably overexpressed in a set of proneural and mesenchymal BTIC lines. Marker expression was investigated by immunocytochemistry and Western blot. Proliferation was monitored by crystal violet staining and migration by spheroid assay. Genome wide transcriptome analysis was performed by next generation RNA sequencing on a HiSeq (Illumina). Results: Overexpression of LAP ­(full-length protein) induced proneural BTICs to switch towards a mesenchymal phenotype, whereas overexpression of LIP had no such effect. Increased LAP led to enhanced migration in the majority of cell lines irrespective of subtype, whereas LIP mostly decreased migration. Rather the reverse effect was observed regarding proliferation. RNASeq analysis revealed highly differential consequences of LAP and LIP overexpression regarding expressed genes and principal component analysis. TGFβ signaling proved to be one of the most significantly altered pathways both in LAP and LIP cells. However, TGFβ treatment had either no effect or inhibited proliferation or migration independent of C/EBPβ isoform levels. Conclusions: We could show for the first time that overexpression of C/EBPβ is sufficient to induce a mesenchymal phenotype in proneural BTICs and that the LAP isoform is responsible for this transdifferentiation. Independent of glioma subtype, LAP and LIP can elicit opposing effects. Nevertheless, both isoforms might contribute to tumor progression, since shifting the balance between LAP and LIP might add to BTICs capability to adapt to microenvironmental cues, e.g. by adopting a more migratory or proliferative phenotype. In contrast to the findings in breast CA, TGFβ acted independently of C/EBPβ isoforms. Ongoing experiments will provide further insight into downstream effector molecules and regulatory mechanisms for each isoform in GBM.

MP07-06 STUDY ON SINGLE NUCLEOTIDE POLYMORPHISMS WITHIN THE NOVEL TESTIS-SPECIFIC HASPIN GENE ENCODING A SERINE/THREONINE PROTEIN KINASE IN HUMAN MALE INFERTILITY

You have accessJournal of UrologyInfertility: Basic Research & Pathophysiology I1 Apr 2017MP07-06 STUDY ON SINGLE NUCLEOTIDE POLYMORPHISMS WITHIN THE NOVEL TESTIS-SPECIFIC HASPIN GENE ENCODING A SERINE/THREONINE PROTEIN KINASE IN HUMAN MALE INFERTILITY Yasushi Miyagawa, Tetsuji Soda, Norichika Ueda, Shinichiro Fukuhara, Hiroshi Kiuchi, Akira Tsujimura, Hiromitsu Tanaka, and Norio Nonomura Yasushi MiyagawaYasushi Miyagawa More articles by this author , Tetsuji SodaTetsuji Soda More articles by this author , Norichika UedaNorichika Ueda More articles by this author , Shinichiro FukuharaShinichiro Fukuhara More articles by this author , Hiroshi KiuchiHiroshi Kiuchi More articles by this author , Akira TsujimuraAkira Tsujimura More articles by this author , Hiromitsu TanakaHiromitsu Tanaka More articles by this author , and Norio NonomuraNorio Nonomura More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2017.02.272AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES It has been reported that many testis-specific functional genes are drastically expressed during spermatogenesis, and defects in their expression cause male infertility. Haspin, encoding a germ cell-specific protein kinase, was cloned from a subtracted cDNA library constructed from mouse testis. Genomic analyses revealed that mouse Haspin is an intron-less gene located within the 26th intron of the integrin alpha E (Itgae) gene on chromosome 6, which is conserved in rats and humans. It was shown that human HASPIN phosphorylates histone H3 at threonine 3 and is required for this phosphorylation event in mitotic cells. HASPIN is found at the centrosomes and spindles during mitosis, where it integrates the regulation of chromosome and spindle function during mitosis and meiosis. The present study assessed whether HASPIN is a cause of infertility in Japanese males. METHODS Japanese subjects with nonobstructive infertility (n = 282) were divided into subgroups according to their degree of defective spermatogenesis: 192 (68%) of these patients had nonobstructive azoospermia, while 90 (32%) had severe oligospermia (<5 × 106 cells/ml). The control group consisted of fertile males who had fathered children born at a maternity clinic (n = 262). Their HASPIN coding sequence (CDS) was screened by the direct sequencing of PCR amplified DNA. This study was conducted with approval from the institutional review board and an independent ethics committee at Osaka University. RESULTS Polymorphisms were found at 10 positions within the HASPIN CDS. Among those polymorphisms, there were six nt changes causing an amino acid substitution, one insertion (TCCCGACGA) leading to the addition of three amino acids (aspartic acid- aspartic acid-proline: DDP), and three silent mutations. There were no correlations among the polymorphisms in terms of their co-occurrence. Three single nucleotide polymorphisms (SNPs) (c365C > A, c560T > C, and c2205A > G) and the insertion resulting in three additional amino acids (c204-/TCCCGACGA) were identified in Japanese males for the first time. Unexpectedly, c2143G > A (rs376754182) was present only in homozygous form in the infertile group. CONCLUSIONS In this study, we found 10 polymorphisms within the HASPIN CDS. Among those, 5 were found only in the infertile group, 3 of which were nonsynonymous. These polymorphisms found only in the infertile patients may be a cause of male infertility, although significant differences in the frequencies of the genotypes were not identified. This is the first analysis of HASPIN genetic polymorphisms in male infertile population and these results will contribute significantly to future large-scale studies on the genetic background of infertility in Japanese males and on functional analyses of the role of HASPIN in cell cycle progression. © 2017FiguresReferencesRelatedDetails Volume 197Issue 4SApril 2017Page: e83 Advertisement Copyright & Permissions© 2017MetricsAuthor Information Yasushi Miyagawa More articles by this author Tetsuji Soda More articles by this author Norichika Ueda More articles by this author Shinichiro Fukuhara More articles by this author Hiroshi Kiuchi More articles by this author Akira Tsujimura More articles by this author Hiromitsu Tanaka More articles by this author Norio Nonomura More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Cloning and expression analysis of a Toll-like receptor 21 (TLR21) gene from turbot, Scophthalmus maximus

Toll-like receptor 21 (TLR21) is a non-mammalian TLR recognizing unmethylated CpG DNA and considered as a functional homolog of mammalian TLR9. In the present study, a TLR21 gene was cloned from turbot, Scophthalmus maximus, its immune responsive expression was subsequently studied in vivo. The turbot (Sm)TLR21 gene is an intronless gene with a length of 3527 bp and encodes a peptide of 984 amino acids. The deduced protein possesses a signal peptide sequence, a leucine-rich repeat (LRR) domain composed of 16 LRR motifs, a transmembrane (TM) region and a Toll/interleukin-1 receptor (TIR) domain. Phylogenetic analysis grouped it with other teleost TLR21s. Quantitative real-time PCR (qPCR) analysis demonstrated the constitutive expression of SmTLR21 mRNA in all twelve examined tissues with higher levels in the lymphomyeloid-rich tissues like spleen and head kidney. Further, upon stimulation with polyinosinic: polycytidylic acid [poly(I:C)], turbot reddish body iridovirus (TRBIV) and CpG oligodeoxynucleotides (CpG-ODN) 2395, the SmTLR21 mRNA expression was up-regulated in the gills, head kidney, spleen and muscle. The maximum increases of SmTLR21 transcript levels ranged from 1.3 to 8.1-fold and appeared at 3 h to 5 day post-injection depending on different organs and stimuli. These findings suggest that SmTLR21 may play an important role in the immune responses to the infections of a broad range of pathogens that include RNA and DNA viruses and bacteria.

Possible role of rare variants in Trace amine associated receptor 1 in schizophrenia

Schizophrenia (SZ) is a chronic mental illness with behavioral abnormalities. Recent common variant based genome wide association studies and rare variant detection using next generation sequencing approaches have identified numerous variants that confer risk for SZ, but etiology remains unclear propelling continuing investigations. Using whole exome sequencing, we identified a rare heterozygous variant (c.545G>T; p.Cys182Phe) in Trace amine associated receptor 1 gene (TAAR1 6q23.2) in three affected members in a small SZ family. The variant predicted to be damaging by 15 prediction tools, causes breakage of a conserved disulfide bond in this G-protein-coupled receptor. On screening this intronless gene for additional variant(s) in ~800 sporadic SZ patients, we identified six rare protein altering variants (MAF<0.001) namely p.Ser47Cys, p.Phe51Leu, p.Tyr294Ter, p.Leu295Ser in four unrelated north Indian cases (n=475); p.Ala109Thr and p.Val250Ala in two independent Caucasian/African-American patients (n=310). Five of these variants were also predicted to be damaging. Besides, a rare synonymous variant was observed in SZ patients. These rare variants were absent in north Indian healthy controls (n=410) but significantly enriched in patients (p=0.036). Conversely, three common coding SNPs (rs8192621, rs8192620 and rs8192619) and a promoter SNP (rs60266355) tested for association with SZ in the north Indian cohort were not significant (P>0.05).TAAR1 is a modulator of monoaminergic pathways and interacts with AKT signaling pathways. Substantial animal model based pharmacological and functional data implying its relevance in SZ are also available. However, this is the first report suggestive of the likely contribution of rare variants in this gene to SZ.

Validation of cebpa mutation testing for use in a clinical setting

Mutations in the CCAAT/enhancer binding protein α (CEBPA) gene have become increasingly important as prognostic factors in acute myeloid leukaemia (AML). Along with FLT3-ITD and NPM1, testing for CEBPA should be standard of care for cytogenetically normal individuals. This intronless gene is however GC-rich throughout its coding region with mutations occurring across its entirety.1 Multiple studies have nevertheless revealed clustering of mutations in two main hot spots, the N-terminal region and C-terminal basic leucine zipper. Furthermore, two prognostic subgroups have been noted, those harbouring a single mutation and other cases with double mutations.2 Molecular challenges, therefore, continue to defy a cost effective, robust detection method for testing mutations in this gene.

Enhanced at Puberty-1 (Eap1) Expression Critically Regulates the Onset of Puberty Independent of Hypothalamic Kiss1 Expression

Background/Aims: Enhance at puberty-1 (Eap1) is an intronless gene that regulates the onset of puberty through a network of hypothalamic genes. However, precise mechanistic events essential for Eap1-regulation of puberty have not been fully elucidated. Eap1 is thought to promote the initiation of puberty through regulation of the hypothalamic metastasis-suppressor KiSS1. We aim to investigate this hypothesis by genetically perturbing Eap1 through RNA interference in vivo. Methods: We first engineered and optimized four sets of shRNAs that target rat Eap1 mRNA as well as one negative control shRNA. After generating lentiviral (LV) particles, we examined the suppression of Eap1 in NRK-54E cell line to select the most efficient one. Sequencelly, LV-Eap1-shRNA or controls including LV-eGFP and saline were intraventricular microinjected into 21-day-old rats. Rats were raised in appropriate conditions and we examined the time of vaginal opening, ovary physiology as well as hypothalamic puberty-regulatory genes at three developmental stages: juvenile (postnatal day PND25), early puberty (PND35), adult (PND42). Results: Hypothalamic suppression of Eap1 delayed the onset of rat vaginal opening. Hematoxylin and eosin (H&E) staining revealed a significant reduction of corpus luteum (CL) at PND35, but at PND42 CL levels were normal relative to control. In conjunction with differences in phenotype and ovary morphology, GnRH expression and transcripts were also reduced at PND25 and PND35, while their levels were similar to control at PND42. KiSS1 mRNA and protein levels were not significantly different at all three developmental stages. Conclusion: Eap1 expression critically regulates puberty as well as GnRH expression. However, Eap1-regulation of puberty may not necessitate KiSS1/GPR54 signaling.

DNA barcoding for the species identification of commercially important fishery products in Indonesian markets

SummaryThe DNA barcoding approach was used for the species identification of 44 Indonesian commercial fishery products. Additionally, the intronless nuclear rhodopsin gene fragment (RH1) was added to the analysis to enable the identification of species not yet barcoded and possible hybrids. The 655‐bp cytochrome C oxidase subunit I (COI) gene fragment marker was successfully amplified and used to identify 86% of the total fish samples at the species level using the BOLD and BLAST public databases. Moreover, the RH1 marker was used to complete COI analysis. For a number of fish species, the COI sequences (six species) and RH1 sequences (eight species) were the first entries submitted to GenBank. This study demonstrated that COI barcoding is a promising tool for Indonesian fishery products and confirmed that it could be adopted in the future for regular seafood control as part of the Indonesian integrated food traceability system.