Gene (v.497, #1)
Do microRNAs regulate bone marrow stem cell niche physiology?
by S.K. Laine; T. Hentunen; T. Laitala-Leinonen (pp. 1-9).
The adult bone marrow, situated within the bone cavity, comprises three distinct stem cell populations: hematopoietic stem cells (HSCs), mesenchymal stromal/stem cells (MSCs) and endothelial progenitor/stem cells (EPCs). HSCs are a well-characterized population of self-renewing cells that give rise to all blood cells. The definition of MSCs is more complex due to the limited understanding of MSC properties. In general, MSCs are considered multipotent stromal cells that are able to differentiate into various cell types, including osteoblasts, chondrocytes and adipocytes. Compared to HSCs and MSCs, EPCs are a newly discovered population of stem/progenitor cells with the capacity to differentiate into endothelial cells, the cells forming the inner lining of a blood vessel.Although functionally different, HSCs, MSCs and EPCs, like stem cells in general, share the ability to self-renew and differentiate into one or more cell types. The homeostasis inside the bone marrow and within the entire body is sustained by an intricate network of growth factors and transcription factors that orchestrate the proliferation and differentiation of these multipotent stem/progenitor cells. Increasing evidence indicates that microRNAs (miRNAs), small non-coding RNAs, are among the key players of this concert. This review summarizes the current insights into miRNA-mediated regulation of bone marrow stem/progenitor cell maintenance and differentiation. Furthermore, the potential contribution of miRNAs in bone marrow stem cell niches is discussed.► MicroRNAs regulate the self-renewal and differentiation of bone marrow stem cells. ► Bone marrow stem cells reside in stem cell niches. ► MicroRNAs may be involved in the regulation of niche function.
Keywords: Abbreviations; miRNA; microRNA; HSC; hematopoietic stem cell; MSC; mesenchymal stem cell; EPC; endothelial progenitor cell; UTR; untranslated regionMicroRNA; Mesenchymal stem cell; Hematopoietic stem cell; Endothelial progenitor cell; Niche
Instruction of mesenchymal cell fate by the transcription factor C/EBPβ
by Jeske J. Smink; Achim Leutz (pp. 10-17).
The transcription factor CCAAT/enhancer binding protein beta (C/EBPβ) plays a role in the differentiation of a large variety of cell types. C/EBPβ was initially described as an early inducer of adipocyte differentiation, however, recent data have shown that this is not the only mesenchymal cell lineage where C/EBPβ has an instructive function. Mouse models and tissue culture studies have now established a regulatory role of C/EBPβ in osteoblast and in chondrocyte differentiation. These three different cell lineages are derived from the same precursor, the mesenchymal stem cell (MSC). This review will focus on the emerging role of C/EBPβ and its different protein isoforms in various mesenchymal cell lineages and its function in adipocyte, chondrocyte and osteoblast differentiation. Moreover, the mesenchymal stem cell has attracted the attention of regenerative medicine in recent years, and the possible role of C/EBPβ in this respect will be discussed.►The role of C/EBPb in mesenchymal cell lineage decision is discussed. ► The action of C/EBPb in adipocytes, chondrocytes and osteoblasts is discussed. ► A possible dual role of C/EBPb as a repressor and activator is discussed. ► The potential implications of all this on regenerative medicine are discussed.
Keywords: Abbreviations; ATF4; activating transcription factor 4; BAT; brown adipose tissue; bZIP; basic leucine zipper; cAMP; adenosine 3′,5′-cyclic monophosphate (cyclic AMP); CBP; CREB binding protein; CD-RAP; cartilage-derived retinoic acid sensitive protein; C/EBP; CCAAT/enhancer binding protein; Ebf; early B cell factor; GR; glucocorticoid receptor; HDAC1; histone deacetylase 1; KLF; Krüppel-like factor; LAP; liver activating protein; LIP; liver inhibitory protein; MAFbx; F-box protein 32; MEF; mouse embryonic fibroblasts; MSC; mesenchymal stem cell; mRNA; messenger RNA; mTOR; mammalian target of rapamycin kinase; Myb; myeloblastosis oncogene; PPAR; peroxisome proliferator-activated receptor; RXR; retinoid X receptor; Sox9; SRY-box containing gene 9; SWI/SNF; switching/sucrose nonfermenting; uORF; upstream open reading frameC/EBPbeta; Mesenchymal stem cells; Osteoblasts; Chondrocytes; Adipocytes; Cell fate
CUX1 transcription factors: From biochemical activities and cell-based assays to mouse models and human diseases
by Laura Hulea; Alain Nepveu (pp. 18-26).
ChIP-chip and expression analyses indicated that CUX1 transcription factors regulate a large number of genes and microRNAs involved in multiple cellular processes. Indeed, in proliferating cells CUX1 was shown to regulate several genes involved in DNA replication, progression into S phase and later, the spindle assembly checkpoint that controls progression through mitosis. siRNA-mediated knockdown established that CUX1 is required for cell motility. Moreover, higher expression of short CUX1 isoforms, as observed in many cancers, was shown to stimulate cell migration and invasion. In parallel, elevated expression particularly in higher grade tumors of breast and pancreatic cancers implicated CUX1 in tumor initiation and progression. Indeed, transgenic mouse models demonstrated a causal role of CUX1 in cancers originating from various cell types. These studies revealed that higher CUX1 expression or activity not only stimulates cell proliferation and motility, but also promotes genetic instability. CUX1 has also been implicated in the etiology of polycystic kidney diseases, both from a transgenic approach and the analysis of CUX1 activity in multiple mouse models of this disease. Studies in neurobiology have uncovered a potential implication of CUX1 in cognitive disorders, neurodegeneration and obesity. CUX1 was shown to be expressed specifically in pyramidal neurons of the neocortex upper layers where it regulates dendrite branching, spine development, and synapse formation. In addition, modulation of CUX1 expression in neurons of the hypothalamus has been associated with changes in leptin receptor trafficking in the vicinity of the primary cilium resulting in altered leptin signaling and ultimately, eating behavior. Overall, studies in various fields have allowed the development of several cell-based assays to monitor CUX1 function and have extended the range of organs in which CUX1 plays an important role in development and tissue homeostasis.► CUX1 accelerates the start of DNA replication and promotes genetic instability. ► CUX1 stimulates cell migration and invasion. ► CUX1 expression is elevated in breast and pancreatic tumors of higher grade. ► CUX1 stimulates dendrite branching and synapse formation in the neocortex. ► CUX1 may regulate leptin signaling and obesity via its effect on the primary cilium.
Keywords: Abbreviations; ADPKD; autosomal dominant polycystic kidney disease; AFP; alpha-fetoprotein; CDK1; cyclin-dependent kinase 1; CDP; CCAAT-displacement protein; ChIP; chromatin immunoprecipitation; CR; Cut repeat; CUTL1; Cut-like 1; CUX1; Cut homeobox 1; CUX2; Cut homeobox 2; EMSA; electrophoretic mobility shift assay; mRNA; messenger RNA; EPM1; progressive myoclonus epilepsy type 1; Ftm; mouse ortholog of human RPGRIP1L; FTO; Fat Mass and Obesity-associated; GRIA3; glutamate receptor, ionotrophic, AMPA 3; IGF1; insulin-like growth factor 1; miR; microRNA; MMTV; mouse mammary tumor virus long terminal repeat; PAR2; proteinase-activated receptor 2; PAR2-AP; PAR2-activating peptide; PARs; proteinase-activated receptors; Pkd1; polycystic kidney disease 1 (autosomal dominant); PKDs; polycystic kidney diseases; qPCR; quantitative real time polymerase chain reaction; RPGRIP1L; retinitis pigmentosa GTPase regulator-interacting protein-1 like; shRNA; short hairpin RNA; siRNA; small interfering RNA; Stat3; signal transducer and activator of transcription 3; VDR; vitamin D-receptorCell cycle; Cancer; Genomic instability; Kidney diseases; Neurological disorders; Obesity
KlRox1p contributes to yeast resistance to metals and is necessary for KlYCF1 expression in the presence of cadmium
by Ana M. Rodríguez Torres; Mónica Lamas Maceiras; Esther Rodríguez Belmonte; Laura Núñez Naveira; Moisés Blanco Calvo; Cerdan M. Esperanza Cerdán (pp. 27-37).
We have characterized the KlROX1 gene from Kluyveromyces lactis and verified that it does not regulate the hypoxic response in this yeast, oppositely to the Saccharomyces cerevisiae homologue ScROX1. The KlROX1 promoter is not regulated by KlHap1p or KlRox1p in response to changes aerobiosis/hypoxia. Besides, KlRox1p expression only partially represses ScANB1 in S. cerevisiae and does not regulate the ScANB1 and KlHEM13 promoters in K. lactis. KlRox1p does not interact either with KlTup1p or KlSsn6p or with their homologues ScTup1p and ScSsn6p, which are components of the general co-repressor factor that mediates the transcriptional repression exerted by ScRox1p in S. cerevisiae. We have found that KlROX1 mediates the response to arsenate and cadmium and, in the presence of cadmium, it is necessary for KlYCF1 expression, a gene encoding a protein with homology to the yeast cadmium and arsenite vacuolar transporter. EMSA assays show that KlRox1p binds, through its HMG domain, to a DNA sequence present in the KlYCF1 promoter. Although in S. cerevisiae the function of ScRox1p in cadmium resistance was already known and linked to regulation of ScFET4 expression, we have found that ScRox1p also regulates ScYCF1transcription and binds to its promoter. ► Rox1pfunction in Kluyveromyces lactis and Saccharomyces cervisiae is compared. ► KlRox1p and its homolog ScRox1p take part in the response to metals in yeasts. ► K. lactis and S. c erevisiae Rox1p regulate YCF1 gen expression in both yeasts. ► K. lactis and S. cerevisiae Rox1p bind to the YCF1 promoters. ► Regulatory mechanisms in this response differ in both yeasts.
Keywords: Abbreviations; As (V); arsenate oxyanion AsO43; −; As (III); arsenite AsO33; −; A.U.; arbitrary units; C; Crick strand; Ca; Candida albicans; Cd (II); cadmium; CM; complete synthetic medium; CM-; medium prepared as CM but with omission of the amino acid or compound cited afterward; cpm; counts per minute; EUROSCARF; European; Saccharomyces cerevisiae; archive for functional analysis; HMG; high mobility group; kanMX4; kanamycin resistance cassette; Kl; K. lactis; A; 600; Absorbance at 600; nm; ORF; open reading frame; ONPG; ortho-nitrophenyl-β-; d; -galactopyranoside; PCR; polymerase chain reaction; PPP; pentose phosphate pathway; ROS; reactive oxygen species; Sc; S. cerevisiae; SD; standard deviation; SDS; sodium dodecyl sulfate; SGD; Saccharomyces; Genome Database; RSA; regulatory sequence analysis; W; Watson strand; WGD; whole genome duplication; wt; wild typeHypoxia; Metals; Transcriptional regulators; Kluyveromyces lactis; Saccharomyces cerevisiae; High-mobility-groups
The R453Q and D151A polymorphisms of Hexose-6-Phosphate Dehydrogenase Gene ( H6PD) influence the polycystic ovary syndrome (PCOS) and obesity
by Martinez-Garcia M.A. Martínez-García; San-Millan J.L. San-Millán; H.F. Escobar-Morreale (pp. 38-44).
Hexose-6-phosphate dehydrogenase (H6PDH) influences 11β-hydroxysteroid dehydrogenase activity, a key enzyme in the peripheral metabolism of cortisol that modulates insulin sensitivity in adipose tissue. To study the associations of R453Q and D151A polymorphisms in the H6PDH gene ( H6PD) with polycystic ovary syndrome (PCOS) and their influence on clinical and metabolic variables, we genotyped 237 patients with PCOS and 135 control women for the R453Q (rs6688832) and D151A (rs34603401) variants in H6PD. The R453Q genotypes were distributed differently in patients and controls ( χ2=9.55, P=0.002). Genotypes of D151A were distributed evenly in women with PCOS and controls, but showed a different distribution in non-obese and obese women ( χ2=3.95, P=0.047), especially within the PCOS subgroup ( χ2=4.65, P=0.031). A backward stepwise likelihood ratio logistic regression model (Nagelkerke's R2=0.490; χ2=164; P<0.0001) retained free testosterone (OR=1.13; 95% CI: 1.10–1.17) and H6PD Q453 alleles (OR=0.46; 95% CI: 0.27–0.79) as statistically significant predictors for PCOS, whereas homeostasis model assessment of insulin resistance and the H6PD D151A variant were excluded by the model. Both H6PD variants were associated with several phenotypic variables, including fasting insulin, homeostasis model assessment of insulin resistance and androstenedione levels. In summary, the R453Q and D151A variants of the H6PD gene are associated with PCOS and obesity, respectively, and may contribute to the PCOS phenotype by influencing obesity, insulin resistance and hyperandrogenism.► Hexose-6-phosphate dehydrogenase influences peripheral cortisol metabolism. ► Hexose-6-phosphate dehydrogenase is encoded by H6PD. ► Q alleles of the R453Q variant in H6PD protect against PCOS. ► A alleles of the D151A variant in H6PD are associated with obesity. ► H6PD R453Q and D151A variants influence insulin resistance and hyperandrogenism.
Keywords: Abbreviations; 11β-HSD1; 11β-hydroxysteroid dehydrogenase; BMI; body mass index; CI; confidence interval; CRD; cortisone reductase deficiency; GLM; general linear model; H6PDH; hexose-6-phosphate dehydrogenase; H6PD; hexose-6-phosphate dehydrogenase; HSD11B1; 11β-hydroxysteroid dehydrogenase gene; OR; odds ratio; PCOS; polycystic ovary syndrome; PCR; polymerase chain reactionAdrenal androgens; Androgen excess; Insulin resistance; Metabolism
Loss of the Prader–Willi obesity syndrome protein necdin promotes adipogenesis
by Jason Russell Bush; Rachel Wevrick (pp. 45-51).
We investigated the role of necdin during adipogenic differentiation. Necdin is one of several genes inactivated in children with Prader–Willi syndrome, who are predisposed to increased adiposity at the expense of lean mass. Necdin promotes neuronal and muscle differentiation and survival through interactions with a variety of proteins, including cell surface receptors, modifiers of protein stability, and transcription factors. In pre-adipocytes, necdin over-expression inhibits adipogenesis, while reducing necdin levels enhances adipogenic differentiation in tissue culture cells. We now directly demonstrate a role for necdin in inhibiting adipogenesis using cells derived from necdin deficient mice.► Necdin is inactivated in people with Prader–Willi obesity syndrome. ► Necdin enhances myogenic differentiation and suppresses adipogenic differentiation. ► Cells from mice lacking necdin have increased adipogenic potential. ► Necdin may inhibit adipogenesis by interacting with Wnt signaling through Dkk3.
Keywords: Abbreviations; CM; conditioned medium; Dkk; Dickkopf; Irs; insulin receptor substrate; MAGE; melanoma antigen gene; MDI; isobutylmethylxanthine, dexamethasone, and insulin; MEFs; mouse embryonic fibroblasts; PWS; Prader–Willi syndromeGenetic obesity; Mouse embryonic fibroblast; Adipogenesis
The evolution of MHC diversity: Evidence of intralocus gene conversion and recombination in a single-locus system
by Angela Bahr; Anthony B. Wilson (pp. 52-57).
Gene conversion, the unidirectional exchange of genetic material between homologous sequences, is thought to strongly influence patterns of genetic diversity. The high diversity of major histocompatibility complex (MHC) genes in many species is thought to reflect a long history of gene conversion events both within and among loci. Theoretical work suggests that intra- and interlocus gene conversion leave characteristic signatures of nucleotide diversity, but empirical studies of MHC variation have rarely been able to analyze the effects of conversion events in isolation, due to the presence of multiple gene copies in most species. The potbellied seahorse ( Hippocampus abdominalis), a species with a single copy of the MH class II beta-chain gene (MHIIb), provides an ideal system in which to explore predictions on the effects of intralocus gene conversion on patterns of genetic diversity. The genetic diversity of the MHIIb peptide binding region (PBR) is high in the seahorse, similar to other vertebrate species. In contrast, the remainder of the gene shows a total absence of synonymous variation and low levels of intronic sequence diversity, concentrated in 3 short repetitive regions and 1–12 SNPs per intron. The distribution of substitutions across the gene results in a patchwork pattern of shared polymorphism between otherwise divergent sequences. The pattern of nucleotide diversity observed in the seahorse MHIIb gene is congruent with theoretical expectations for intralocus gene conversion, indicating that this evolutionary mechanism has played an important role in MHC gene evolution, contributing to both the high diversity in the PBR and the low diversity outside this region. Neutral variation at this locus may be further reduced due to biases in nucleotide composition and functional constraints.► Influence of intralocus gene conversion on the evolution of a single-locus MHC system. ► Full-length gDNA analysis: Extremely low levels of variability outside the PBR. ► Prominent signature of intralocus conversion with patchwork nucleotide variation. ► Skewed nucleotide composition in exons and introns: Impacts distribution of variation. ► Intralocus recombination alone can generate the patterns of variation typical of MHC.
Keywords: Abbreviations; MHC/MH; major histocompatibility (complex); MHIIb; major histocompatibility class II beta-chain; PBR; peptide binding region; PBS; peptide binding sitesGene conversion; Major histocompatibility complex; Molecular evolution; Hippocampus abdominalis
Calculating phenotypic similarity between genes using hierarchical structure data based on semantic similarity
by Shanzhen Zhang; Zhiqiang Chang; Zhenqi Li; Huizi DuanMu; Zihui Li; Kening Li; Yufeng Liu; Fujun Qiu; Yan Xu (pp. 58-65).
Phenotypic similarity is correlated with a number of measures of gene function, such as relatedness at the level of direct protein–protein interaction. The phenotypic effect of a deleted or mutated gene, which is one part of gene annotation, has caught broad attention. However, there have been few measures to study phenotypic similarity with the data from Human Phenotype Ontology (HPO) database, therefore more analogous measures should be developed and investigated. We used five semantic similarity-based measures (Jiang and Conrath, Lin, Schlicker, Yu and Wu) to calculate the human phenotypic similarity between genes (PSG) with data from HPO database, and evaluated their accuracy with information of protein–protein interaction, protein complex, protein family, gene function or DNA sequence. Compared with the gene pairs that were random selected, the results of these methods were statistically significant (all P<0.001). Furthermore, we assessed the performance of these five measures by receiver operating characteristic (ROC) curve analysis, and found that most of them performed better than the previous methods. This work had proved that these measures based on semantic similarity for calculation of PSG were effective for hierarchical structure data. Our study contributes to the development and optimization of novel algorithms of PSG calculation and provides more alternative methods to researchers as well as tools and directions for PSG study.► We calculated similarity between HPO terms based on semantic similarity. ► We evaluated the performance of five methods for calculating PSG. ► This work proved that these methods were effective for hierarchical structure data.
Keywords: Abbreviations; AUC; Area under Curve; CPco; Complex Proportion of co-occurrence; FN; False Negative; FP; False Positive; GO; Gene Ontology; GSN; Gold Standard Negative; GSP; Gold Standard Positive; HPO; Human Phenotype Ontology; IC; Information Content; IPco; Interaction Proportion of co-occurrence; JC; Jiang and Conrath; LR; Likelihood Ratios; MeSH; Medical Subject Headings; OMIM; Online Mendelian Inheritance in Man; Pco; Proportion of Co-occurrence; PSG; Phenotypic Similarity between Genes; ROC; Receiver Operating Characteristic; TN; True Negative; TP; True Positive; UMLS; Unified Medical Language SystemHereditary disease; Human phenotype; Gene similarity; Method evaluation
A 40-bp insertion/deletion polymorphism in the constitutive promoter of MDM2 confers risk for hepatocellular carcinoma in a Chinese population
by Dong Dong; Xueren Gao; Zhansheng Zhu; Qiang Yu; Shizhong Bian; Yuzhen Gao (pp. 66-70).
The pathogenesis of HCC is a multistage process with the involvement of genetic factors. The aim of the present study is to investigate the possible association between a 40-bp insertion/deletion polymorphism (indel) at constitutive promoter of MDM2 and risk of hepatocellular carcinoma (HCC) in a Chinese population. Using 420 HCC patients and 423 control subjects, we genotyped the indel polymorphism (rs3730485) using polymerase chain reaction method. Logistic regression was used to analyze the association between the polymorphism and HCC susceptibility. Under co-dominant model, we found that the ins/del and del/del genotype of indel was associated with a significantly increased risk of HCC compared with its homozygote ins/ins (OR=1.39, 95%C.I.=1.03–1.87; OR=1.68, 95%C.I.=1.03–2.73, respectively). Presence of 40-bp deletion allele of MDM2 seemed to confer higher risk for HCC when compared with non-carriers (OR=1.30, 95%C.I.=1.06–1.60, P=0.011). Further stratification analysis showed that this association was more pronounced in patients with a family history of HCC, early tumor stage and higher serum alpha-fetoprotein (AFP). These findings indicated that the MDM2 indel polymorphism may be a genetic modifier for developing HCC in Chinese population.►The 40-bp indel polymorphism within MDM2 is associated with the occurrence of HCC. ►The association is more pronounced in patients with early tumor stage. ►rs3730485 is associated with elevated serum AFP level (≥400μg/L) of HCC patients.
Keywords: Abbreviation; HCC; hepatocellular carcinoma; HBV; hepatitis B virus; HCV; hepatitis C virus; HDV; hepatitis D virus; HIV; Human immunodeficiency virus; AFP; alpha-fetoprotein; MDM2; murine double minute 2; SNP; single nucleotide polymorphism; Indel; insertion deletion polymorphism MDM2; Indel polymorphism; rs3730485; Hepatocellular carcinoma
Analysis of the role of p38 MAP kinase in epidermal growth factor-induced JB6 Cl41 cell transformation by cDNA array
by Zhiwei He; Ping Cui; Caiguo Ye; Wei-Ya Ma; Ann. Bode; Zigang Dong (pp. 71-78).
To further explore the mechanism of p38 MAP kinase in regulation of JB6 Cl41 cell transformation. cDNA array was employed to scan the differential expression genes between DN-p38 cells and CMV-neo JB6 Cl41 cells after EGF stimuli. We found that up-expression genes including oncogenes and tumor suppressor genes, p53-associated protein, transcription repressors, apoptosis-associated genes, and growth arrest and DNA damage-inducible protein 153 were detected in DN-p38 cells, but low expression in CMV-neo JB6 Cl41 cells after EGF treatment. Meanwhile, some proto-oncogenes, such as c-Myc, and signal transducer and activator of transcription 1 (STAT1) were lowly expressed in EGF-stimulated DN-p38 cells, but had relatively high expression level in CMV-neo JB6 Cl41 cells under the same stimuli. Four of the differential expression genes were further confirmed by quantitative RT-PCR analysis. Our results indicate that p38 MAP kinase is involved in EGF-induced JB6 Cl41 cell transformation through effecting on more genes expression levels including transcription factors, proto-oncogene, apoptosis-related genes and growth arrest genes.► We found that more genes and pathways are regulated by p38 MAP kinase. ► p38 MAP kinase plays a key role in the EGF-induced JB6 Cl41 cell transformation. ► p38 MAP kinase may be a target in cancer prevention. ► cDNA array is still a useful tool for finding new targets at transcription level.
Keywords: Abbreviation; p38 MAPK; p38 mitogen-activated protein kinase; DN; dominant negative; EGF; epidermal growth factor; STAT1; signal transducer and activator of transcription 1; ATF-2; activating transcription factor 2; ERK; extracellular signal-regulated kinase; JNK; c-Jun N-terminal kinase; PKB; protein kinase B; MEN; Eagle's minimal essential medium; BME; Basal Medium Eagle; FBS; Fetal bovine serum; RT-PCR; reverse transcription polymerase chain reaction.; PVDF; polyvinylidene difluoridep38 MAP kinase; Gene expression; Epidermal growth factor; Cell transformation
DAG1, no gene for RNA regulation?
by Andrea Brancaccio (pp. 79-82).
DAG1 encodes for a precursor protein that liberates the two subunits featured by the dystroglycan (DG) adhesion complex that are involved in an increasing number of cellular functions in a wide variety of cells and tissues. Aside from the proteolytic events producing the α and β subunits, especially the former undergoes extensive “post-production” modifications taking place within the ER/Golgi where its core protein is both N- and O-decorated with sugars. These post-translational events, that are mainly orchestrated by a plethora of certified, or putative, glycosyltransferases, prelude to the excocytosis-mediated trafficking and targeting of the DG complex to the plasma membrane. Extensive genetic and biochemical evidences have been accumulated so far on α-DG glycosylation, while little is know on possible regulatory events underlying the chromatine activation, transcription or post-transcription (splicing and escape from the nucleus) of DAG1 or of its mRNA. A scenario is envisaged in which cells would use a sort of preferential, and scarcely regulated, route for DAG1 activation, that would imply fast mRNA transcription, maturation and export to the cytosol, and would prelude to the multiple time-consuming enzymatic post-translational activities needed for its glycosylation. Such a provocative view might be helpful to trigger future work aiming at disclosing the complete molecular mechanisms underlying DAG1 activation and at improving our knowledge of any pre-translational step that is involved in dystroglycan regulation.
Keywords: Dystroglycan; Large introns; Transcription; Splicing; Nucleus Escape; Post-translational modifications
Does the growth temperature of a prokaryote influence the purine content of its mRNAs?
by Kiran Narasinha Mahale; Vivek Kempraj; Debjani Dasgupta (pp. 83-89).
The formation and breaking of hydrogen bonds between nucleic acid bases are dependent on temperature. The high G+C content of organisms was surmised to be an adaptation for high temperature survival because of the thermal stability of G:C pairs. However, a survey of genomic GC% and optimum growth temperature (OGT) of several prokaryotes revoked any direct relation between them. Significantly high purine (R=A or G) content in mRNAs is also seen as a selective response for survival among thermophiles. Nevertheless, the biological relevance of thermophiles loading their unstable mRNAs with excess purines (purine-loading or R-loading) is not persuasive. Here, we analysed the mRNA sequences from the genomes of 168 prokaryotes (as obtained from NCBI Genome database) with their OGTs ranging from −5°C to 100°C to verify the relation between R-loading and OGT. Our analysis fails to demonstrate any correlation between R-loading of the mRNA pool and OGT of a prokaryote. The percentage of purine-loaded mRNAs in prokaryotes is found to be in a rough negative correlation with the genomic GC% ( r2=0.655, slope=−1.478, P<000.1). We conclude that genomic GC% and bias against certain combinations of nucleotides drive the mRNA-synonymous (sense) strands of DNA towards variations in R-loading.► An updated analysis of 168 prokaryotic mRNA pools for purine-loading. ► No correlation between purine-loading and OGT of prokaryotes. ► Dataset of 53 mesophiles (OGT=37°C) show nearly all patterns of purine-loading. ► Genomic GC% in a negative correlation with the percentage of purine-loaded mRNAs. ► GC%, YY dimers and G-rich tracts drive mRNAs towards variations in R-loading.
Keywords: Abbreviations; R; purines = adenine (A) or guanine (G); Y; pyrimidines = cytosine (C) or thymine (T); GC%; percentage of guanine and cytosine in a nucleic acid; OGT; optimum growth temperature; R-loading; purine loading; Y-loading; pyrimidine loading; YY dimer; pyrimidine dimer; TT dimer; thymine dimerPurine loading; Szybalski; Optimum growth temperature; GC%; Chargaff; Thermophiles
A large deletion causes apparent homozygosity for the D1152H mutation in the cystic fibrosis transmembrane regulator ( CFTR) gene
by Anna Diana; Riccardina Tesse; Angela M. Polizzi; Teresa Santostasi; Antonio Manca; Giuseppina Leonetti; Manuela Seia; Luigi Porcaro; Luciano Cavallo (pp. 90-92).
We report the case of a patient with an apparent homozygosity for the D1152H mutation located in exon 18 of the cystic fibrosis transmembrane conductance regulator ( CFTR) gene. The parents had no personal history of cystic fibrosis (CF) and referred to our laboratory after the diagnosis of fetal bowel hyperechogenicity. The proband presented with meconium ileus and normal sweat chloride test. Sequencing of the CFTR exon 18 together with quantitative genomic assays, such as real-time PCR and the multiplex ligation probe amplification (MLPA) techniques, were performed and revealed that the father was heterozygous for the D1152H mutation and the mother carried a large deletion of the CFTR gene encompassing the genomic sequence including the same mutation. The child inherited D1152H from his father and the large deletion of the CFTR gene from his mother. We suggest that D1152H likely acts as a mild mutation with a dominant effect on the severe deletion of exon 18, considering that after 3years of clinical examinations the child shows no classical signs and symptoms of CF. Not testing for large deletions in subjects with apparent homozygosity for a mutated CFTR allele could lead to the misidentification of CFTR mutation carrier status.► Association between fetal bowel hyperechogenicity and cystic fibrosis. ► Variable phenotype in patient bearing the D1152H in exon 18 of CFTR gene. ► Importance of investigation for large deletion in unknown alleles of CFTR gene.
Keywords: Abbreviations; CF; cystic fibrosis; CFTR; cystic fibrosis transmembrane conductance regulator; MI; meconium ileus; PI; pancreatic insufficiency; UPD7; uniparental disomy for chromosome 7; RDB; reverse dot blot; DGGE; denaturing gradient gel electrophoresis; PCR; polymerase chain reaction; MLPA; multiplex ligation probe amplification; CBAVD; congenital bilateral absence of vas deferens; DHPLC; denaturing high-performance liquid chromatographyCFTR; Cystic fibrosis; Homozygosis; Large deletion; Phenotype
Association between C3orf21, TP63 polymorphisms and environment and NSCLC in never-smoking Chinese population
by Yongjun Zhang; Cuiping Gu; Hua Shi; Aiqin Zhang; Xiangming Kong; Wenlong Bao; Dehou Deng; Lili Ren; Danlin Gu (pp. 93-97).
Recently, two genome-wide association studies in Asia identified gene polymorphisms known as rs4488809, rs9816619 in TP63 and rs2131877, rs952481 in C3orf21. It has been proposed that these polymorphisms are susceptibility loci for non-small cell lung cancer (NSCLC) development among Japanese and Korean populations. We ask whether susceptibility to NSCLC is limited to the Chinese population or whether the environment also affects genetic polymorphisms. We conducted a matched case–control study to explore this question. Results show that polymorphism of TP63 was not associated with NSCLC development, whereas variant genotypes of C3orf21 were nominally associated with a reduced risk of lung adenocarcinoma (OR=0.619, 95% CI=0.390–0.976). These results strongly suggest that environmental agents interact with human genetic polymorphism independent of ethnic background. In addition, the C3orf21 gene may be a potential susceptibility marker for lung adenocarcinoma independent of ethnic background and environmental agents.► TP63 was not associated with NSCLC risk in never-smoking Chinese. ► C3orf21 was susceptibility gene for lung adenocarcinoma in never-smoking Chinese. ► Environmental agents affect genetic polymorphism.
Keywords: Abbreviations; C3rof21; chromosome 3 open reading frame 21; CYP1A1; cytochrome P450, family 1, subfamily A, polypeptide 1; EGFR; epidermal growth factor receptor; HWE; Hardy–Weinberg equilibrium; NSCLC; non-small cell lung cancer; SNP; single nucleotidepolymorphism; TP63; tumor protein p63; VEGFR; vascular endothelial growth factor receptorC3orf21; Chinese; Environment; Genetic polymorphism; Non-small cell lung cancer; TP63
Polymorphisms of the insulin-like growth factor-binding protein 3 gene ( IGFBP3) in gayal ( Bos frontalis)
by Dongmei Xi; Min Wu; Yueyuan Fan; Qing Liu; Jing Leng; Xiao Gou; Huaming Mao; Weidong Deng (pp. 98-102).
The gene coding for insulin-like growth factor-binding protein 3 (IGFBP3) is important for regulation of growth, development and metabolism in mammals. The present investigation was conducted to study nucleotide polymorphism of the IGFBP3 in gayal ( Bos frontalis) and to compare the variations with those which occur in other ruminants. A fragment of 645 base pairs of the IGFBP3 covering a part of exon 2, the complete intron 2 and exon 3 and a part of intron 3 was amplified, sequenced (n=46) and digested (n=79) with HaeIII restriction enzyme from 125 collected gayal samples. Nine single nucleotide polymorphisms (SNPs) [C14T, A122C, C137T, G144C, C155T, G213A, C279A, G334A and G460A] were identified and located in intron 2, revealing high genetic variability. The alignment of nucleotide sequences was found to be very similar to those for other bovid species. Sequencing and HaeIII digestion showed that frequency of alleles C and A [consisting of fragments of sizes 56, 64, 228, 264, 282, 298 and 497bp (CC genotype)] was 0.96 and 0.04 for the SNP C279A. Moreover, the genotype frequency of the SNP C279A in gayal was compared with that in other ruminants and it appears that this polymorphism may be associated with low fat content and rapid growth in this rare species.► We firstly have cloned the IGFBP3 gene from rare gayal ( Bos frontalis). ► The gayal IGFBP3 gene has high genetic variability. ► The gayal SNP C279A may be associated with their low fat content and rapid growth.
Keywords: Abbreviations; He; gene heterozygosity; Ho; gene homozygosity; H–W; Hardy–Weinberg; IGFBP3; insulin-like growth factor-binding protein 3 gene; Ne; effective allele numbers; PCR; polymerase chain reaction; PIC; polymorphism information content; RFLP; restriction fragment length polymorphism; SNPs; single nucleotide polymorphisms.Gayal (; Bos frontalis; ); Insulin-like growth factor-binding protein 3; gene (; IGFBP3; ); Polymorphisms
Comparative analysis of the structural and expressional parameters of microRNA target genes
by Young-Joon Mok; Seung Gu Park; Sun Shim Choi (pp. 103-109).
MicroRNAs (miRNAs) generally pair with the 3′UTRs of their target mRNAs to repress gene expression. It has reported that miRNA targets (TGs) are longer and evolve more slowly than non-targets (NTGs). We confirmed the observation and also found novel structural and expressional characteristics of TGs. The length difference between TGs and NTGs was greatest for the 3′UTRs, although a difference was also observed for CDSs and introns. Widely expressed genes were shorter for both TGs and NTGs; however, TGs were significantly longer than NTGs in all ranges of expression. TGs were more likely than NTGs to be widely expressed, which might explain why TGs evolve more slowly than NTGs. Finally, we found that TG mRNAs have faster decay rates. In addition, the decay rate of a TG mRNA transcript was found to be positively correlated with the number or density of target sites located in that TG's mRNA transcript.► The size difference between TGs and NTGs is greatest for the 3′UTRs. ► TGs are significantly longer than NTGs in all ranges of expression. ► TGs are more likely than NTGs to be widely expressed. ► TG mRNAs have faster decay rates. ► The decay rate of a TG mRNA is positively correlated with the number or density of target sites.
Keywords: Abbreviations; TG; microRNA target gene; NTG; microRNA non-target gene; pTG; predicted microRNA target gene; pNTG; predicted microRNA non-target gene; rTG; real microRNA target gene; prTG; predicted microRNA target gene plus real microRNA target gene; FGA; fixed group analysismiRNA targets; miRNA nontargets; Structural parameters; Expressional parameters; Comparative analysis; Evolutionary charateristics
Somatic mosaicism in two unrelated patients with X-linked chronic granulomatous disease characterized by the presence of a small population of normal cells
by Masafumi Yamada; Yuka Okura; Yasuto Suzuki; Shinobu Fukumura; Toru Miyazaki; Hisami Ikeda; Shun-Ichiro Takezaki; Nobuaki Kawamura; Ichiro Kobayashi; Tadashi Ariga (pp. 110-115).
X-linked chronic granulomatous disease (X-CGD) is a primary immunodeficiency disease of phagocytes caused by mutations in the cytochrome b 558 β ( CYBB) gene. We, for the first time, detected somatic mosaicism in two unrelated male patients with X-CGD caused by de novo nonsense mutations (p.Gly223X and p.Glu462X) in the CYBB gene. In each patient, a small subset of granulocytes was normal in terms of respiratory burst (ROB) activity, gp91phox expression, and CYBB sequences. Cells with wild-type CYBB sequence were also detected in buccal swab specimens and in peripheral blood mononuclear cells. The normal cells were shown to be of the patient origin by fluorescent in situ hybridization analysis of X/Y chromosomes, and by HLA DNA typing. Two possible mechanisms for this somatic mosaicism were considered. The first is that the de novo disease-causing mutations in CYBB occurred at an early multicellular stage of embryogenesis with subsequent expansion of the mutated cells, leaving some unmutated cells surviving. The second possibility is that the de novo mutations occurred in oocytes which was followed by reversion of the mutations in a small subset of cells in early embryogenesis.► We, for the first time, report somatic mosaicism in two male patients with X-CGD. ► Cells with normal DNA sequence also had normal gp91phox expression and ROB activity. ► Cells with normal DNA sequence were also present in buccal swab specimens and PBMC. ► FISH and HLA DNA typing studies indicate these cells are of the patient origin. ► De novo mutations or reversion of mutations during embryogenesis may have occurred.
Keywords: Abbreviations; X-CGD; X-linked chronic granulomatous disease; CYBB; cytochrome b; 558; β; ROB; respiratory burst; PBMC; peripheral blood mononuclear cells; PID; primary immunodeficiency disease; EBV-LCLs; EBV-transformed lymphoblastoid cell linesX-linked chronic granulomatous disease (X-CGD); Cytochrome b; 558; β; (; CYBB; ); Somatic mosaicism; De novo; mutation; Reversion
Genomic characteristics comparisons of 12 food-related filamentous fungi in tRNA gene set, codon usage and amino acid composition
by Wanping Chen; Ting Xie; Yanchun Shao; Fusheng Chen (pp. 116-124).
Filamentous fungi are widely exploited in food industry due to their abilities to secrete large amounts of enzymes and metabolites. The recent availability of fungal genome sequences has provided an opportunity to explore the genomic characteristics of these food-related filamentous fungi. In this paper, we selected 12 representative filamentous fungi in the areas of food processing and safety, which were Aspergillus clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, A. terreus, Monascus ruber, Neurospora crassa, Penicillium chrysogenum, Rhizopus oryzae and Trichoderma reesei, and did the comparative studies of their genomic characteristics of tRNA gene distribution, codon usage pattern and amino acid composition. The results showed that the copy numbers greatly differed among isoaccepting tRNA genes and the distribution seemed to be related with translation process. The results also revealed that genome compositional variation probably constrained the base choice at the third codon, and affected the overall amino acid composition but seemed to have little effect on the integrated physicochemical characteristics of overall amino acids. The further analysis suggested that the wobble pairing and base modification were the important mechanisms in codon–anticodon interaction. In the scope of authors' knowledge, it is the first report about the genomic characteristics analysis of food-related filamentous fungi, which would be informative for the analysis of filamentous fungal genome evolution and their practical application in food industry.► Genomic characteristics of 12 food-related filamentous fungi were investigated. ► tRNA gene distribution seemed to be related with translation process. ► Codon usage pattern and amino acid composition were affected by GC content. ► tRNA gene set, codon usage and amino acid composition showed close correlations.
Keywords: Abbreviations; A; adenosine; C; cytidine; G; guanosine; RSCU; Relative synonymous codon usage; T; thymidine; tRNA; transfer RNA; U; uridineFilamentous fungi; Food; tRNA gene; Codon usage; Amino acid composition
Isolation and molecular characterisation of flavonoid 3′-hydroxylase and flavonoid 3′, 5′-hydroxylase genes from a traditional Chinese medicinal plant, Epimedium sagittatum
by Wenjun Huang; Wei Sun; Ying Wang (pp. 125-130).
The epimedii herb, a traditional Chinese medicinal plant, has significant pharmacological effects on human health. The bioactive components in the herb ( Epimedium sagittatum (Sieb. et Zucc.) Maxim) are mainly prenylated flavonol glycosides, which are end-products of the flavonoid biosynthetic pathway. This has not been clearly elucidated until recently. The genes encoding flavonoid 3′-hydroxylase ( F3′H) and flavonoid 3′, 5′-hydroxylase ( F3′5′H) involved in the flavonoid biosynthetic pathway, designated as EsF3′H and EsF3′5′H, were isolated from E. sagittatum using a homology-based cloning method and deposited in the GenBank databases (GenBank ID: HM011054 and HM011055), respectively. EsF3′H and EsF3′5′H proteins shared high homology with other plant-specific flavonoid hydroxylases and were clustered into the CYP75B and CYP75A group, respectively. In addition, four conserved cytochrome P450-featured motifs were found in the amino acid sequences of both genes. Transcription levels of both genes were detected in all tissues tested and were high in most of the pigmented tissues. Moreover, the expression levels of both EsF3′H and EsF3′5′H correlated positively with the anthocyanin accumulation pattern in leaves from E. sagittatum. The cloning and molecular characterisation of EsF3′H and EsF3′5′H genes will accelerate progress in the study of the flavonoid biosynthetic pathway to elucidate the molecular mechanisms of the biosynthesis of the bioactive components in E. sagittatum. ► F3′H and F3′5′H genes from Epimedium sagittatum are isolated. ► EsF3′H and EsF3′5′H show high homology with other flavonoid hydroxylases proteins. ► EsF3′H and EsF3′5′H are indicated the CYP75B and CYP75A family, respectively. ► EsF3′H and EsF3′5′H are highly expressed in the pigmented tissues. ► The expression levels of both correlate with the anthocyanin accumulation pattern.
Keywords: Abbreviations; CTAB; cetyl trimethyl ammonium bromide; CYP; cytochrome P450; RACE; rapid amplification of cDNA ends; qRT-PCR; quantitative reverse transcription-polymerase chain reaction; F3′H; flavonoid 3′-hydroxylase; F3′5′H; flavonoid 3′,5′-hydroxylase; FLS; flavonol synthase; DFR; dihydroflavonol 4-reductaseAnthocyanin; CYP75; Epimedium; Flavonoid biosynthesis