Diagnostic utility of DREAM gene mRNA levels in thyroid tumours

ABSTRACT Objective The transcriptional repressor DREAM is involved in thyroid-specific gene expression, thyroid enlargement and nodular development, but its clinical utility is still uncertain. In this study we aimed to investigate whether DREAM mRNA levels differ in different thyroid tumors and how this possible difference would allow the use of DREAM gene expression as molecular marker for diagnostic and/or prognosis purpose. Materials and methods We quantified DREAM gene mRNA levels and investigated its mutational status, relating its expression and genetic changes to diagnostic and prognostic features of 200 thyroid tumors, being 101 malignant [99 papillary thyroid carcinomas (PTC) and 2 anaplastic thyroid carcinomas] and 99 benign thyroid lesions [49 goiter and 50 follicular adenomas (FA)]. Results Levels of mRNA of DREAM gene were higher in benign (0.7909 ± 0.6274 AU) than in malignant (0.3373 ± 0.6274 AU) thyroid lesions (p < 0.0001). DREAM gene expression was able to identify malignancy with 66.7% sensitivity, 85.4% specificity, 84.2% positive predictive value (PPV), 68.7% negative predictive value (NPV), and 75.3% accuracy. DREAM mRNA levels were also useful distinguishing the follicular lesions FA and FVPTC with 70.2% sensitivity, 73.5% specificity, 78.5% PPV, 64.1% NPV, and 71.6% accuracy. However, DREAM gene expression was neither associated with clinical features of tumor aggressiveness, nor with recurrence or survival. Six different genetic changes in non-coding regions of DREAM gene were also found, not related to DREAM gene expression or tumor features. Conclusion We suggest that DREAM gene expression may help diagnose thyroid nodules, identifying malignancy and characterizing follicular-patterned thyroid lesions; however, it is not useful as a prognostic marker.

Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models / 癌症

By altering the electrostatic charge of histones or providing binding sites to protein recognition molecules, Chromatin marks have been proposed to regulate gene expression, a property that has motivated researchers to link these marks to cis-regulatory elements. With the help of next generation sequencing technologies, we can now correlate one specific chromatin mark with regulatory elements (e.g. enhancers or promoters) and also build tools, such as hidden Markov models, to gain insight into mark combinations. However, hidden Markov models have limitation for their character of generative models and assume that a current observation depends only on a current hidden state in the chain. Here, we employed two graphical probabilistic models, namely the linear conditional random field model and multivariate hidden Markov model, to mark gene regions with different states based on recurrent and spatially coherent character of these eight marks. Both models revealed chromatin states that may correspond to enhancers and promoters, transcribed regions, transcriptional elongation, and low-signal regions. We also found that the linear conditional random field model was more effective than the hidden Markov model in recognizing regulatory elements, such as promoter-, enhancer-, and transcriptional elongation-associated regions, which gives us a better choice.

In silico genome-wide screening for TnrA-regulated genes of Bacillus clausii

Bacillus clausii TnrA transcription factor is required for global nitrogen regulation. In order to obtain an overview of gene regulation by TnrA in B. clausii KSM-K16, the entire genome of B. clausii was screened for the consensus sequence, 5'-TGTNAN7TNACA-3' known as the TnrA box, and 13 transcription units were found containing a putative TnrA box. The TnrA targets identified in this study were tnrA, glnA, nrgA, nasFDEB, puc genes, licT, the two operons of the oligopeptide ABC transporter, lytR, transcriptional regulator of the Lrp/AsnC family, sodium-dependent transporter of SNF family, hyu genes and a biochemically uncharacterized protein

Relationship between Sp3 and the transcriptional regulation of enamelin gene / 中华口腔医学杂志

<p><b>OBJECTIVE</b>To investigate the role of Sp3 in the transcriptional regulation of enamelin gene.</p><p><b>METHODS</b>By bioinformatic analysis, a putative responsive element for Sp3 was identified. Electrophoretic mobility shift assay was used to examine the interaction between Sp3 and enamelin. 5'-flanking regulatory region of enamelin was cloned and ligated into pGL3-basic luciferase vector. Sp3 and the Enam-luc were cotransfected into mouse ameloblast-like cell line, and the activity of luciferase was examined.</p><p><b>RESULTS</b>The results showed that Sp3 could not directly bind to the enamelin regulation region and activate enamelin transcription.</p><p><b>CONCLUSIONS</b>Sp3 might not be involved in transcriptional regulation of enamelin gene via an indirect interaction.</p>

Influence of the polymorphisms of the alpha-major regulatory element HS-40 on in vitro gene expression

The α-MRE is the major regulatory element responsible for the expression of human α-like globin genes. It is genetically polymorphic, and six different haplotypes, named A to F, have been identified in some population groups from Europe, Africa and Asia and in native Indians from two Brazilian Indian tribes. Most of the mutations that constitute the α-MRE haplotypes are located in flanking sequences of binding sites for nuclear factors. To our knowledge, there are no experimental studies evaluating whether such variability may influence the α-MRE enhancer activity. We analyzed and compared the expression of luciferase of nine constructs containing different α-MRE elements as enhancers. Genomic DNA samples from controls with A (wild-type α-MRE) and B haplotypes were used to generate C-F haplotypes by site-directed mutagenesis. In addition, three other elements containing only the G→A polymorphism at positions +130, +199, and +209, separately, were also tested. The different α-MRE elements were amplified and cloned into a plasmid containing the luciferase reporter gene and the SV40 promoter and used to transiently transfect K562 cells. A noticeable reduction in luciferase expression was observed with all constructs compared with the A haplotype. The greatest reductions occurred with the F haplotype (+96, C→A) and the isolated polymorphism +209, both located near the SP1 protein-binding sites believed not to be active in vivo. These are the first analyses of α-MRE polymorphisms on gene expression and demonstrate that these single nucleotide polymorphisms, although outside the binding sites for nuclear factors, are able to influence in vitro gene expression.

Bioinformatics scan of factors with inhibitory effect on lrp16 gene expression / 中国实验血液学杂志

The main purpose of the this study was to find the candidate cis-elements in negative regulation region throngh analysing the DNA sequences of lrp16 gene promoter so as to provide the experimental basis for screening drugs with inhibitory effect on lrp16 gene expression. The open reading frame (ORF) sequences in uncoding DNA and mRNA sequences of 5' flanking region in lrp16 gene were cloned by the data in GeneBank and Internet; the possibly existing cis-element in thsi region was searched in databank of human transcriptional factor by using TESS and Genomax online promoter analysis software; the drugs related to inhibition of lrp16 gene expression were screened by using SAGE and GEO databank. The results showed that there were many cis-elements in the negative regulation region, including T-Ag, PU.1, c-Ets, XPF-1, P2 alphaA, IL6-6RE and RAR. In cultured cell lines, hormone or its inhibitor such as corticosteroid, tamoxifen, forskolin, phenylephrine, inflammatory factors such as IFNgamma and TNFalpha, and chemotherapeutics 5-fluorouracil could down-regulate the lrp16 gene expression as compared with absent ones. It is concluded that cis-elements including T-Ag, PU.1, c-Ets, XPF-1, P2 alphaA, IL6-6RE and RAR may inhibit lrp16 expression and hormone or its inhibitor such as corticosteroid, tamoxifen, forskolin, phenylephrine, inflammatory factors such as IL6, IFNgamma and TNFalpha, and chemotherapeutics 5-fluorouracil may participate in the regulation of lrp16 gene expression in negative manner.

Progress of researches on liver-specific transcriptional regulatory sequence / 生物医学工程学杂志

Gene therapy is a fast developing therapeutics in recent years. Now, the point at issue that restricts the development of gene therapy is the safety and effectivity of gene expression in space, time series and location. Tissular or cellular specific transcriptional regulatory element can make precise and effective expression of exogenous gene in specified tissue and cell, thus increasing the safety and effectivity of gene expression. This has been a hot spot in gene therapy. Now, researches indicate that hepatic tissue has liver-specific transcriptional regulatory sequence. The regulatory sequences can promote gene expression only in hepatic tissue; they are widely used in transgenic animal and gene therapy. They can serve as a basis for the researches in the pathogenic mechanism and gene therapy of liver-related diseases. New achievements in the studies on liver-specific transcriptional regulatory sequence are reviewed in this article.

Parsing regulatory DNA: general tasks, techniques, and the PhyloGibbs approach.

In this review, we discuss the general problem of understanding transcriptional regulation from DNA sequence and prior information. The main tasks we discuss are predicting local regions of DNA, cis-regulatory modules (CRMs) that contain binding sites for transcription factors (TFs), and predicting individual binding sites. We review various existing methods, and then describe the approach taken by PhyloGibbs, a recent motif-finding algorithm that we developed to predict TF binding sites, and PhyloGibbs-MP, an extension to PhyloGibbs that tackles other tasks in regulatory genomics, particularly prediction of CRMs.

Effect of alpha-synuclein on the promoter activity of tyrosine hydroxylase gene / 神经科学通报·英文版

<p><b>OBJECTIVE</b>To approach the associated mechanism by which alpha-synuclein (alpha-Syn) might regulate the metabolism of dopamine.</p><p><b>METHODS</b>A DNA fragment, located at -495 to +25 of the human tyrosine hydroxylase (TH) gene, was amplified by PCR and inserted into the pGL(3)-Basic luciferase reporter vector. The recombinant plasmid pGL(3)-THprom was transfected into a dopaminergic cell line MES23.5 or a alpha-Syn over-expressed MES23.5 (named MES23.5/halpha-Syn(+)). The promoter activity was detected by the Dual Luciferase Assay System.</p><p><b>RESULTS</b>The luciferase activities in the MES23.5 cells transfected with pGL(3)-Basic, pGL(3)-THprom, and pGL(3)-Control vectors were 5.60+/-0.67, 26.80+/-4.11, and 32.90+/-4.75, respectively. On the other hand, the luciferase activity of pGL(3)-THprom in the MES23.5 (26.80+/-4.11) was significantly higher than that in the MES23.5/halpha-Syn(+) (14.40+/-0.61) (P<0.01).</p><p><b>CONCLUSION</b>These results indicate that the - 495 to +25 region in the TH gene possesses promoter activity for controlling the gene expression, and that alpha-Syn may negatively regulate the metabolism of dopamine by affecting the function of TH promoter as a trans-acting factor.</p>

Comparative analysis of regulatory motif discovery tools for transcription factor binding sites / 基因组蛋白质组与生物信息学报·英文版

In the post-genomic era, identification of specific regulatory motifs or transcription factor binding sites (TFBSs) in non-coding DNA sequences, which is essential to elucidate transcriptional regulatory networks, has emerged as an obstacle that frustrates many researchers. Consequently, numerous motif discovery tools and correlated databases have been applied to solving this problem. However, these existing methods, based on different computational algorithms, show diverse motif prediction efficiency in non-coding DNA sequences. Therefore, understanding the similarities and differences of computational algorithms and enriching the motif discovery literatures are important for users to choose the most appropriate one among the online available tools. Moreover, there still lacks credible criterion to assess motif discovery tools and instructions for researchers to choose the best according to their own projects. Thus integration of the related resources might be a good approach to improve accuracy of the application. Recent studies integrate regulatory motif discovery tools with experimental methods to offer a complementary approach for researchers, and also provide a much-needed model for current researches on transcriptional regulatory networks. Here we present a comparative analysis of regulatory motif discovery tools for TFBSs.

Cloning and sequence analysis of the Antheraea pernyi nucleopolyhedrovirus gp64 gene.

Frequent outbreaks of the purulence disease of Chinese oak silkworm are reported in Middle and Northeast China. The disease is produced by the pathogen Antheraea pernyi nucleopolyhedrovirus (AnpeNPV). To obtain molecular information of the virus, the polyhedra of AnpeNPV were purified and characterized. The genomic DNA of AnpeNPV was extracted and digested with HindIII. The genome size of AnpeNPV is estimated at 128 kb. Based on the analysis of DNA fragments digested with HindIII, 23 fragments were bigger than 564 bp. A genomic library was generated using HindIII and the positive clones were sequenced and analysed. The gp64 gene, encoding the baculovirus envelope protein GP64, was found in an insert. The nucleotide sequence analysis indicated that the AnpeNPV gp64 gene consists of a 1,530 nucleotide open reading frame (ORF), encoding a protein of 509 amino acids. Of the eight gp64 homologues, the AnpeNPV gp64 ORF shared the most sequence similarity with the gp64 gene of Anticarsia gemmatalis NPV, but not Bombyx mori NPV. The upstream region of the AnpeNPV gp64 ORF encoded the conserved transcriptional elements for early and late stage of the viral infection cycle. These results indicated that AnpeNPV belongs to group I NPV and was far removed in molecular phylogeny from the BmNPV.

Mapping of regulatory domain of T-protein from Escherichia coli / 浙江大学学报·医学版

<p><b>OBJECTIVE</b>To map the regulatory domain of Escherichia coli T-protein.</p><p><b>METHODS</b>Fragmentation cloning was employed in cloning of 11 fragments from T-protein. The regulatory activity of each fragment was determined respectively.</p><p><b>RESULTS</b>The regulatory domain of T-protein was located in the C-terminal 270 amino acids, which was the same location as PDH domain.</p><p><b>CONCLUSION</b>T-protein has no independent regulatory domain.</p>

Effects of Mycobacterium tuberculosis infection on the transcriptional expression of human macrophage gene encoding ion channels and related regulatory elements / 生理学报

Expression microarray was employed in this study to investigate whether the ion channels and their regulatory elements encoding genes participate in the immune response to Mycobacterium tuberculosis infection. The results of a virulent strain were compared with those of the clinically isolated strains. The data demonstrate that K(+), Na(+), Ca(2+) and Cl(-) channels and their regulatory elements, such as the G protein, receptor and second messenger, protein kinase and protein phosphatase were involved in the immune reaction. The clinical strain affected more types of ion channels and respective regulatory elements. The data provides clues for further scrutiny into the role of ion channels and related elements in the interaction between Mycobacterium tuberculosis and host macrophage.