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.
Binding Sites ; Chromatin ; genetics ; Enhancer Elements, Genetic ; Epigenomics ; Histones ; genetics ; Humans ; Markov Chains ; Models, Genetic ; Models, Statistical ; Promoter Regions, Genetic ; Regulatory Elements, Transcriptional

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.
Gene Expression Regulation ; Humans ; Ion Channels ; genetics ; Macrophages ; immunology ; microbiology ; Mycobacterium tuberculosis ; pathogenicity ; Regulatory Elements, Transcriptional ; Tuberculosis ; genetics ; immunology ; microbiology

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.
Cell Line ; Computational Biology ; Gene Expression Regulation ; Humans ; Neoplasm Proteins ; drug effects ; genetics ; Open Reading Frames ; Regulatory Elements, Transcriptional

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.
Gene Expression ; Gene Expression Regulation ; Gene Regulatory Networks ; Genetic Therapy ; Humans ; Liver ; metabolism ; Oligonucleotide Array Sequence Analysis ; methods ; Regulatory Elements, Transcriptional ; genetics ; Transcription Factors ; metabolism ; Transcription, Genetic

OBJECTIVETo approach the associated mechanism by which alpha-synuclein (alpha-Syn) might regulate the metabolism of dopamine.

METHODSA 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.

RESULTSThe 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).

CONCLUSIONThese 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.

Animals ; Cell Line, Tumor ; Dopamine ; biosynthesis ; Down-Regulation ; genetics ; Gene Expression Regulation, Enzymologic ; genetics ; Genes, Reporter ; genetics ; Genetic Vectors ; genetics ; Hybridomas ; Luciferases ; genetics ; Mice ; Neurons ; metabolism ; Parkinson Disease ; genetics ; metabolism ; physiopathology ; Promoter Regions, Genetic ; genetics ; Rats ; Regulatory Elements, Transcriptional ; genetics ; Substantia Nigra ; metabolism ; physiopathology ; Transfection ; Tyrosine 3-Monooxygenase ; genetics ; alpha-Synuclein ; genetics

OBJECTIVETo map the regulatory domain of Escherichia coli T-protein.

METHODSFragmentation cloning was employed in cloning of 11 fragments from T-protein. The regulatory activity of each fragment was determined respectively.

RESULTSThe regulatory domain of T-protein was located in the C-terminal 270 amino acids, which was the same location as PDH domain.

CONCLUSIONT-protein has no independent regulatory domain.

Cloning, Molecular ; Deoxyribonucleases, Type I Site-Specific ; analysis ; chemistry ; genetics ; Escherichia coli Proteins ; analysis ; chemistry ; genetics ; Nucleic Acid Conformation ; Peptide Fragments ; chemistry ; genetics ; Protein Binding ; genetics ; Regulatory Elements, Transcriptional ; genetics

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.
Algorithms ; Amino Acid Motifs ; Base Sequence ; Binding Sites ; Computational Biology ; Internet ; Molecular Sequence Data ; Protein Binding ; Regulatory Elements, Transcriptional ; genetics ; Sequence Analysis, DNA ; methods ; Sequence Homology, Nucleic Acid ; Transcription Factors ; metabolism

Using overlapping and mutant oligonucleotides as probes, gel mobility assays and competition experiments identified a sequence from -47 to -32 bp upstream of the LIM2 CAP site, which a lens protein complex bound with high affinity which appeared to bind only to the "sense" strand of the double-stranded DNA molecule. This sequence consisted of a string of four guanine residues followed by seven other nucleotides (AACCTAA) and followed by another four guanines, i.e. GGGGAACCTAAGGGG, called the Hsu element. Promoter-CAT constructs containing this sequence or mutations of the sequence indicated that the Hsu element is located within the basal promoter, and is essential for expression of the LIM2 gene. The trans factors binding to the Hsu element are present throughout development, and appear to be lens-specific. Since the LIM2 gene promoter does not contain a classic TATA box, the Hsu element may serve as the site for binding the RNA polymerase complex.
Base Sequence ; Eye Proteins ; genetics ; Humans ; Membrane Proteins ; Molecular Sequence Data ; Promoter Regions, Genetic ; TATA Box

BACKGROUND: Rosacea is a chronic inflammatory disease characterized by centrofacial erythema. Excess cathelicidin is suggested to be important to the pathophysiology of the disease. Recently, presence of a vitamin D response element was revealed in the cathelicidin gene promoter. OBJECTIVE: The aim of this study was to determine whether vitamin D and cathelicidin are associated with rosacea, both serologically and histopathologically. METHODS: Subjects with rosacea and without chronic skin disorders were enrolled in the patient and control groups, respectively. Serum 25-hydroxy-vitamin D and cathelicidin levels were measured. Tissue expression of cathelicidin and vitamin D receptor were measured with immunostaining-intensity-distribution index. RESULTS: The mean serum 25-hydroxyvitamin D level of patients with rosacea was 12.18±5.65 ng/ml, which is lower than that of the controls (17.41±6.75 ng/ml). Mean serum cathelicidin levels in patients with rosacea and the controls were 85.0±26.1 ng/ml and 55.0±23.3 ng/ml, respectively. Cathelicidin expression in rosacea tissue was significantly higher than that in control tissue (5.21 vs. 4.03). No significant difference was observed in vitamin D receptor expression. CONCLUSION: Higher cathelicidin expression in rosacea supports the hypothesis that an abnormal inflammatory response of the innate immune system is important in pathogenesis of rosacea, but the role of high cathelicidin serum levels is complicated. Serum vitamin D was lower in patients with rosacea, although serum cathelicidin was higher than that of the controls. This suggests that the role of vitamin D level in the pathogenesis of rosacea merits further investigation.
Erythema ; Humans ; Immune System ; Receptors, Calcitriol ; Rosacea* ; Skin ; Vitamin D Response Element ; Vitamin D* ; Vitamins*

The strongest signal of plant promoter is searched with the model of single motif with two types. It turns out that the dominant type is the TATA-box. The other type may be called TATA-less signal, and may be used in gene finders for promoter recognition. While the TATA signals are very close for the monocot and the dicot, their TATA-less signals are significantly different. A general and flexible multi-motif model is also proposed for promoter analysis based on dynamic programming. By extending the Gibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed for searching signals in plant promoters.
Algorithms ; Amino Acid Motifs ; Computational Biology ; methods ; Genes, Plant ; Genomics ; methods ; Models, Genetic ; Models, Statistical ; Plants ; genetics ; Promoter Regions, Genetic ; Software ; TATA Box