Bioinformatic analysis of the hsa-miR-1908 upstream promoter region / 临床儿科杂志

Objective To predict the functions of hsa-miR-1908 promoter using various bioinformatic tools, and to provide clues for further study on transcriptional regulation mechanism of miR-1908 in human adipocytes. Methods The promoter se-quence of miR-1908 was obtained from Ensemble, and then the CpG islands and transcription factor binding sites were pre-dicted by a variety of online bioinformatic tools. Results The length of the miR-1908 promoter sequence was 1 458 bp. The CpG islands, which inhibited the transcription of miR-1908, were located at (438-756) bp, (836-937) bp and (979-1374) bp. Meanwhile, 15 transcription factor binding sites were found in the promoter sequence of miR-1908. Conclusions miRNA up-stream promoter related bioinformatics can not only improve the efficiency of microRNA promoter research, but also provide further important information on transcriptional regulation of miR-1908.

Construction of Iuciferase reporter vectors harboring DC-SIGN promoters without AP-1 or ETS-1 transcription factor binding site and detection of their activity / 中华微生物学和免疫学杂志

Objective To detect the role of AP-1 or ETS-1 transcription factor binding sites (TFBS) in activity of DC-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) pro-moter. Methods Genomic DNA was extracted from peripheral blood. Complete DC-SIGN promoter and those without AP-1 or ETS-1 TFBS were amplified by PCR using designed primers. The PCR products were digested with MLu Ⅰ and Bgl Ⅱ and then ligated into MLu Ⅰ and Bgl Ⅱ digested pGL-3/Basic and pGL-3/En-hancer vectors. Transfection in Hacat and 293 cells was accomplished with Trans Fast liposome. Activity of luciferase was detected after 48 h. Results The DC-SIGN promoters without AP-1 or ETS-1 TFBS and the recombined pGL-3 vectors were correctly constructed. The activity of DC-SIGN promoters without AP-1 was reduced 20% (293) and 10% (Hacat), which was 40%-50% with enhancer. The activity of DC-SIGN pro-moters without ETS-1 was nearly vanished, no matter with or without enhancer. Conclusion ETS-1 TFBS, not AP-1 TFBS, plays an important role in activity of DC-SIGN promoter.

Calibrating Thresholds to Improve the Detection Accuracy of Putative Transcription Factor Binding Sites

To understand the mechanism of transcriptional regulation, it is essential to detect promoters and regulatory elements. Various kinds of methods have been introduced to improve the prediction accuracy of regulatory elements. Since there are few experimentally validated regulatory elements, previous studies have used criteria based solely on the level of scores over background sequences. However, selecting the detection criteria for different prediction methods is not feasible. Here, we studied the calibration of thresholds to improve regulatory element prediction. We predicted a regulatory element using MATCH, which is a powerful tool for transcription factor binding site (TFBS) detection. To increase the prediction accuracy, we used a regulatory potential (RP) score measuring the similarity of patterns in alignments to those in known regulatory regions. Next, we calibrated the thresholds to find relevant scores, increasing the true positives while decreasing possible false positives. By applying various thresholds, we compared predicted regulatory elements with validated regulatory elements from the Open Regulatory Annotation (ORegAnno) database. The predicted regulators by the selected threshold were validated through enrichment analysis of muscle-specific gene sets from the Tissue-Specific Transcripts and Genes (T-STAG) database. We found 14 known muscle-specific regulators with a less than a 5% false discovery rate (FDR) in a single TFBS analysis, as well as known transcription factor combinations in our combinatorial TFBS analysis.

Analysis of the transcription factor binding sites in the promoter region of genes encoding the co-expressive proteins induced by N-methyl-N'-nitro-N-nitrosoguanidine / 中国病理生理杂志

AIM: To find out common transcription factor binding sites in the promoter regions of the encoding genes of the co-expressive proteins induced by N-methyl-N'-nitro-N- nitrosoguanidine (MNNG). METHODS: Using phylogenetic footprinting and TRANSFAC position weight matrix (PWM) searching program to predict the common transcription factor binding sites among the promoter regions of the genes encoding the co-expressive proteins. The predictive results were validated with electrophoresis mobility shift assay (EMSA). RESULTS: Eleven common transcription factor binding sites were predicted in the promoters of the co-expressive proteins, among them, besides the activator protein 1(AP1) which was previously identified to be activated in MNNG pretreated cells in this laboratory, the nuclear factor Y (NFY) and GATA binding factor (GATA) consensus oligonucleotides binding activity were found being increased in the nuclear extract of cells pre-treated with MNNG as demonstrated by EMSA. CONCLUSION: Phylogenetic footprinting can effectively decrease the false positive rate in predicting transcription factor binding sites. It is possible that NFY and GATA transcription factor binding sites are involved in the co-regulation of the MNNG induced co- expressive proteins. [

Application of bioinformatics in transcriptional regulation research / 中国病理生理杂志

Gene transcriptional regulation research is one of the major challenges in the post-genome era. Bioinformatics has become more important with the rapid accumulation of complete genome sequences and the advances of computational methods and related databases. The current computational approaches in promoter prediction, transcription factor binding site identification, composite elements prediction, co-regulation of gene expression analysis and phylogenetic footprinting in the regulatory region analysis are discussed in this review.