Cells exposed to oxidative stress or electrophilic xenobiotics respond by transcriptionally up-regulating a battery of genes that contain a cis-acting element in their promoter region known as the antioxidant/electrophile response element (ARE). Mutational analysis of the promoter regions of ARE-containing genes led to the creation of two different models for the ARE; a core ARE (cARE: RTGACnnn...

UNLABELLED 'Melina' assists users to compare the results of four public softwares for DNA motif extraction in order to both confirm the reliability of each finding and avoid missing important motifs. It is also useful to optimize the sensitivity of software with a series of different parameter settings. AVAILABILITY Melina is available at http://www.hgc.ims.u-tokyo.ac.jp/Melina/.

The methylation status in the human-muscle enolase gene (ENO3) was assayed. Previous sequence data and MspI cleavage sites indicate the presence of a 5' CpG-rich island of at least 4 kb: none of 22 characterized MspI CCGG sites is methylated in any of muscle, sperm or brain DNA. However a complex pattern of complete and partial methylation of MspI sites that is different between tissues is obse...

The temporal and spatial expression pattern of the Drosophila melanogaster alpha 2-tubulin gene (alpha 2) has been investigated by examining the expression of an alpha 2-lacZ fusion gene. When this fusion gene is introduced into the germ line by P-element mediated transformation, expression is only detected in chordotonal organs and testes. Chordotonal organs, which are sensory organs of the pe...

DNA methylation (DNAm) is a term used to describe the heritable covalent addition of a methyl group to cytosines at CpG dinucleotides in mammals. While methods for examining DNAm status at specific loci have existed for several years, recent technological advances have begun to enable the examination of DNAm across the genome. In this unit, we describe comprehensive high-throughput arrays for r...

Regarding host aspects, there has been strong evidence for a genetic component in the etiology of caries. The salivary protein lactotransferrin (LTF) exhibits antibacterial activity, but there is no study investigating the association of polymorphisms in the promoter region of LTF gene with caries. The objective of this study was firstly to search the promoter region of the human LTF gene for v...

Gene clusters could be derived based on expression profiles, function categorization and promoter regions. To obtain thorough understanding of gene expression and regulation, the three aspects should be combined in an organic way. In this study, we explored the possible ways to analyze the large-scale gene expression data. Three approaches were used to analyze yeast temporal expression data: 1)...

We measured the in vivo production of RNA molecules tagged with MS2d-GFP in Escherichia coli, driven by the lar promoter, under weak and medium induction. The distributions of intervals between consecutive productions of RNAs are found to be sub-exponential, and the process of RNA production is found to be sub-Poissonian. We discuss possible models of transcription initiation and, based on our ...

Abstract Background Co-localized combinations of histone modifications (“chromatin states”) have been shown to correlate with promoter and enhancer activity. Changes in chromatin states over multiple time points state trajectories”) previously analyzed at enhancers separately. With the advent series Hi-C data it is now possible connect promoters analyze trajectories promoter-enhancer pairs. Res...

Background: There are different etiological factors in spontaneous recurrent abortion which are one of the complications in pregnancy. Primary embryo development in uterine tube and oviduct are affected by different factors such as embryotrophic elements. ETF3 as a embryotrophic factor that contains a complex of complement 3 protein and its derivatives specially iC3b, causes embryo trophoblast ...