UNLABELLED In this paper we propose a new method for recognition of prokaryotic promoter regions with startpoints of transcription. The method is based on Sequence Alignment Kernel, a function reflecting the quantitative measure of match between two sequences. This kernel function is further used in Dual SVM, which performs the recognition. Several recognition methods have been trained and test...

The DNA sequence just adjacent to the transcriptional start sites (TSSs), what we call the promoter, plays an important role in transcription regulation. Although many attempts have been made to detect functional signals in promoter regions aiming to understand the mechanisms of transcription regulation, those attempts remain challenges because the grammars or semantics of promoter sequences ar...

Negative cofactor 2 (NC2) forms a stable complex with TATAbinding protein (TBP) on promoters in vitro. Its association with TBP prevents the binding of TFIIB and leads to inhibition of preinitiation complex formation. Here, we investigate the association of NC2 subunitwith human RNA polymerase II promoter regions by using gene-specific ChIP and genome-wide promoter ChIPchip analyses. We find NC...

Both OTX2 and MYC are important oncogenes in medulloblastoma, the most common malignant brain tumor in childhood. Much is known about MYC binding to promoter regions, but OTX2 binding is hardly investigated. We used ChIP-on-chip data to analyze the binding patterns of both transcription factors in D425 medulloblastoma cells. When combining the data for all promoter regions in the genome, OTX2 b...

Many molecular studies describe how components of the proximal promoter affect transcriptional processes. However, these studies do not account for the likely effects of distant enhancers or chromatin structure, and thus it is difficult to conclude that the sequence variation in proximal promoters acts to modulate transcription in the natural context of the whole genome. This problem, the biolo...

1.Kawamoto, S. 1996. Neuron-specific alternative splicing of nonmuscle myosin II heavy chain-B pre-mRNA requires a cis-acting intron sequence. J. Biol. Chem. 271:1761317616. 2.Kido, M., K.A. Rich, G. Lang, E. Barron, D.B. Kohn, M.R. Al-Ubaidi and J.C. Blanks. 1996. Use of a retroviral vector with an internal opsin promoter to direct gene expression to retinal photoreceptor cells. Curr. Eye Res....

Emiliania huxleyi (E. huxleyi), the most abundant coccolithophorid, has served as a model system for environmental studies pertaining to global carbon cycling, oceanic sulfur bio-transformations, and paleoclimatology. It has also potential applications in material sciences and biomedical studies. E. huxleyi was selected by the Department of Energy in 1999 for genome sequencing, which was recent...

This study attempts to discover putative binding site on how combinations of the known regulatory sites and over-represented repetitive elements are distributed in the promoter regions of groups of functionally related genes. The association rules mined would facilitate to predict putative regulatory elements and identify genes potentially co-regulated by the putative regulatory elements. The o...

A 47-base-pair (bp) conserved sequence in the 5'-flanking regions of three transcriptional units coding for nodulation functions (nodABC, nodEFG, and nodH) has been identified in Rhizobium meliloti strain 41. The conserved region contains subsequences of 7 bp, 5 bp, and 25 bp. The conserved 25-bp sequence was synthesized and used as a hybridization probe; three additional copies of the sequence...

The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence ...