Signals in the promoter regions of several cancerous genes.

The eukaryotic core promoter regions are complex and fuzzy, usually lacking any conserved regions. However, they contain signals in the form of short stretches of nucleic acid sequences, for transcription start sites (TSS) that are recognized by the transcription factors (TFs). The core promoter region thus plays an important role in biological pathways (gene network and activation). It has been reported that these signals are composed of nucleotide hexamers in the promoter sequence (smaller sequences are likely to have too little information to be useful and longer sequences are too complex to be recognized by proteins) reasonably close to the TSS. The signals (nucleotide hexamers) have been identified by a similarity search on the eukaryotic promoter database (EPD, Homo sapiens). The signals have been classified, depending on their base composition. They have been have clustered using an algorithm, such that there are two and three nucleotide differences between the classes and a single nucleotide difference within a class. We have reclassified the hexamers taking the highest frequent hexamers present in the EPD (Homo sapiens) as the class representatives. Also we have tried to find whether the same composition is reflected on the miRNAs but found that they probably have other functions unrelated to promoter recognition. In this report melanoma carcinoma pathway has been chosen as the reference pathway and the promoters of the driver genes has been searched for the presence of the major classes. A few of these were found and are reported here. Several non-cancerous genes have also been studied as reference and comparison.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites / 基因组蛋白质组与生物信息学报·英文版

Vertebrate genomes are characterized with CpG deficiency, particularly for GC-poor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5' T to 5' A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5' Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected (obs/exp) values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes (except sea urchin) but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5' T and 5' A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation. CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions.

Synonymous codon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of GC3 rich genes towards protein stability.

The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was used to assess the significance of deviation of the observed and expected frequencies of 59 codons at the level of individual synonymous families in the four different protein secondary structural classes. It was observed that synonymous codon families show non-randomness in codon usage in four different secondary structural classes. However,when the genes were classified according to their GC3 levels there was an increase in non-randomness in high GC3 group of genes. The non-randomness in codon usage was further tested among the same protein secondary structures belonging to four different protein folding classes of high GC3 group of genes. The results show that in each of the protein secondary structural unit there exist some synonymous family that shows class specific codon-usage pattern. Moreover, there is an increased non-random behaviour of synonymous codons in sheet structure of all secondary structural classes in high GC3 group of genes. Biological implications of these results have been discussed.

GC-rich heterochromatin in silver stained nucleolar organizer regions (NORs) fluoresces with Chromomycin A3 (CMA3) staining in three species of teleostean fishes (Pisces).

In a bid to ascertain the molecular architecture of the silver positive regions (NORs) in chromosomes of three species of fish, namely, Hemibagrus menoda (Hamilton), Sperata seenghala (Sykes) (Fam: Bagridae) and Mastacembelus armatus (Lacep6de) (Fam: Mastacembelidae), an additional staining methodology using a fluorochrome dye (Chromomycin A3) was deployed along with the AgNO3 technique. The nucleolar organizing regions (NORs) were located terminally at the shorter arms (Tp) of one pair of submetacentric chromosomes (No.3) in H. menoda (2n=58), at the longer arms (Tq) of one pair of submetacentric chromosomes (No.5) in S. seenghala (2n=50) and at the shorter arm (Tp) of one pair of homologous submetacentric chromosomes (No.6) in M. armatus (2n=48). Staining with Chromomycin A3 produced bright fluorescing zones in GC-rich heterochromatin of Ag-positive NORs. The results indicate a more general trend of existence of an overlapping region between NOR and GC-rich fluorescing zones, the active sites of rRNA genes (rDNA) in this primitive group of vertebrates although exceptions to this situation has been reported in a couple of extant fish species earlier. More data utilizing such combined methodologies are warranted to understand the structural organization of fish chromosomes more precisely.

GC-box is not a key cis-acting element in human insulin gene promoter / 南方医科大学学报

<p><b>OBJECTIVE</b>To identify whether GC-box (-348 to -338) in human insulin gene promoter is a key cis-acting element.</p><p><b>METHODS</b>Human insulin gene promoter was sub-cloned into secreted alkaline phosphatase (SEAP) reporter plasmid. The deletion and mutation of GC-box in insulin gene promoter was performed. The activity of human insulin gene promoter was determined by evaluating the activity of SEAP in the supernatant of cell culture after the reporter plasmids were transfected in beta cell line betaTC3.</p><p><b>RESULT</b>Deletion and mutation of GC box in human insulin gene promoter did not result in significant changes of the activity of the promoter in betaTC3.</p><p><b>CONCLUSION</b>The GC-box is not a key cis-acting element in human insulin gene promoter.</p>