Localizing hotspots of antisense transcription.

Analysis of the transcriptome by computational and experimental methods has established that sense-antisense transcriptional units are a common phenomenon. Although the regulatory potential of antisense transcripts has been experimentally verified in a number of studies, the biological importance of sense-antisense regulation of gene expression is still a matter of debate. Here, we report the identification of sequence features that are associated with antisense transcription. We show that the sequence composition of the first exon and the 5'end of the first intron of many human genes is similar to the sequence composition observed in promoter regions as measured by the density of known transcription regulatory motifs. Cloned intron-derived fragments were found to possess bidirectional promoter activity. In agreement with the reported abundance of antisense transcripts overlapping the 5'UTR, mapping of the 5'ends of antisense transcripts to the corresponding sense transcripts revealed that the first exon and the 5'end of the first intron are hotspots of antisense transcription as measured by the number of antisense transcription start sites per unit sequence. CpG dinucleotide suppression that is typically weak in non-methylated promoter regions is similarly weakened upstream as well as downstream of the first exon. In support of antisense transcripts playing a regulatory role, we find that 5'UTRs and first exons of genes with overlapping antisense transcripts are significantly longer than the genomic average. Interestingly, a similar size distribution of 5'UTRs and first exons is observed for genes silenced by CpG island methylation in human cancer.

Lap2alpha expression is controlled by E2F and deregulated in various human tumors.

Deregulation of the retinoblastoma (pRB) tumor suppressor pathway is frequently observed in human cancer and associated with aberrant activity of E2F transcription factors. We have performed microarray based analysis with the aim of identifying potential downstream mediators of the tumor suppressing activity of pRB. Here we report that the expression of LAP2 (lamina-associated polypeptide 2) is under direct control of E2F transcription factors. Chromatin immunoprecipitation assays show that the LAP2 promoter is bound by endogenous E2F in vivo. The LAP2 promoter is transactivated by ectopically expressed E2F and mutation of E2F binding sites eliminates this effect. We studied the expression level of LAP2alpha in human tumors by tissue microarray analysis and found LAP2alpha over expression in a significant percentage of primary larynx, lung, stomach, breast, and colon cancer tissues. In agreement with its regulation by E2F, LAP2alpha over expression in primary tumors was found to be correlated with tumor proliferation rate.

GenePicker: replicate analysis of Affymetrix gene expression microarrays.

UNLABELLED: GenePicker allows efficient analysis of Affymetrix gene expression data performed in replicate, through definition of analysis schemes, data normalization, t-test/ANOVA, Change-Fold Change-analysis and yields lists of differentially expressed genes with high confidence. Comparison of noise and signal analysis schemes allows determining a signal-to-noise ratio in a given experiment. Change Call, Fold Change and Signal mean ratios are used in the analysis. While each parameter alone yields gene lists that contain up to 30% false positives, the combination of these parameters nearly eliminates the false positives as verified by northern blotting, quantitative PCR in numerous independent experiments as well as by the analysis of spike-in data. AVAILABILITY: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html. SUPPLEMENTARY INFORMATION: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html.