To analyze the relationship between antisense transcription and alternative splicing, we developed a computational approach for the detection of antisense-correlated exon splicing events using Affymetrix exon array data. Our analysis of expression data from 176 lymphoblastoid cell lines revealed that the majority of expressed sense-antisense genes exhibited alternative splicing events that were...

Transcript abundance of the gene encoding -galactosidase II, a -galactosidase/exo-galactanase (EC 3.2.1.23) present during tomato (Lycopersicon esculentum) fruit ripening, was suppressed by expression of an antisense tomato -galactosidase 4 (TBG4) cDNA driven by the cauliflower mosaic virus 35S promoter. RNA gel-blot analysis was used to evaluate TBG4 mRNA levels in transgenic fruit. All of the...

Natural antisense transcripts are frequently transcribed from many genes in eukaryotes. Although natural antisense transcripts have been recognized for a long time, their importance has been overlooked due to their heterogeneity, low expression level, and unknown function. Genes induced in responses to various external stimuli are transcriptionally regulated by the activation of a gene promoter...

MicroRNAs are small non-coding RNA molecules involved in the epigenetic regulation of carcinogenesis. miR-204-5p was shown to be among most downregulated miRs melanoma versus benign melanocytic lesions. SIRT1 as a gene target regulates proliferation, apoptosis, migration cancer cells whereas BCL2 is well known by it’s antiapoptotic functions. Therefore B16-bearing mice were treated synthetic mi...

Mammalian genomes encode numerous natural antisense long noncoding RNAs (lncRNAs) that regulate gene expression. Recently, an antisense lncRNA to mouse Ubiquitin carboxyl-terminal hydrolase L1 (Uchl1) was reported to increase UCHL1 protein synthesis, representing a new functional class of lncRNAs, designated as SINEUPs, for SINE element-containing translation UP-regulators. Here, we show that a...

Eukaryotic topoisomerase I (TOP1), a DNA unwinding enzyme, plays an essential role in several cellular functions; however, regulation of TOP1 activity remains unknown. In an effort to identify potential regulators of TOP1 activity, the transcriptional activity of a TOP1 pseudogene in chromosome 1 was studied. By using primers unique to the TOP1 pseudogene, strand-specific polymerase chain react...

PURPOSE There are two types of cyclic AMP (cAMP)-dependent protein kinase (PKA), type I (PKA-I) and type II (PKA-II), which share a common catalytic (C) subunit but contain distinct regulatory (R) subunits, RI versus RII, respectively. Evidence suggests that increased expression of PKA-I and its regulatory subunit (RIalpha) correlates with tumorigenesis and tumor growth. We investigated the eff...

Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNAFISH, we observed changes in sense transcript distributions in n...

Antisense technology is based on the ability to design potent, sequence-specific inhibitors. The G-clamp heterocycle modification, a cytosine analog that clamps on to guanine by forming an additional hydrogen bond, was rationally designed to enhance oligonucleotide/RNA hybrid affinity. A single, context-dependent substitution of a G-clamp heterocycle into a 15-mer phosphorothioate oligodeoxynuc...

The majority of mouse genes are estimated to undergo bidirectional transcription; however, their tissue-specific distribution patterns and physiological significance are largely unknown. This is in part due to the lack of methodology to routinely assess the expression of natural antisense transcripts (NATs) on a large scale. Here we tested whether commercial DNA arrays can be used to monitor an...