2004
DOI: 10.1038/sj.onc.1207880
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Abstract: A large fraction of transcripts are expressed antisense to introns of known genes in the human genome. Here we show the construction and use of a cDNA microarray platform enriched in intronic transcripts to assess their biological relevance in pathological conditions. To validate the approach, prostate cancer was used as a model, and 27 patient tumor samples with Gleason scores ranging from 5 to 10 were analyzed. We find that a considerably higher fraction (6.6%, [23/346]) of intronic transcripts are significa… Show more

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Cited by 154 publications
(157 citation statements)
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“…To date, antisense transcripts have been observed for up to 75% of the mammalian transcriptome in data sets generated by both sequence-based and hybridization-based methods (Katayama et al 2005). Given the high prevalence of antisense transcription in the mammalian genome, and the link between antisense transcripts and disease (Tufarelli et al 2003;Reis et al 2004), Tag-seq was well suited to the study of cancer-relevant gene expression in the context of the CGAP project. We found known and novel S-AS gene pairs for which the ratio of expression changed significantly between The enrichment of miRNA targeting sites increased further for those genes with differential expression values in the top 20% and even further for those in the top 10%.…”
Section: Discussionmentioning
confidence: 99%
See 1 more Smart Citation
“…To date, antisense transcripts have been observed for up to 75% of the mammalian transcriptome in data sets generated by both sequence-based and hybridization-based methods (Katayama et al 2005). Given the high prevalence of antisense transcription in the mammalian genome, and the link between antisense transcripts and disease (Tufarelli et al 2003;Reis et al 2004), Tag-seq was well suited to the study of cancer-relevant gene expression in the context of the CGAP project. We found known and novel S-AS gene pairs for which the ratio of expression changed significantly between The enrichment of miRNA targeting sites increased further for those genes with differential expression values in the top 20% and even further for those in the top 10%.…”
Section: Discussionmentioning
confidence: 99%
“…We first analyzed the AS tags with a focus on their differential expression in libraries representing cancerous and normal tissue samples. Previous studies have shown that the ratio of sense to antisense transcripts changes between normal and malignant tissue samples , and that antisense transcripts can be implicated in disease processes (Tufarelli et al 2003;Reis et al 2004). Our goal was to highlight the potential of the Tag-seq approach to identify known and novel antisense transcripts whose expression ratios changed significantly with respect to the sense gene, between normal and diseased states, between different stages of disease progression, or between cancer subtypes.…”
Section: Sense-antisense Transcripts In Cancer Librariesmentioning
confidence: 99%
“…Several microRNAs (miRNAs) are now associated with the progression and classification of this and other malignancies (Lu et al, 2005;Volinia et al, 2006;Porkka et al, 2007;Shi et al, 2007;Ozen et al, 2008;Prueitt et al, 2008;Tong et al, 2009). Evidence is accumulating that small nuclear RNA and small nucleolar RNA (snoRNA) are also employed in cis and trans gene regulation and alternative splicing besides their established function in ribosomal RNA modification (Reis et al, 2004;Mattick and Makunin, 2006;Dong et al, 2008;Ender et al, 2008). Nevertheless, the assessment of the complete small ncRNA transcriptome involved in the formation and differentiation of different types and subtypes of PCa has remained a challenge.…”
Section: Introductionmentioning
confidence: 99%
“…miRNAs are also linked to neoplastic transformation (Lu et al, 2005;Meltzer, 2005;Volinia et al, 2006). In addition, one type of ncRNAs transcribed from the introns of known genes correlate with the degree of differentiation of prostate cancer (Reis et al, 2004) or protect cells from Fas-mediated apoptosis (Yan et al, 2005). Another class of ncRNAs that have received relatively sparse attention are the large ncRNAs that, like mRNAs, are usually produced by RNA polymerase II, but lack significant and utilized open reading frames (ORFs).…”
Section: Introductionmentioning
confidence: 99%