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ABSTRACT: Altered antisense-to-sense transcript ratios in breast cancer

OTHER RELATED OMICS DATASETS IN: GSE25292

PROVIDER: PRJNA134891 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR077867.fastq.gz	Fastqsanger.gz
	SRR077868.fastq.gz	Fastqsanger.gz
	SRR077869.fastq.gz	Fastqsanger.gz
	SRR079377.fastq.gz	Fastqsanger.gz
	SRR079378.fastq.gz	Fastqsanger.gz

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Expression patterns of sense-antisense transcripts in normal and cancer tissues

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Project description:We characterized the expression patterns of sense-antisense transcripts, based on available cDNA sequences, in colon (colorectal) cancer tissues and in normal tissues surrounding the cancer tissues. Although expression balances (ratios) of most of sense and antisense transcript pairs did not change between patients or between normal and cancer tissues, we found 68 sense-antisense transcripts whose expression balances were altered specifically in colon cancer tissues. We conducted DNA microarray analyses by using the same set of probes designed for 2621 sense-antisense pairs to detect transcripts expressed in colon cancer tissues. These probes comprise 2358 pairs for the detection of protein-coding transcripts only, 250 pairs for the detection of protein-coding transcripts paired with non-protein-coding transcripts, and 13 pairs for the detection of non-protein-coding transcripts only.

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Project description:<p>High throughput RNA Sequencing has revealed that the human genome is widely transcribed. However, the extent of natural antisense transcription, the molecular mechanisms by which natural antisense transcripts (NATs) might affect their cognate sense genes, and the role of NATs in cancer are less well understood. Here, we use strand-specific paired-end RNA sequencing (ssRNASeq) on a cohort of 376 cancer patients covering 9 tissue types to comprehensively characterize the landscape of antisense expression. Our results reveal that greater than 60% of annotated transcripts have measureable antisense expression and the expression of sense and antisense transcript pairs is in general positively correlated. Furthermore, by studying the expression of sense/antisense pairs across tissues we identify lineage-specific, ubiquitous and cancer-specific antisense loci. Our results raise the possibility that NATs participate in the regulation of well-known tumor suppressors and oncogenes. Finally, this study provides a catalogue of cancer related genes with significant antisense transcription (oncoNAT). This resource will allow researchers to investigate the molecular mechanisms of sense/antisense regulation and further advance our understanding of their role in cancer.</p>

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CTCF blocks anti-sense transcription initiation at divergent gene promoters [ChIP-Seq]

Project description:Transcription is typically divergent, initiating at closely spaced oppositely oriented core promoters to produce sense and unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and coordinated with sense transcription is largely unknown. Here by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters, the great majority of which bear proximal CTCF binding sites. Genome editing, chromatin conformation studies and 5’ transcript mapping revealed that CTCF directly suppresses uasTrx initiation in manner independent of its chromatin architectural function. Primary transcript RNA FISH revealed co-bursting of sense and anti-sense transcripts is disfavored, suggesting CTCF-regulated competition for transcription initiation. In sum, CTCF shapes the noncoding transcriptional landscape by suppressing upstream antisense transcription.

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