Antisense RNAs influence promoter usage of their counterpart sense genes in cancer
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ABSTRACT:
PROVIDER: PRJNA729482 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14511540_1.fastq.gz | Fastqsanger.gz | |||
| SRR14511540_2.fastq.gz | Fastqsanger.gz | |||
| SRR14511541_1.fastq.gz | Fastqsanger.gz | |||
| SRR14511541_2.fastq.gz | Fastqsanger.gz | |||
| SRR14511542_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Antisense RNAs influence promoter usage of their counterpart sense genes in cancer
| PRJNA729482 | ENA
Project description:Natural antisense transcripts (NATs) are those RNAs transcribed from the same locus, but in the opposite direction to a sense gene transcript. non-coding NATs (ncNATs) have been reported to modulate key biological events such as cell differentiation and carcinogenesis through gene expression regulation; nevertheless, their actual impact on cancer remains largely unknown. Due to their low expression levels and their overlap with sense genes, the study of ncNATs using RNA-seq is challenging. Public databases frequently register incomplete sequences of ncNATs, and mostly in a not tissue-specific manner. In the present study, we aim to better characterize the nature of ncNATs expressed in liver and hepatocellular carcinoma (HCC). For that, we performed strand-specific RNA-seq in 6 pairs of HCC - normal adjacent liver tissues from 6 HCC patients. Knowing the strand origin of the reads, we will be able to determine the actual nature and span of those ncNATs expressed in the liver and in HCC.
2021-11-15 | GSE174338 | GEO
Project description:Multiple noncoding natural antisense transcripts (ncNAT) are known to modulate key biological events such as cell growth or differentiation. However, the actual impact of ncNATs on cancer progression remains largely unknown. In this study, we identified a complete list of differentially expressed ncNATs in hepatocellular carcinoma. Among them, a previously undescribed ncNAT HNF4A-AS1L suppressed cancer cell growth by regulating its sense gene HNF4A, a well-known cancer driver, through a promoter-specific mechanism. HNF4A-AS1L selectively activated the HNF4A P1 promoter via HNF1A, which upregulated expression of tumor suppressor P1-driven isoforms, while having no effect on the oncogenic P2 promoter. RNA-seq data from 23 tissue and cancer types identified approximately 100 ncNATs whose expression correlated specifically with the activity of one promoter of their associated sense gene. Silencing of two of these ncNATs ENSG00000259357 and ENSG00000255031 (antisense to CERS2 and CHKA, respectively) altered the promoter usage of CERS2 and CHKA. Altogether, these results demonstrate that promoter-specific regulation is a mechanism used by ncNATs for context-specific control of alternative isoform expression of their counterpart sense genes. SIGNIFICANCE: This study characterizes a previously unexplored role of ncNATs in regulation of isoform expression of associated sense genes, highlighting a mechanism of alternative promoter usage in cancer.
| S-EPMC9397637 | biostudies-literature
Project description:Increasing numbers of sense–antisense transcripts (SATs), which are transcribed from the same chromosomal location but in opposite directions, have been identified in various eukaryotic species, but the biological meanings of most SATs remain unclear. To improve understanding of natural sense–antisense transcription, we performed comparative expression profiling of SATs conserved among humans and mice. Using custom oligo-arrays loaded with probes that represented SATs with both protein-coding and non-protein–coding transcripts, we showed that 33% of the 291 conserved SATs displayed identical expression patterns in the two species. Among these SATs, expressional balance inversion of sense–antisense genes was mostly observed in testis at a tissue-specific manner. Northern analyses of the individual conserved SAT loci revealed that: (1) a smeary hybridization pattern was present in mice, but not in humans, and (2) small RNAs (about 60 to 80 nt) were detected from the exon-overlapping regions of SAT loci. In addition, further analyses showed marked alteration of sense–antisense expression balance throughout spermatogenesis in testis. These results suggest that conserved SAT loci are rich in potential regulatory roles that will help us understand this new class of transcripts underlying the mammalian genome. Keywords: Expression profile of mouse and human sense-antisense transcript
2008-02-20 | GSE9581 | GEO
Project description:Comparison of sense (forward probes) and antisense (reverse probes on U74 v1 gene arrays) transcripts in mouse kidney and brain. Positive calls related to antisense transcripts were compared to the cognate signals on the 430 version of mouse genome arrays to obtain genes that co expressed sense and antisense transcripts. This had to be done manually because divergent probe IDs on the two chip generations. Keywords: Qualitative comparison of expression
2006-11-07 | GSE6106 | GEO
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.
2011-03-01 | GSE14398 | GEO
Project description:Transcription profiling of sense and antisense transcripts of 10 tissues each from human, mouse, and rat. This SuperSeries is composed of the following subset Series: GSE41462: Antisense exon profiling across human, mouse, and rat GSE41464: Sense exon profiling across human, mouse, and rat We profiled the sense and antisense transcription level of 10 tissues each from human, mouse, and rat. Only Affymetrix core probesets were used. Two technical replicates per sample. Reference for protocol: Ge, X., Rubinstein, W.S., Jung, Y.C., and Wu, Q. (2008). Genome-wide analysis of antisense transcription with Affymetrix exon array. BMC Genomics 9, 27.
2012-10-10 | E-GEOD-41409 | biostudies-arrayexpress
Project description:Expression of Mouse and Human Sense-Antisense Transcript
| PRJNA103413 | ENA
Project description:Comparison of sense (forward probes) and antisense (reverse probes on U74 v1 gene arrays) transcripts in mouse kidney and brain. Positive calls related to antisense transcripts were compared to the cognate signals on the 430 version of mouse genome arrays to obtain genes that co expressed sense and antisense transcripts. This had to be done manually because divergent probe IDs on the two chip generations. Experiment Overall Design: The first Affymetrix U74 mouse gene chips contains reversely oriented probe sets. These probes will hybridize to natural antisense transcripts that overlap with the sense transcript in the cognate area. Affymetrix provided a mask to identify the reverse probes. Positive calls with these reverse probes will give an estimate of the antisense transcriptome in that particular tissue. Comparison of the reversely oriented probes with correctly annotated probes will reveal the expression ratio of sense and antisense transcripts.
2008-06-14 | E-GEOD-6106 | biostudies-arrayexpress
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.
2011-03-01 | E-GEOD-14398 | biostudies-arrayexpress