Expression of Mouse and Human Sense-Antisense Transcript
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ABSTRACT:
PROVIDER: PRJNA103413 | ENA |
REPOSITORIES: ENA
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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. 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: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:Increasing numbers of senseâantisense 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 senseâantisense 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-proteinâcoding 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 senseâantisense 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 senseâantisense 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 The RNA samples used for the mouse oligo-array experiments came from the brain, NIH3T3 cells (fibroblast cell line), liver, heart, and testis. RNA from mouse tissue (C57BL/6J, 8 to 10 weeks, male and female mixed) and mouse fibroblast line NIH3T3 was isolated by using Trizol reagent (Invitrogen). The mouse custom oligo DNA microarray chip (microarray format: 11K) contained 3896 probes that represented genes in 1948 exon-overlapping SAT (sense-antisense transcript) pairs.The same total RNA samples were reciprocally labeled with Cy3 or Cy5, hybridized to the oligo DNA on the chip, and dye-normalized. The data on all genes on the chip were used to enable the Feature Extraction software to produce the processed signals. The total mean signal on the mouse chip in each hybridization experiment was adjusted with to a value of 4872.3. The RNA samples used for human microarray experiments came from brain, HF19 cells (fibroblast cell line), heart, liver and testis. The total brain, heart, and testis RNA used in the array experiments was purchased from Ambion. Total RNA was isolated from the fibroblast cells by using Trizol reagent (Invitrogen). The same total RNA samples were labeled with single color Cy3, hybridized to the oligo DNA on the chip, and dye-normalized; the processed signals were obtained by using Feature Extraction software (Agilent Technologies). The custom oligo DNA microarray chip (microarray format: 11K) contained 2793 probes for 1486 pairs of exon-overlapping SATs. The data on all genes on the chip were used to enable the Feature Extraction software to produce the processed signals. For further analysis, the Cy3-labeled processed signal was used as the processed signal from the expression of a particular gene. The total mean signal on the human chip in each hybridization experiment was adjusted to 1491.6, so that the relative differences in gene expression could be compared among cell lines and tissues.
2010-06-25 | E-GEOD-9581 | biostudies-arrayexpress
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:Transcription profiling of sense and antisense transcripts of 10 tissues each from human, mouse, and rat. This SuperSeries is composed of the SubSeries listed below.
2012-10-10 | GSE41409 | 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:<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>
| phs000937 | dbGaP
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
Project description:Sense-antisense transcript (SAT) pairs are pairs of transcripts that fully or partially overlap but are transcribed in opposite directions. Although SAT expression occurs in various species, most SAT pairs have not been examined in detail. Because our previous studies revealed some tissue specificity in SAT expression, SAT pairs might be involved in cell differentiation and the maintenance of tissue-specific gene expression programs. To analyze such tissue-specific SAT pairs, we assessed the expression profiles of SATs from 12 tissues of normal mice at a genome-wide scale and found that a considerable number of SAT pairs showed expression patterns unique to testis. This finding prompted us to study the relationship between SAT expression pattern and another epigenetic gene regulatory mechanism, DNA methylation. We conducted a comparative global analysis of the DNA methylation status of CpG island (CGI)-associated SAT loci from various tissues and found that in 99 of the 4911 SAT pairs studied, DNA methylation could cooperatively suppress its downstream “sense” transcription together with the “antisense” transcriptional activity in a tissue-specific manner. The tissue-specific differentially methylated regions (T-DMRs) of these SAT pairs mainly occurred outside of the defined CGIs. In addition, some of these T-DMRs are situated at the 5′ region of the antisense transcripts. This positioning implies a novel mechanism for DNA methylation to regulate gene transcription, in which DNA methylation inhibits an opposing transcriptional activity and therefore maintains stable expression of a tissue-specific gene.
2010-08-26 | GSE14392 | GEO