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Novel endogenous antisense transcripts (data for the mouse mammary tumors)

ABSTRACT: Recent transcriptomic analyses have uncovered widespread occurrence of natural antisense transcripts (NATs), which are transcribed from the opposite strand of another discrete transcribed region. We describe a novel probe-design technique for DNA microarray analysis that specifically targets the complementary strand of annotated genes, and show that this technique can successfully identify novel NAT expression in normal and tumor samples. Northern and in situ hybridization analyses of selected examples (Acaa1, Aard, and Thbd) confirmed their transcription and dynamic expression in a tissue- and cell-type-specific manner. Our data highlight the importance of NAT expression in the regulation of cellular processes and in oncogenesis. The fundamental basis of the technology described in this paper is applicable to all genes and sample types for the identification of NAT expression that is not possible by conventional cDNA/EST/CAGE information.

ORGANISM(S): Mus musculus

PROVIDER: GSE14557 | GEO | 2009/08/24

SECONDARY ACCESSION(S): PRJNA114397

REPOSITORIES: GEO

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Novel endogenous antisense transcripts (data for the mouse normal tissues)

2009-08-24 | GSE14372 | GEO

Novel endogenous antisense transcripts (data for the mouse mammary tumors)

Project description:Recent transcriptomic analyses have uncovered widespread occurrence of natural antisense transcripts (NATs), which are transcribed from the opposite strand of another discrete transcribed region. We describe a novel probe-design technique for DNA microarray analysis that specifically targets the complementary strand of annotated genes, and show that this technique can successfully identify novel NAT expression in normal and tumor samples. Northern and in situ hybridization analyses of selected examples (Acaa1, Aard, and Thbd) confirmed their transcription and dynamic expression in a tissue- and cell-type-specific manner. Our data highlight the importance of NAT expression in the regulation of cellular processes and in oncogenesis. The fundamental basis of the technology described in this paper is applicable to all genes and sample types for the identification of NAT expression that is not possible by conventional cDNA/EST/CAGE information. Total RNA for the GRS mammary tumor microarray experiments was isolated from normal and cancerous mammary glands of dissected GRS/A mice, by using Trizol reagent (Invitrogen Corporation). Unpublished data has been masked in the supplementary feature extraction files.

2010-05-06 | E-GEOD-14557 | biostudies-arrayexpress

Novel endogenous antisense transcripts (data for the mouse normal tissues)

Project description:Recent transcriptomic analyses have uncovered widespread occurrence of natural antisense transcripts (NATs), which are transcribed from the opposite strand of another discrete transcribed region. We describe a novel probe-design technique for DNA microarray analysis that specifically targets the complementary strand of annotated genes, and show that this technique can successfully identify novel NAT expression in normal and tumor samples. Northern and in situ hybridization analyses of selected examples (Acaa1, Aard, and Thbd) confirmed their transcription and dynamic expression in a tissue- and cell-type-specific manner. Our data highlight the importance of NAT expression in the regulation of cellular processes and in oncogenesis. The fundamental basis of the technology described in this paper is applicable to all genes and sample types for the identification of NAT expression that is not possible by conventional cDNA/EST/CAGE information. Total RNA for the mouse (C57BL/6J) microarray experiments was isolated from SL10 cells (fibroblast cell line), brain, heart, intestine, kidney, liver, lung, placenta (d.p.c. 10.5 and 13.5), spleen, stomach, testis, and thymus. Testis was from C57BL/6J males (8 to 10 weeks), placenta was from pregnant mice, and the other tissue was from both male and female mice. Unpublished data has been masked in the supplementary feature extraction files.

2010-05-06 | E-GEOD-14372 | biostudies-arrayexpress

The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

Project description:Naturally occurring Antisense Transcripts (NATs) compose an emerging group of regulatory RNAs. These regulatory elements appear in all organisms examined, but little is known about global expression of NATs in fungi. Analysis of currently available EST sequences suggests that 352 cis NATs are present in Aspergillus flavus. An Affymetrix GeneChip® microarray containing probes for these cis NATs, as well as all predicted genes in A. flavus, allowed a whole genome expression analysis of these elements in response to two ecologically important temperatures for the fungus. RNA expression analysis showed that 32 NATs and 2709 genes were differentially expressed between 37°C, the optimum temperature for growth, and 28°C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. These NATs correspond to sense genes with diverse functions including transcription initiation, carbohydrate processing and binding, temperature sensitive morphogenesis, and secondary metabolism. This is the first report of a whole genome transcriptional analysis of NAT expression in a fungus and shows that although less than 10% of putative NATs are differentially expressed in response to temperature, some of the NAT-cis gene interactions are likely to be important. Keywords: temperature response

2009-03-25 | GSE12594 | GEO

The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

Project description:Naturally occurring Antisense Transcripts (NATs) compose an emerging group of regulatory RNAs. These regulatory elements appear in all organisms examined, but little is known about global expression of NATs in fungi. Analysis of currently available EST sequences suggests that 352 cis NATs are present in Aspergillus flavus. An Affymetrix GeneChipÂ® microarray containing probes for these cis NATs, as well as all predicted genes in A. flavus, allowed a whole genome expression analysis of these elements in response to two ecologically important temperatures for the fungus. RNA expression analysis showed that 32 NATs and 2709 genes were differentially expressed between 37Â°C, the optimum temperature for growth, and 28Â°C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. These NATs correspond to sense genes with diverse functions including transcription initiation, carbohydrate processing and binding, temperature sensitive morphogenesis, and secondary metabolism. This is the first report of a whole genome transcriptional analysis of NAT expression in a fungus and shows that although less than 10% of putative NATs are differentially expressed in response to temperature, some of the NAT-cis gene interactions are likely to be important. Keywords: temperature response 3 samples (reps) for each temperature treatment were analyzed with a total of 6 samples.

2010-06-21 | E-GEOD-12594 | biostudies-arrayexpress

Exosomal natural antisense transcripts released from colorectal cancer SW480 cells into culture supernatants

2015-05-19 | GSE68979 | GEO

Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

Project description:We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots. We examined the abundance of NATs in etiolated seedlings and seedlings undergoing de-etiolation in continuous white light for 1/6h. Seedlings were further dissected into cotyledons, hypocotyls and roots. RNAs from 3 biological replicates of each of the 3 organs were separately hybridized to ATH NAT arrays to profile light-regulated NAT pairs.

2013-12-23 | E-GEOD-49382 | biostudies-arrayexpress

The Landscape of Antisense Gene Expression in Human Cancers

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

Stranded RNASeq of human mammary primary tumors ER+ and paired adjacent healthy tissues

Project description:Non-coding RNAs (ncRNA) represent at least 1/5 of the mammalian transcript amount, and about 90% of the genome length is actively transcribed. Many ncRNAs have been demonstrated to play a role in cancer. Among them, natural antisense transcripts (NAT) are RNA sequences which are complementary and overlapping to those of protein-coding transcripts (PCT). NATs were punctually described as regulating gene expression, and are expected to act more frequently in cis than other ncRNAs that commonly function in trans. In this work, 22 breast cancers expressing estrogen receptors and their paired healthy tissues were analyzed by strand-specific RNA sequencing to highlight the potential role of NATs in gene regulations occurring in breast cancer.

2017-11-30 | GSE103001 | GEO

Exosomal natural antisense transcripts released from colorectal cancer SW480 cells into culture supernatants

Project description:In the present study, natural antisense transcripts (NATs), transcribed from reverse strand deoxynucleic acids (DNAs) of genes, into exosomes released from colorectal cancer SW480 cells were searched using an sense/antisense-custom microarray. SW480 cells were cultured with serum-free RPMI1640 for 48 h. Then, culture media were collected, centrifugated, and filtrated using 0.22-um filters. Exosomes from culture media were collected by ultracentrifugation.

2015-05-19 | E-GEOD-68979 | biostudies-arrayexpress

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