Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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. 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 Unpublished data has been masked in the supplementary feature extraction files.

ORGANISM(S): Mus musculus

SUBMITTER: Rintaro Saito

PROVIDER: E-GEOD-14557 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes.

Numata Koji K Osada Yuko Y Okada Yuki Y Saito Rintaro R Hiraiwa Noriko N Nakaoka Hajime H Yamamoto Naoyuki N Watanabe Kazufumi K Okubo Kazue K Kohama Chihiro C Kanai Akio A Abe Kuniya K Kiyosawa Hidenori H

BMC genomics 20090822

<h4>Background</h4>Recent transcriptomic analyses in mammals have uncovered the widespread occurrence of endogenous antisense transcripts, termed natural antisense transcripts (NATs). NATs are transcribed from the opposite strand of the gene locus and are thought to control sense gene expression, but the mechanism of such regulation is as yet unknown. Although several thousand potential sense-antisense pairs have been identified in mammals, examples of functionally characterized NATs remain limi ...[more]

PMID: 19698135

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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. Twelve tissues (brain, thymus, heart, lung, liver, spleen, stomach, kidney, small intestine, testis, and placentae [10.5 and 13.5 days postcoitum (dpc)]) of C57BL/6J Jc1 and a mouse fibroblast cell line (SL10) were used for the mouse expression oligo-microarray. The expression array data were obtained by both oligo-dT and random priming methods, except for SL10 (olio-dT only). Twelve tissues (brain, thymus, heart, lung, liver, spleen, stomach, kidney, small intestine, testis, and placentae [10.5 and 13.5 days postcoitum (dpc)]) were used for DIP chip experiments. Nine of twelve tissues were separately analyzed classified on the basis of sex. A technical duplication of DIP chip analysis was performed by using the same genomic DNA of male kidney.

Dataset Information

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

Publications

Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes.

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