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Computational discovery of sense-antisense transcription in the human and mouse genomes.

ABSTRACT: BACKGROUND:Overlapping but oppositely oriented transcripts have the potential to form sense-antisense perfect double-stranded (ds) RNA duplexes. Over recent years, the number and variety of examples of mammalian gene-regulatory phenomena in which endogenous dsRNA duplexes have been proposed or demonstrated to participate has greatly increased. These include genomic imprinting, RNA interference, translational regulation, alternative splicing, X-inactivation and RNA editing. We computationally mined public mouse and human expressed sequence tag (EST) databases to search for additional examples of bidirectionally transcribed genomic regions. RESULTS:Our bioinformatics approach identified over 217 candidate overlapping transcriptional units, almost all of which are novel. From experimental validation of a subset of our predictions by orientation-specific RT-PCR, we estimate that our methodology has a specificity of 84% or greater. In many cases, regions of sense-antisense overlap within the 5'- or 3'-untranslated regions of a given transcript correlate with genomic patterns of mouse-human conservation. CONCLUSIONS:Our results, in conjunction with the literature, bring the total number of predicted and validated examples of overlapping but oppositely oriented transcripts to over 300. Several of these cases support the hypothesis that a subset of the instances of substantial mouse-human conservation in the 5' and 3' UTRs of transcripts might be explained in part by functionality of an overlapping transcriptional unit.

SUBMITTER: Shendure J

PROVIDER: S-EPMC126869 | biostudies-literature | 2002 Aug

REPOSITORIES: biostudies-literature

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Computational discovery of sense-antisense transcription in the human and mouse genomes.

Shendure Jay J Church George M GM

Genome biology 20020822 9

<h4>Background</h4>Overlapping but oppositely oriented transcripts have the potential to form sense-antisense perfect double-stranded (ds) RNA duplexes. Over recent years, the number and variety of examples of mammalian gene-regulatory phenomena in which endogenous dsRNA duplexes have been proposed or demonstrated to participate has greatly increased. These include genomic imprinting, RNA interference, translational regulation, alternative splicing, X-inactivation and RNA editing. We computation ...[more]

PMID: 12225583

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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.

Dataset Information

Computational discovery of sense-antisense transcription in the human and mouse genomes.

Publications

Computational discovery of sense-antisense transcription in the human and mouse genomes.

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