Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression patterns of cancer-related genes and their putative antisense transcripts in normal and colon cancer tissues

ABSTRACT: Background: Recent studies have identified thousands of sense-antisense gene pairs across different genomes by computational mapping of cDNA sequences. These studies have shown that approximately 25% of all transcriptional units in the human and mouse genomes are involved in cis-sense-antisense pairs. However, the number of known sense-antisense pairs remains limited because currently available cDNA sequences represent only a fraction of the total number of transcripts comprising the transcriptome of each cell type. Results: To discover novel antisense transcripts encoded in the antisense strand of important genes, such as cancer-related genes, we conducted expression analyses of antisense transcripts using our custom microarray platform along with 2376 probes designed specifically to detect the potential antisense transcripts of 501 well-known genes suitable for cancer research. Using colon cancer tissue and normal tissue surrounding the cancer tissue obtained from 6 patients, we found that antisense transcripts without poly(A) tails are expressed from approximately 80% of these well-known genes. This observation is consistent with our previous finding that many antisense transcripts expressed in a cell are poly(A)-. We also identified 101 and 71 antisense probes displaying a high level of expression specifically in normal and cancer tissues respectively. Some of these probes showed characteristic expression patterns which are anti-correlated with the expression patterns of the sense genes. Conclusion: Our microarray analysis identified novel antisense transcripts with expression profiles specific to cancer tissue, some of which might play a role in the regulatory networks underlying oncogenesis and thus are potential targets for further experimental validation. 501 probes targeting well-known genes suitable for cancer researches were designed. Additionally 2,376 probes targeting putative transcription units on the antisense strand of these genes were designed. Samples were obtained from colon cancer tissues and normal tissues surrounding cancer tissues of six patients.

ORGANISM(S): Homo sapiens

SUBMITTER: Rintaro Saito

PROVIDER: E-GEOD-14397 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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Expression patterns of cancer-related genes and their putative antisense transcripts in normal and colon cancer tissues

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