Most comprehensive genome-wide experimental analyses of sense-antisense transcripts to date

A team of scientists led by Dr. Kuniya Abe from the RIKEN BioResource Center in Japan has performed one of the most comprehensive genome-wide experimental analyses of sense-antisense transcripts to date. Their findings are published in the April issue of the journal Genome Research.

Sense-antisense transcripts, or SATs, are pairs of RNA molecules generated from opposite DNA strands at the same locus. The number of SATs identified in the past several years has grown substantially, and they are now believed to comprise at least 8% of human genes. Many SAT pairs have been implicated in various stages of gene regulation, including transcription, mRNA processing, splicing, stability, transport, and translation. Various examples of such overlapping genes have been documented in all life forms – from viruses and prokaryotes to plants and animals.

To date, most studies on SAT pairs have utilized purely in silico approaches; very few have experimentally validated the existence of overlapping RNA molecules in vivo. With this in mind, Dr. Hidenori Kiyosawa, the lead author on the paper, set out to confirm the presence of SATs in a variety of mouse tissue types and cell cultures, as well as to identify common characteristics of these unique transcripts.

Employing a custom-made microarray chip designed to detect strand-specific expression of 1947 SAT pairs, the researchers discovered that most of the SATs were widely expressed in mouse brain, heart, and testis, as well as in mouse embryonic stem cells and fibroblasts. While some SATs were expressed at a consistent level in all cells and tissues tested, others exhibited marked tissue-specific expression patterns.

Upon close examination of several SAT pairs, Abe's group found that the transcripts shared several striking characteristics. Northern blot hybridization analyses of six randomly chosen SAT pairs revealed that the SAT loci generated multiple transcripts of various sizes, in contrast to a single transcript that is expected under the traditional one gene-one transcript model. Furthermore, the SATs tended to be poly(A)-negative and enriched in the nucleus, which strongly suggests a functional role for these transcripts in gene regulation.

Abe and Kiyosawa also evaluated four Arabidopsis SAT pairs and demonstrated that these molecular characteristics were largely conserved in plants.

"Conventional belief in molecular biology suggests that poly(A)+ mRNAs are major mediators in flows of genetic information," Abe explains. "However, the information obtained from this study implies that some classes of poly(A)-negative nuclear RNA may have important biological functions."

Among these functions may be the regulation of gene expression on a domain level, such as that which has been documented for several imprinted loci. Antisense transcripts have been shown to alter the methylation status of the overlapping partner gene. SATs might also trigger posttranscriptional gene regulation via RNA interference (RNAi) by virtue of their ability to form double-stranded RNA (dsRNA) molecules.

A large proportion of these antisense RNAs represent non-coding RNAs. Thus, the researchers expect that these results will lead to a better understanding of roles of non-coding RNAs in gene regulation.