’Pregnant’ protein-coding genes carry RNA ’babies’

Scientists characterize large numbers of independently expressed, non-protein-coding RNA genes in the introns of protein-coding genes

Scientists from the Chinese Academy of Sciences have performed a comprehensive analysis of small, non-protein-coding RNAs in the model nematode, C. elegans. They characterize 100 heretofore-undescribed transcripts, including two novel classes; they provide insights into the genomic structure and transcriptional regulation of non-coding RNAs; and they underscore the importance of non-coding RNAs in nematode development. Their work appears this month in the journal Genome Research.

“The significance of non-protein-coding RNAs as central components of various cellular processes has risen sharply over the recent years,” explains Prof. Runsheng Chen, principal investigator on the study. Excluding microRNAs (miRNAs), or small transcripts that have recently received widespread attention and are known to play important roles in transcriptional regulation, small non-coding RNAs (or ncRNAs) in C. elegans have not been extensively investigated – until now.

Using a new, high-throughput procedure to clone small, full-length ncRNAs, Chen’s laboratory isolated and characterized 161 unique transcripts. A major advantage of the new cloning procedure is that it achieves an extraordinarily high detection rate for ncRNAs by current standards. “Studies published over recent years have only been able to reach a detection rate of about 3%, but our method reached a detection rate of 30% – a 10-fold increase in cloning efficiency,” explains Chen. “It’s like going from a Model T Ford to a Ferrari in one fell swoop!”

Of the 161 transcripts detected by Chen’s group, 100 were novel and 61 were previously known or predicted. Among the 100 novel genes, 30 had no known function, whereas 70 belonged to the ubiquitous class of small nucleolar RNAs (snoRNAs). Based on sequence and structural features, Chen and his colleagues were able to classify more than half of the 30 unknown RNAs into two new categories: stem-bulge RNAs (sbRNAs) and small nuclear-like RNAs (snlRNAs). Both classes of transcripts exhibited enhanced expression during the later stages of worm development, indicating a functional role for these transcripts in developmental processes.

“The interesting thing about nematodes is that their genomic organization of both snoRNAs and other ncRNAs is quite different from other animals,” says Chen. In contrast to the genomes of other metazoans, where most snoRNAs are found in introns and are under the control of independent promoters, nematode snoRNA loci are both intergenic and intronic (with and without promoters). Interestingly, plant snoRNAs are primarily located in intergenic regions. Other ncRNA genes (i.e., non-snoRNA genes) are mainly located in intergenic regions in both plants and animals. But in nematodes, Chen’s team found that many of these other ncRNA genes are located in the introns of host protein-coding genes and are under the control of independent promoter elements.

Finally, Chen and his colleagues estimated that 2700 ncRNA genes are present in the C. elegans genome. “One particularly intriguing aspect of the non-coding transcriptome is its potential to fill the regulatory gap created by the surprisingly low number of protein-coding genes in higher organisms,” says Chen. “Between one-celled yeast, thousand-celled nematodes, and trillion-celled mammals, there is a difference of a mere 6,000 to 19,000 to 25,000 in protein-coding gene numbers. We think that regulation by non-coding RNA accounts for this discrepancy and helps to explain the additional biological complexity of higher organisms.”