As the herculean genome sequencing efforts closed in on a draft of the human genome sequence back in 2000, the estimated numbers of “genes” that comprised our genome dropped quicker than the market cap of the biotech heavy Nasdaq after Clinton/Blair announced the sequences of these little gems would reside in the public domain.
Shortly after, groups like RIKEN, armed with a lab full of sequencers, began taking a deep looking into the transcriptome by sequencing as many full-length cDNA clones they could get their hands on while other curious research teams at Affymetrix took full advantage of their access to tiling arrays for probing (yes we like to insert a little microarray humor where possible) the transcriptome. Their results started to support what non-coding RNA enthusiasts like John Mattick were thinking for years.
“And the more I thought and read about it, the more I was convinced that the genome was not junk but largely comprises information that intellectually and biochemically had slipped under the radar of biochemists,” explained John Mattick, a major advocate for non-coding RNAs playing a central role in a diverse range of cellular processes.
Probing Functional ncRNA Xistence
Mattick isn’t just talking about the small RNAs that have been in vogue the last few years either. He and his colleagues have been vocal proponents of the idea that there exist tens, if not hundreds of thousands, of longer, functional non-coding RNAs working their magic in our cellular systems.
Sure some of these non-coding RNAs don’t exhibit much conservation, leading many to question their function, but lately we’ve see data emerge supporting strong conservation in novel classes like large intervening non-coding RNAs (lincRNAs). Moreover, as Mattick pointed out in a Nature Genetics Review (2009 Mar;10(3):155-9) last month, important non-coding RNAs like Xist don’t necessarily have to hold up to the same percent of conservation as their protein-coding relatives so long as their key functional regions are maintained.
Lately it seems not a week goes by without seeing new data supporting non-coding RNA involvement in key activities like laying down chromatin modifications in transcriptional gene silencing, or regulating DNA methylation as the broader research community rapidly warms up to the idea that our genomic real estate serves more purpose than housing a mere 20,000 protein encoding blueprints.
Don’t Call it a Comeback, They’ve Been Here for Years!
If non-coding RNA has been around forever, why has it taken so long to grab its share of the limelight? Its a combination of technology accessibility and research momentum and its hard to address the latter without the former. Most labs couldn’t dream of conducting some of the analyses that the early movers pulled off, even if they did believe there was gold in all that transcription. Fortunately, moving forward they won’t have to, as the recent advancements in high throughput RNA sequencing (RNA-Seq) and higher density tiling arrays have made it possible for more than just the well funded labs to start transcriptome profiling studies.
In addition to the data heavy, open transcriptome profiling platforms, we’re starting to see some dedicated platforms emerge for making sense of longer non-coding RNAs. The NCode™ Noncoding RNA Arrays were launched recently by Life Technologies, are produced by Agilent (how’s that for teamwork?), and have probes for interrogating about 17,000 human (10,000 for mouse) long non-coding RNAs from a variety of published sources*. They use the same microarray labeling/detection methods that have been used for profiling mRNA and make profiling longer non-coding RNAs even more straight forward and cost-effective.
Dr. Ranjan Perera, the Director of Genomics and R&D Labs at the Anderson Cancer Institute in Savannah, and Dr. Brian Nickoloff, a Director at the Oncology Institute at the Loyola University of Chicago Medical Center have been using the NCode™ Arrays to identify key non-coding RNAs that play a key function in our body’s largest organ, our skin.
“We have been taking a close look at non-coding RNAs in differentiating keritinocytes,” added Perera. “Right now I think these arrays are the only focused tool available for profiling non-coding RNAs.”
Regardless of the approach, the research momentum and technology advances appear to be pushing non-coding RNA research toward a tipping point and we at EpiGenie are more than happy to tag along for the ride!
Want a more intelligent commentary on non-coding RNA? Check out, Dr. John Mattick’s interview in Life’s Quest Magazine special issue on Epigenetics.
*Functional Annotation of Mouse (FANTOM3) project, Human Full-length cDNA Annotation Invitational (H-Invitational) project, antisense ncRNAs from cDNA and EST database for mouse and human using a computation pipeline (Engstrom et al. 2006), human snoRNAs and scaRNAs derived from snoRNA-LBME-db, RNAz (Washietl et al. 2005), Noncoding RNA Search (Torarinsson, et al. 2006), and EvoFold (Pedersen et al. 2006).