research highlights

SMALL RNAs Partners in time, partners in crime

Phylogenetic profiling implicates diverse Ruvkun’s team generated profiles for in small-RNA pathways. worm RNAi components across 86 species, In his search for genetic culprits, Gary finding many new candidates. Tabach also Ruvkun of Harvard University has resorted developed a statistical method to combine to criminal profiling. Faced with long lists expression and interaction of suspects involved in RNA interference data with the phylogenetic profile to predict (RNAi), he needed a way to prioritize can- function. The team experimentally evalu- didates from noisy functional screens in the ated a large fraction of the top candidates, roundworm Caenorhabditis elegans. RNAi including splicing factors that support an is used by many organisms to regulate gene RNAi mechanism that monitors intron expression or silence foreign RNA. While on presence to distinguish invading viral the trail of the Argonaute that bind from host genes. RNA to trigger silencing, Ruvkun stumbled Ruvkun’s excitement about the approach across a database showing their distribution is captured in his favorite candidate: phos- in seven disparate species, and he realized phoglycerate mutase, a sugar metabolism that many hits from his screens shared the protein. “As a developmental biologist, if same evolutionary profile. you were to ask me 20 years ago, ‘Do you Phylogenetic profiling has been around want to work on phosphoglycerate mutase?’ for at least 15 years, since Eugene Koonin I’d shout out, ‘NO’!” says Ruvkun. “But here and his group at the US National Center for we are; its phylogenetic profile is gorgeous.” Biotechnology Information outlined the Worm phosphoglycerate mutase has the concept of clusters of orthologous groups same profile as RNA-dependent RNA poly- (COGs). In Koonin’s original approach, merase, the amplification engine of RNAi. proteins that cluster by their shared pres- “There’s a 100% correlation—if you have ence or absence across evolutionary lineag- the worm kind, you do RNAi like a race es are thought to do similar things because, car, and if you’re the human kind, you do for example, they act in the same protein RNAi like a jalopy,” says Ruvkun, raising the complexes or pathways. If at least one mem- provocative question of why glycolysis is so ber of a cluster has a known function, the different between humans, who do not have same function can be inferred for the other these polymerases, and worms.

© 2013 Nature America, Inc. All rights reserved. America, Inc. © 2013 Nature members. Unlike sequence similarity, phylogenetic The approach has had success in , profiling can be used to pin the same func- the first organisms to have their genomes tion on seemingly unrelated proteins, and

npg sequenced. The clear loss and retention pat- Ruvkun believes that it should be used as a tern of Argonautes actually led Koonin and gene annotation tool. Only genes conserved his group, who developed the COG data- outside their immediate evolutionary base that Ruvkun stumbled on, to predict neighborhood are eligible, though, exclud- their role in RNAi early on. In , ing roughly half of the worm . profiling has been largely restricted to pro- The current work is limited to a gene- teins related to the loss or retention of entire and organism-centric view of evolved structures such as mitochondria. functions. But the approach can be applied Generalizing the approach fell to lead to other processes and may eventually be postdoc Yuval Tabach. Using his biostatis- broadened to an all-against-all comparison. tics savvy, Tabach found a way to represent Phylogenetic profiling has found new cul- protein sequence divergence and partial prits in a well-studied area, positioning it loss rather than only total loss or reten- as a good way to bring diverse proteins and tion. Candidates are then ranked by how the people who study them together to the similar their profile is to that of a known same crime scene. worm RNAi protein. Tabach also included Tal Nawy normalizations to make more meaningful evolutionary inferences. For instance, con- RESEARCH PAPERS Tabach, Y. et al. Identification of small RNA pathway servation between two proteins is normal- genes using patterns of phylogenetic conservation ized by the evolutionary distance between and divergence. Nature advance online publication the two species. (23 December 2012).

108 | VOL.10 NO.2 | FEBRUARY 2013 | nature methods