No abstract

Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ~500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.

The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3D maps for other organisms. Data are provided for human and plant (Arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and eukarya. Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis. Displaying positions of modified nucleotides is fully manageable. Views of each modified nucleotide are controlled by individual buttons and buttons also control the visibility of different ribosomal molecular components. A section called ‘Paint Your Own’ enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known. This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins. The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/

One of the largest families of small RNAs in eukaryotes is the H/ACA small nucleolar RNAs (snoRNAs), most of which guide RNA pseudouridine formation. So far, an effective computational method specifically for identifying H/ACA snoRNA gene sequences has not been established. We have developed snoGPS, a program for computationally screening genomic sequences for H/ACA guide snoRNAs. The program implements a deterministic screening algorithm combined with a probabilistic model to score gene candidates. We report here the results of testing snoGPS on the budding yeast Saccharomyces cerevisiae. Six candidate snoRNAs were verified as novel RNA transcripts, and five of these were verified as guides for pseudouridine formation at specific sites in ribosomal RNA. We also predicted 14 new base-pairings between snoRNAs and known pseudouridine sites in S.cerevisiae rRNA, 12 of which were verified by gene disruption and loss of the cognate pseudouridine site. Our findings include the first prediction and verification of snoRNAs that guide pseudouridine modification at more than two sites. With this work, 41 of the 44 known pseudouridine modifications in S.cerevisiae rRNA have been linked with a verified snoRNA, providing the most complete accounting of the H/ACA snoRNAs that guide pseudouridylation in any species.

One of the exciting frontiers in the field of RNA editing is the phenomenon of RNA-guided nucleotide modification. In this type of editing, a nucleotide in a precursor RNA is converted to another form by an RNA-protein complex (RNP) 1 (1). The RNPs that mediate these reactions include a guide RNA that provides site specificity through base pairing with the substrate and a set of proteins, one of which catalyzes the modification reaction. The phenomenon was first discovered in the modification of ribosomal RNA (rRNA) in the nucleolus of eukaryotic cells (Fig. 1). Two common alterations are relevant, formation of 2Ј-O-methylated nucleosides (Nm; the guided mechanism was reported in 1996) and conversion of uridine to pseudouridine (⌿; the guided process was reported in 1997) (2-4). These modifications are mediated by two large, heterogeneous populations of RNPs that are modification type-specific and sitespecific. The RNPs contain a small nucleolar RNA (snoRNA) and several associated proteins, and the snoRNA-protein complexes are called snoRNPs ("snorps"). The snoRNA provides the guide function, and an integral snoRNP protein catalyzes the modification reaction. When discovered, this type of reaction scheme was not only novel but in sharp contrast to the rRNA modification schemes used by Eubacteria, where the synthesis of Nm and ⌿ is mediated (thus far) by protein enzymes that do not include an RNA co-factor (5). Guided modification was subsequently discovered to apply to the U6 snRNA (small nuclear RNA in vertebrates and Caenorhabditis elegans) and likely to mRNA (mammals, trypanosomes) (6 -9). Strikingly, from an evolutionary perspective, the new paradigm was also discovered (in 2000) to apply to Archaeal organisms where substrates include tRNA as well as rRNA (10).Recent advances have revealed guided modification to be more complex and widespread and are almost certainly a harbinger of exciting new developments to come. Key developments include: 1) identification of new guide RNAs that reside in mammalian Cajal bodies (these RNAs are specific for the four snRNAs transcribed by RNA polymerase II (pol II), which are thought to undergo maturation and possibly RNP assembly at this location (11)); 2) evidence that the trypanosome transspliced leader is a substrate for guided modification (9); and 3) successful development of the first cell-free Nm modification system, using recombinant archaeal components (12). Taken together, these findings argue that additional modifying RNPs and substrates subjected to RNA-guided modification will be discovered. In this minireview we describe the present state of knowledge about the various RNP-modifying complexes, the processes they mediate, where in the cell these reactions occur, and the range of substrates. Because of limited space the reader is also referred to other recent reviews (1,(13)(14)(15)(16)(17)(18).