Identifying potential tRNA genes in genomic DNA sequences

Draft genome sequence of Xylella fastidiosa strain ATCC 35874 isolated from infected red oak in Washington, DC

We report here the draft genome sequence of Xylella fastidiosa strain ATCC 35874. The strain was originally isolated from infected red oak in Washington, DC, and obtained from the American Type Culture Collection. The ATCC 35874 genome contains 2,543,332 bp and has a G + C content of 51.72%.

Draft Genome Sequence of a Xylella fastidiosa Strain Causing Bacterial Leaf Scorch of American Elm in Washington, DC

Here, we report the draft genome sequence of Xylella fastidiosa strain ATCC 35873, which was obtained from the American Type Culture Collection and was originally isolated from a symptomatic American elm tree grown in Washington, DC. The ATCC 35873 genome contains 2,454,216 bp and has a GC content of 51.68%.

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded. With the massive increase in quantity and phylogenetic diversity of genomes, the accurate detection and functional prediction of tRNAs has become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype- and clade-specific models, greatly improving tRNAscan-SE’s ability to identify and classify both typical and atypical tRNAs. We employ a new comparative multi-model strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models, allowing functional prediction based on both the anticodon and the highest-scoring isotype model. Comparative model scoring has also enhanced the program's ability to detect tRNA-derived SINEs and other likely pseudogenes. For the first time, tRNAscan-SE also includes fast and highly accurate detection of mitochondrial tRNAs using newly developed models. Overall, tRNA detection sensitivity and specificity is improved for all isotypes, particularly those utilizing specialized models for selenocysteine and the three subtypes of tRNA genes encoding a CAU anticodon. These enhancements will provide researchers with more accurate and detailed tRNA annotation for a wider variety of tRNAs, and may direct attention to tRNAs with novel traits.

Conserved long-range base pairings are associated with pre-mRNA processing of human genes

The ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3'-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation.

The Expansion of Inosine at the Wobble Position of tRNAs, and Its Role in the Evolution of Proteomes

The modification of adenosine to inosine at the first position of transfer RNA (tRNA) anticodons (I34) is widespread among bacteria and eukaryotes. In bacteria, the modification is found in tRNAArg and is catalyzed by tRNA adenosine deaminase A, a homodimeric enzyme. In eukaryotes, I34 is introduced in up to eight different tRNAs by the heterodimeric adenosine deaminase acting on tRNA. This substrate expansion significantly influenced the evolution of eukaryotic genomes in terms of codon usage and tRNA gene composition. However, the selective advantages driving this process remain unclear. Here, we have studied the evolution of I34, tRNA adenosine deaminase A, adenosine deaminase acting on tRNA, and their relevant codons in a large set of bacterial and eukaryotic species. We show that a functional expansion of I34 to tRNAs other than tRNAArg also occurred within bacteria, in a process likely initiated by the emergence of unmodified A34-containing tRNAs. In eukaryotes, we report on a large variability in the use of I34 in protists, in contrast to a more uniform presence in fungi, plans, and animals. Our data support that the eukaryotic expansion of I34-tRNAs was driven by the improvement brought by these tRNAs to the synthesis of proteins highly enriched in certain amino acids.

Codon adaptation to tRNAs with Inosine modification at position 34 is widespread among Eukaryotes and present in two Bacterial phyla

The modification of adenosine to inosine at position 34 of tRNA anticodons has a profound impact upon codon-anticodon recognition. In bacteria, I34 is thought to exist only in tRNA^Arg, while in eukaryotes the modification is present in eight different tRNAs. In eukaryotes, the widespread use of I34 strongly influenced the evolution of genomes in terms of tRNA gene abundance and codon usage. In humans, codon usage indicates that I34 modified tRNAs are preferred for the translation of highly repetitive coding sequences, suggesting that I34 is an important modification for the synthesis of proteins of highly skewed amino acid composition. Here we extend the analysis of distribution of codons that are recognized by I34 containing tRNAs to all phyla known to use this modification. We find that the preference for codons recognized by such tRNAs in genes with highly biased codon compositions is universal among eukaryotes, and we report that, unexpectedly, some bacterial phyla show a similar preference. We demonstrate that the genomes of these bacterial species contain previously undescribed tRNA genes that are potential substrates for deamination at position 34.

Characterization of a new chlorovirus type with permissive and non-permissive features on phylogenetically related algal strains

A previous report indicated that prototype chlorovirus PBCV-1 replicated in two Chlorella variabilis algal strains, NC64A and Syngen 2-3, that are ex-endosymbionts isolated from the protozoan Paramecium bursaria. Surprisingly, plaque-forming viruses on Syngen 2-3 lawns were often higher than on NC64A lawns from indigenous water samples. These differences led to the discovery of viruses that exclusively replicate in Syngen 2-3 cells, named Only Syngen (OSy) viruses. OSy-NE5, the prototype virus for the proposed new species, had a linear dsDNA genome of 327kb with 44-nucleotide-long, incompletely base-paired, covalently closed hairpin ends. Each hairpin structure was followed by an identical 2612 base-paired inverted sequence after which the DNA sequence diverged. OSy-NE5 encoded 357 predicted CDSs and 13 tRNAs. Interestingly, OSy-NE5 attached to and initiated infection in NC64A cells but infectious progeny viruses were not produced; thus OSy-NE5 replication in NC64A is blocked at some later stage of replication.

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

Methanogenesis is the primary biogenic source of methane in the atmosphere and a key contributor to climate change. The long-standing dogma that methanogenesis originated within the Euryarchaeota was recently challenged by the discovery of putative methane-metabolizing genes in members of the Bathyarchaeota, suggesting that methanogenesis may be more phylogenetically widespread than currently appreciated. Here, we present the discovery of divergent methyl-coenzyme M reductase genes in population genomes recovered from anoxic environments with high methane flux that belong to a new archaeal phylum, the Verstraetearchaeota. These archaea encode the genes required for methylotrophic methanogenesis, and may conserve energy using a mechanism similar to that proposed for the obligate H₂-dependent methylotrophic Methanomassiliicoccales and recently described Candidatus 'Methanofastidiosa'. Our findings indicate that we are only beginning to understand methanogen diversity and support an ancient origin for methane metabolism in the Archaea, which is changing our understanding of the global carbon cycle.

tRNAfeature: An algorithm for tRNA features to identify tRNA genes in DNA sequences

The identification of transfer RNAs (tRNAs) is critical for a detailed understanding of the evolution of biological organisms and viruses. However, some tRNAs are difficult to recognize due to their unusual sub-structures and may result in the detection of the wrong anticodon. Therefore, the detection of unusual sub-structures of tRNA genes remains an important challenge. In this study, we propose a method to identify tRNA genes based on tRNA features. tRNAfeature attempts to refold the sequence with single-stranded regions longer than those found in the canonical and conventional structural models for tRNA. We predicted a set of 53926 archaeal, eubacterial and eukaryotic tRNA genes annotated in tRNADB-CE and scanned the tRNA genes in whole genome sequencing. The results indicate that tRNAfeature is more powerful than other existing methods for identifying tRNAs.

Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis

To further our understanding of the RNAi machinery within the human nucleus, we analyzed the chromatin and RNA binding of Argonaute 2 (AGO2) within human cancer cell lines. Our data indicated that AGO2 binds directly to nascent tRNA and 5S rRNA, and to the genomic loci from which these RNAs are transcribed, in a small RNA- and DICER-independent manner. AGO2 chromatin binding was not observed at non-TFIIIC-dependent RNA polymerase III (Pol III) genes or at extra-TFIIIC (ETC) sites, indicating that the interaction is specific for TFIIIC-dependent Pol III genes. A genome-wide analysis indicated that loss of AGO2 caused a global increase in mRNA expression level among genes that flank AGO2-bound tRNA genes. This effect was shown to be distinct from that of the disruption of DICER, DROSHA, or CTCF. We propose that AGO2 binding to tRNA genes has a novel and important regulatory role in human cells.

piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells

BACKGROUND

Piwi-interacting RNAs (piRNAs) are a class of small RNAs; distinct types of piRNAs are expressed in the mammalian testis at different stages of development. The function of piRNAs expressed in the adult testis is not well established. We conducted a detailed characterization of piRNAs aligning at or near the 3' UTRs of protein-coding genes in a deep dataset of small RNAs from adult mouse testis.

RESULTS

We identified 2710 piRNA clusters associated with 3' UTRs, including 1600 that overlapped genes not previously associated with piRNAs. 35% of the clusters extend beyond the annotated transcript; we find that these clusters correspond to, and are likely derived from, novel polyadenylated mRNA isoforms that contain previously unannotated extended 3'UTRs. Extended 3' UTRs, and small RNAs derived from them, are also present in somatic tissues; a subset of these somatic 3'UTR small RNA clusters are absent in mice lacking MIWI2, indicating a role for MIWI2 in the metabolism of somatic small RNAs.

CONCLUSIONS

The finding that piRNAs are processed from extended 3' UTRs suggests a role for piRNAs in the remodeling of 3' UTRs. The presence of both clusters and extended 3'UTRs in somatic cells, with evidence for involvement of MIWI2, indicates that this pathway is more broadly distributed than currently appreciated.

Experimental confirmation of a whole set of tRNA molecules in two archaeal species

Based on the genomic sequences for most archaeal species, only one tRNA gene (isodecoder) is predicted for each triplet codon. This observation promotes analysis of a whole set of tRNA molecules and actual splicing patterns of interrupted tRNA in one organism. The entire genomic sequences of two Creanarchaeota, Aeropyrum pernix and Sulfolobus tokodaii, were determined approximately 15 years ago. In these genome datasets, 47 and 46 tRNA genes were detected, respectively. Among them, 14 and 24 genes, respectively, were predicted to be interrupted tRNA genes. To confirm the actual transcription of these predicted tRNA genes and identify the actual splicing patterns of the predicted interrupted tRNA molecules, RNA samples were prepared from each archaeal species and used to synthesize cDNA molecules with tRNA sequence-specific primers. Comparison of the nucleotide sequences of cDNA clones representing unspliced and spliced forms of interrupted tRNA molecules indicated that some introns were located at positions other than one base 3' from anticodon region and that bulge-helix-bulge structures were detected around the actual splicing sites in each interrupted tRNA molecule. Whole-set analyses of tRNA molecules revealed that the archaeal tRNA splicing mechanism may be essential for efficient splicing of all tRNAs produced from interrupted tRNA genes in these archaea.

Class-specific prediction of ncRNAs

Many RNA families, i.e., groups of homologous RNA genes, belong to RNA classes, such as tRNAs, snoRNAs, or microRNAs, that are characterized by common sequence motifs and/or common secondary structure features. The detection of new members of RNA classes, as well as the comprehensive annotation of genomes with members of RNA classes is a challenging task that goes beyond simple homology search. Computational methods addressing this problem typically use a three-tiered approach: In the first step an efficient and sensitive filter is employed. In the second step the candidate set is narrowed down using computationally expensive methods geared towards specificity. In the final step the hits are annotated with class-specific features and scored. Here we review the tools that are currently available for a diverse set of RNA classes.

Identification of RNA polymerase III-transcribed genes in eukaryotic genomes

The RNA polymerase (Pol) III transcription system is devoted to the production of short, generally abundant noncoding (nc) RNAs in all eukaryotic cells. Previously thought to be restricted to a few housekeeping genes easily detectable in genome sequences, the set of known Pol III-transcribed genes (class III genes) has been expanding in the last ten years, and the issue of their detection, annotation and actual expression has been stimulated and revived by the results of recent high-resolution genome-wide location analyses of the mammalian Pol III machinery, together with those of Pol III-centered computational studies and of ncRNA-focused transcriptomic approaches. In this article, we provide an outline of distinctive features of Pol III-transcribed genes that have allowed and currently allow for their detection in genome sequences, we critically review the currently practiced strategies for the identification of novel class III genes and transcripts, and we discuss emerging themes in Pol III transcription regulation which might orient future transcriptomic studies. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Identification of an entire set of tRNA molecules and characterization of cleavage sites of the intron-containing tRNA precursors in acidothermophilic crenarchaeon Sulfolobus tokodaii strain7

The acidothermophilic crenarchaeon, Sulfolobus tokodaii strain7, was isolated from a hot spring in Beppu, Kyushu, Japan. Whole genomic data of this microorganism indicated that among 46 putative tRNA genes identified, 24 were interrupted tRNA genes containing an intron. A sequence comparison between the cDNA sequences for unspliced and spliced tRNAs indicated that all predicted tRNAs were expressed and all intron portions were spliced in this microorganism. However, the actual cleavage site in the splicing process was not determined for 13 interrupted tRNAs because of the presence of the same nucleotides at both 5' and 3' border regions of each intron. The cleavage sites for all the introns, which were determined by an in vitro cleavage experiment with recombinant splicing endonuclease as well as cDNA sequencing of the spliced tRNAs, indicated that non-canonical BHB structure motifs were also recognized and processed by the splicing machinery in this organism. This is the first report to empirically determine the actual cleavage and splice sites of introns in the whole set of archaeal tRNA genes, and reassigns the exon-intron borders with a novel and more plausible non-canonical BHB structure.

Discovery of permuted and recently split transfer RNAs in Archaea

Background

As in eukaryotes, precursor transfer RNAs in Archaea often contain introns that are removed in tRNA maturation. Two unrelated archaeal species display unique pre-tRNA processing complexity in the form of split tRNA genes, in which two to three segments of tRNAs are transcribed from different loci, then trans-spliced to form a mature tRNA. Another rare type of pre-tRNA, found only in eukaryotic algae, is permuted, where the 3' half is encoded upstream of the 5' half, and must be processed to be functional.

Results

Using an improved version of the gene-finding program tRNAscan-SE, comparative analyses and experimental verifications, we have now identified four novel trans-spliced tRNA genes, each in a different species of the Desulfurococcales branch of the Archaea: tRNA^Asp(GUC) in Aeropyrum pernix and Thermosphaera aggregans, and tRNA^Lys(CUU) in Staphylothermus hellenicus and Staphylothermus marinus. Each of these includes features surprisingly similar to previously studied split tRNAs, yet comparative genomic context analysis and phylogenetic distribution suggest several independent, relatively recent splitting events. Additionally, we identified the first examples of permuted tRNA genes in Archaea: tRNA^iMet(CAU) and tRNA^Tyr(GUA) in Thermofilum pendens, which appear to be permuted in the same arrangement seen previously in red alga.

Conclusions

Our findings illustrate that split tRNAs are sporadically spread across a major branch of the Archaea, and that permuted tRNAs are a new shared characteristic between archaeal and eukaryotic species. The split tRNA discoveries also provide new clues to their evolutionary history, supporting hypotheses for recent acquisition via viral or other mobile elements.

Folding and finding RNA secondary structure

Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed.

Prediction and verification of mouse tRNA gene families

BACKGROUND

Transfer RNA (tRNA) gene predictions are complicated by challenges such as structural variation, limited sequence conservation and the presence of highly reiterated short interspersed sequences (SINEs) that originally derived from tRNA genes or tRNA-like transcription units. Annotation of "tRNA genes" in sequenced genomes generally have not been accompanied by experimental verification of the expression status of predicted sequences.

RESULTS

To address this for mouse tRNA genes, we have employed two programs, tRNAScan-SE and ARAGORN, to predict the tRNA genes in the nuclear genome, resulting in diverse but overlapping predicted gene sets. From these, we removed known SINE repeats and sorted the genes into predicted families and single-copy genes. In particular, four families of intron-containing tRNA genes were predicted for the first time in mouse, with introns in positions and structures similar to the well characterized intron-containing tRNA genes in yeast. We verified the expression of the predicted tRNA genes by microarray analysis. We then confirmed the expression of appropriately sized RNA for the four intron-containing tRNA gene families, as well as the other 30 tRNA gene families creating an index of expression-verified mouse tRNAs.

CONCLUSIONS

These confirmed tRNA genes represent all anticodons and all known mammalian tRNA structural groups, as well as a variety of predicted "rogue" tRNA genes within families with altered anticodon identities.

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

Transfer RNAs (tRNAs) represent the single largest, best-understood class of non-protein coding RNA genes found in all living organisms. By far, the major source of new tRNAs is computational identification of genes within newly sequenced genomes. To organize the rapidly growing collection and enable systematic analyses, we created the Genomic tRNA Database (GtRNAdb), currently including over 74 000 tRNA genes predicted from 740 species. The web resource provides overview statistics of tRNA genes within each analyzed genome, including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments. Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information. The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. The database is publicly available at http://gtrnadb.ucsc.edu.

Small RNA gene identification and mRNA target predictions in bacteria

MOTIVATION

Bacterial small ribonucleic acids (sRNAs) that are not ribosomal and transfer or messenger RNAs were initially identified in the sixties, whereas their molecular functions are still under active investigation today. It is now widely accepted that most play central roles in gene expression regulation in response to environmental changes. Interestingly, some are also implicated in bacterial virulence. Functional studies revealed that a large subset of these sRNAs act by an antisense mechanism thanks to pairing interactions with dedicated mRNA targets, usually around their translation start sites, to modulate gene expression at the posttranscriptional level. Some sRNAs modulate protein activity or mimic the structure of other macromolecules. In the last few years, in silico methods have been developed to detect more bacterial sRNAs. Among these, computational analyses of the bacterial genomes by comparative genomics have predicted the existence of a plethora of sRNAs, some that were confirmed to be expressed in vivo. The prediction accuracy of these computational tools is highly variable and can be perfectible. Here we review the computational studies that have contributed to detecting the sRNA gene and mRNA targets in bacteria and the methods for their experimental testing. In addition, the remaining challenges are discussed.

Computational methods in noncoding RNA research

Non protein-coding RNAs (ncRNAs) are a research hotspot in bioinformatics. Recent discoveries have revealed new ncRNA families performing a variety of roles, from gene expression regulation to catalytic activities. It is also believed that other families are still to be unveiled. Computational methods developed for protein coding genes often fail when searching for ncRNAs. Noncoding RNAs functionality is often heavily dependent on their secondary structure, which makes gene discovery very different from protein coding RNA genes. This motivated the development of specific methods for ncRNA research. This article reviews the main approaches used to identify ncRNAs and predict secondary structure.

An algorithm for searching RNA motifs in genomic sequences

RNA molecules, which are found in all living cells, fold into characteristic structures that account for their diverse functional activities. Many of these RNA structures consist of a collection of fundamental RNA motifs. The various combinations of RNA basic components form different RNA classes and define their unique structural and functional properties. The availability of many genome sequences makes it possible to search computationally for functional RNAs. Biological experiments indicate that functional RNAs have characteristic RNA structural motifs represented by specific combinations of base pairings and conserved nucleotides in the loop regions. The searching for those well-ordered RNA structures and their homologues in genomic sequences is very helpful for the understanding of RNA-based gene regulation. In this paper, we consider the following problem: given an RNA sequence with a known secondary structure, efficiently determine candidate segments in genomic sequences that can potentially form RNA secondary structures similar to the given RNA secondary structure. Our new bottom-up approach searches all potential stem-loops similar to ones of the given RNA secondary structure first, and then based on located stem-loops, detects potential homologous structural RNAs in genomic sequences.

The repertoire of transfer RNA genes is tuned to codon usage bias in the genomes of Phytophthora sojae and Phytophthora ramorum

In all, 238 and 155 transfer (t)RNA genes were predicted from the genomes of Phytophthora sojae and P. ramorum, respectively. After omitting pseudogenes and undetermined types of tRNA genes, there remained 208 P. sojae tRNA genes and 140 P. ramorum tRNA genes. There were 45 types of tRNA genes, with distinct anticodons, in each species. Fourteen common anticodon types of tRNAs are missing altogether from the genome in the two species; however, these appear to be compensated by wobbling of other tRNA anticodons in a manner which is tied to the codon bias in Phytophthora genes. The most abundant tRNA class was arginine in both P. sojae and P. ramorum. A codon usage table was generated for these two organisms from a total of 9,803,525 codons in P. sojae and 7,496,598 codons in P. ramorum. The most abundant codon type detected from the codon usage tables was GAG (encoding glutamic acid), whereas the most numerous tRNA gene had a methionine anticodon (CAT). The correlation between the frequencies of tRNA genes and the codon frequencies in protein-coding genes was very low (0.12 in P. sojae and 0.19 in P. ramorum); however, the correlation between amino acid tRNA gene frequency and the corresponding amino acid codon frequency in P. sojae and P. ramorum was substantially higher (0.53 in P. sojae and 0.77 in P. ramorum). The codon usage frequencies of P. sojae and P ramorum were very strongly correlated (0.99), as were tRNA gene frequencies (0.77). Approximately 60% of orthologous tRNA gene pairs in P sojae and P. ramorum are located in regions that have conserved synteny in the two species.

An algorithm for detecting homologues of known structured RNAs in genomes

Distinct RNA structures are frequently involved in a wide-range of functions in various biological mechanisms. The three dimensional RNA structures solved by X-ray crystallography and various well-established RNA phylogenetic structures indicate that functional RNAs have characteristic RNA structural motifs represented by specific combinations of base pairings and conserved nucleotides in the loop region. Discovery of well-ordered RNA structures and their homologues in genome-wide searches will enhance our ability to detect the RNA structural motifs and help us to highlight their association with functional and regulatory RNA elements. We present here a novel computer algorithm, HomoStRscan, that takes a single RNA sequence with its secondary structure to search for homologous-RNAs in complete genomes. This novel algorithm completely differs from other currently used search algorithms of homologous structures or structural motifs. For an arbitrary segment (or window) given in the target sequence, that has similar size to the query sequence, HomoStRscan finds the most similar structure to the input query structure and computes the maximal similarity score (MSS) between the two structures. The homologousRNA structures are then statistically inferred from the MSS distribution computed in the target genome. The method provides a flexible, robust and fine search tool for any homologous structural RNAs.

Computational analysis of RNAs

Genome sequence analysis of RNAs presents special challenges to computational biology, because conserved RNA secondary structure plays a large part in RNA analysis. Algorithms well suited for RNA secondary structure and sequence analysis have been borrowed from computational linguistics. These "stochastic context-free grammar" (SCFG) algorithms have enabled the development of new RNA gene-finding and RNA homology search software. The aim of this paper is to provide an accessible introduction to the strengths and weaknesses of SCFG methods and to describe the state of the art in one particular kind of application: SCFG-based RNA similarity searching. The INFERNAL and RSEARCH programs are capable of identifying distant RNA homologs in a database search by looking for both sequence and secondary structure conservation.

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

Transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) are two of the largest classes of non-protein-coding RNAs. Conventional gene finders that detect protein-coding genes do not find tRNA and snoRNA genes because they lack the codon structure and statistical signatures of protein-coding genes. Previously, we developed tRNAscan-SE, snoscan and snoGPS for the detection of tRNAs, methylation-guide snoRNAs and pseudouridylation-guide snoRNAs, respectively. tRNAscan-SE is routinely applied to completed genomes, resulting in the identification of thousands of tRNA genes. Snoscan has successfully detected methylation-guide snoRNAs in a variety of eukaryotes and archaea, and snoGPS has identified novel pseudouridylation-guide snoRNAs in yeast and mammals. Although these programs have been quite successful at RNA gene detection, their use has been limited by the need to install and configure the software packages on UNIX workstations. Here, we describe online implementations of these RNA detection tools that make these programs accessible to a wider range of research biologists. The tRNAscan-SE, snoscan and snoGPS servers are available at http://lowelab.ucsc.edu/tRNAscan-SE/, http://lowelab.ucsc.edu/snoscan/ and http://lowelab.ucsc.edu/snoGPS/, respectively.

Approximate matching of structured motifs in DNA sequences

Several methods have been developed for identifying more or less complex RNA structures in a genome. All these methods are based on the search for conserved primary and secondary sub-structures. In this paper, we present a simple formal representation of a helix, which is a combination of sequence and folding constraints, as a constrained regular expression. This representation allows us to develop a well-founded algorithm that searches for all approximate matches of a helix in a genome. The algorithm is based on an alignment graph constructed from several copies of a pushdown automaton, arranged one on top of another. This is a first attempt to take advantage of the possibilities of pushdown automata in the context of approximate matching. The worst time complexity is O(krpn), where k is the error threshold, n the size of the genome, p the size of the secondary expression, and r its number of union symbols. We then extend the algorithm to search for pseudo-knots and secondary structures containing an arbitrary number of helices.

In search of RNase P RNA from microbial genomes

A simple procedure has been developed to quickly retrieve and validate the DNA sequence encoding the RNA subunit of ribonuclease P (RNase P RNA) from microbial genomes. RNase P RNA sequences were identified from 94% of bacterial and archaeal complete genomes where previously no RNase P RNA was annotated. A sequence was found in camelpox virus, highly conserved in all orthopoxviruses (including smallpox virus), which could fold into a putative RNase P RNA in terms of conserved primary features and secondary structure. New structure features of RNase P RNA that enable one to distinguish bacteria from archaea and eukarya were found. This RNA is yet another RNA that can be a molecular criterion to divide the living world into three domains (bacteria, archaea, and eukarya). The catalytic center of this RNA, and its detection from some environmental whole genome shotgun sequences, is also discussed.

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics

We screened for new structural non-coding RNAs (ncRNAs) in the genome sequence of the yeast Saccharomyces cerevisiae using computational comparative analysis of genome sequences from five related species of Saccharomyces. The screen identified 92 candidate ncRNA genes. Thirteen showed discrete transcripts when assayed by northern blot. Of these, eight appear to be novel ncRNAs ranging in size from 268 to 775 nt, including three new H/ACA box small nucleolar RNAs.

A novel method for finding tRNA genes

We describe a novel procedure for generating and optimizing pattern descriptors that can be used to find structural motifs in DNA or RNA sequences. This combines a pattern-description language (based primarily on secondary structure alignment and conservation of some key nucleotides) with a scoring function that relies heavily on estimated folding free energies for the secondary structure of interest. For the cloverleaf secondary structure characteristic of tRNA, we show that a fairly simple pattern descriptor can find almost all known tRNA genes in both bacterial and eukaryotic genomes, and that false positives (sequences that match the pattern but that are probably not tRNAs) can be recognized by their high estimated folding free energies. A general procedure for optimizing descriptors (and hence for finding new structural motifs) is also described. For six bacterial, four eukaryotic, and four archaea genome sequences, our results compare favorably with those of the more complex and specialized tRNAscan-SE algorithm. Prospects for using this general approach to find other RNA structural motifs are discussed.

Regulation by RNA

In recent years, noncoding RNAs (ncRNAs) have been shown to constitute key elements implicated in a number of regulatory mechanisms in the cell. They are present in bacteria and eukaryotes. The ncRNAs are involved in regulation of expression at both transcriptional and posttranscriptional levels, by mediating chromatin modifications, modulating transcription factor activity, and influencing mRNA stability, processing, and translation. Noncoding RNAs play a key role in genetic imprinting, dosage compensation of X-chromosome-linked genes, and many processes of differentiation and development.

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

BACKGROUND

Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs.

RESULTS

I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic programming algorithms for linear sequence alignment. The new algorithm has an O(N2 log N) memory complexity, at the expense of a small constant factor in time.

CONCLUSIONS

Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB.

Searching for RNA genes using base-composition statistics

The hypothesis that genomic regions rich in non-protein-coding RNAs (ncRNAs) can be identified using local variations in single-base and dinucleotide statistics has been investigated. (G+C)%, (G-C)% difference, (A-T)% difference and dinucleotide-frequency statistics were compared among seven classes of ncRNAs and three genomes. Significant variations were observed in (G+C)% and, in Methanococcus jannaschii, in the frequency of the dinucleotide 'CG'. Screening programs based on these two base-composition statistics were developed. With (G+C)% screening alone, a 1% fraction of the M.jannaschii genome containing all 44 known transfer RNAs, ribosomal RNAs and signal recognition particle RNAs could be identified. When (G+C)% combined with CG dinucleotide-frequency screening was used, 43 of the 44 known M.jannaschii structural ncRNAs were again identified, while the number of presumably false hits overlapping a known or putative protein-coding gene was reduced from 15 to 6. In addition, 19 candidate ncRNAs were identified including one with significant homology to several known archaeal RNaseP RNAs.

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens

We have determined the complete 1,694,969-nt sequence of the GC-rich genome of Methanopyrus kandleri by using a whole direct genome sequencing approach. This approach is based on unlinking of genomic DNA with the ThermoFidelase version of M. kandleri topoisomerase V and cycle sequencing directed by 2'-modified oligonucleotides (Fimers). Sequencing redundancy (3.3x) was sufficient to assemble the genome with less than one error per 40 kb. Using a combination of sequence database searches and coding potential prediction, 1,692 protein-coding genes and 39 genes for structural RNAs were identified. M. kandleri proteins show an unusually high content of negatively charged amino acids, which might be an adaptation to the high intracellular salinity. Previous phylogenetic analysis of 16S RNA suggested that M. kandleri belonged to a very deep branch, close to the root of the archaeal tree. However, genome comparisons indicate that, in both trees constructed using concatenated alignments of ribosomal proteins and trees based on gene content, M. kandleri consistently groups with other archaeal methanogens. M. kandleri shares the set of genes implicated in methanogenesis and, in part, its operon organization with Methanococcus jannaschii and Methanothermobacter thermoautotrophicum. These findings indicate that archaeal methanogens are monophyletic. A distinctive feature of M. kandleri is the paucity of proteins involved in signaling and regulation of gene expression. Also, M. kandleri appears to have fewer genes acquired via lateral transfer than other archaea. These features might reflect the extreme habitat of this organism.

RNAMotif, an RNA secondary structure definition and search algorithm

RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural motifs will therefore enhance our understanding of RNA structure and help associate elements of RNA structure with functional and regulatory elements. Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif search algorithm, RNAMotif, and demonstrate its utility with some motif search examples. RNAMotif differs from other motif search tools in two important aspects: first, the structure definition language is more flexible and can specify any type of base-base interaction; second, RNAMotif provides a user controlled scoring section that can be used to add capabilities that patterns alone cannot provide.

Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles

We present here a new approach to the problem of defining RNA signatures and finding their occurrences in sequence databases. The proposed method is based on "secondary structure profiles". An RNA sequence alignment with secondary structure information is used as an input. Two types of weight matrices/profiles are constructed from this alignment: single strands are represented by a classical lod-scores profile while helical regions are represented by an extended "helical profile" comprising 16 lod-scores per position, one for each of the 16 possible base-pairs. Database searches are then conducted using a simultaneous search for helical profiles and dynamic programming alignment of single strand profiles. The algorithm has been implemented into a new software, ERPIN, that performs both profile construction and database search. Applications are presented for several RNA motifs. The automated use of sequence information in both single-stranded and helical regions yields better sensitivity/specificity ratios than descriptor-based programs. Furthermore, since the translation of alignments into profiles is straightforward with ERPIN, iterative searches can easily be conducted to enrich collections of homologous RNAs.

Variation in the spacer regions separating tRNA genes in Renibacterium salmoninarum distinguishes recent clinical isolates from the same location

A means for distinguishing between clinical isolates of Renibacterium salmoninarum that is based on the PCR amplification of length polymorphisms in the tRNA intergenic spacer regions (tDNA-ILPs) was investigated. The method used primers specific to nucleotide sequences of R. salmoninarum tRNA genes and tRNA intergenic spacer regions that had been generated by using consensus tRNA gene primers. Twenty-one PCR products were sequenced from five isolates of R. salmoninarum from the United States, England, and Scotland, and four complete tRNA genes and spacer regions were identified. Sixteen specific PCR primers were designed and tested singly and in all possible pairwise combinations for their potential to discriminate between isolates from recent clinical outbreaks of bacterial kidney disease (BKD) in the United Kingdom. Fourteen of the isolates were cultured from kidney samples taken from fish displaying clinical signs of BKD on five farms, and some of the isolates came from the same farm and at the same time. The tDNA-ILP profiles separated 22 clinical isolates into nine groups and highlighted that some farms may have had more than one source of infection. The grouping of isolates improved on the discriminatory power of previously reported typing methods based on randomly amplified polymorphic DNA analysis and restriction fragment length profiles developed using insertion sequence IS994. Our method enabled us to make divisions between closely related clinical isolates of R. salmoninarum that have identical exact tandem repeat (ETR-A) loci, rRNA intergenic spacer sequences, and IS994 profiles.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Genome sequence of the nematode C. elegans: a platform for investigating biology

The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms. There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly conserved genes provides evidence for a regional organization of the chromosomes.

Computational methods for exon detection

Computer methods for the complete and accurate detection of genes in vertebrate genomic sequences are still a long way to perfection. The intermediate task of identifying the coding moiety of genes (coding exons) is now reasonably well achieved using a combination of methods. After reviewing the intrinsic difficulties in interpreting vertebrate genomic sequences, this article presents the state-of-the-art, with an emphasis on similarity search methods and the resources available through Internet.

The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis

The completion of the entire 4.2-Mb genome sequence of the gram-positive bacterium Bacillus subtilis has been a milestone for biological studies on this model organism. This paper describes bioinformatics work related to this joint European and Japanese project: methods and strategies for gene annotation and detection of sequencing errors, using an integrated cooperative computer environment (Imagene); construction of a specialized database for data management and a WWW server for data retrieval (SubtiList); DNA sequence analysis, yielding striking results on oligonucleotide bias, repeated sequences, and codon usage, all landmarks of evolutionary events shaping the B. subtilis genome.

A chimeric Ty3/Moloney murine leukemia virus integrase protein is active in vivo

This report describes the results of experiments to determine whether chimeras between a retrovirus and portions of Ty3 are active in vivo. A chimera between Ty3 and a Neo(r)-marked Moloney murine leukemia virus (M-MuLV) was constructed. The C-terminal domain of M-MuLV integrase (IN) was replaced with the C-terminal domain of Ty3 IN. The chimeric retroviruses were expressed from an amphotrophic envelope packaging cell line. The virus generated was used to infect the human fibrosarcoma cell line HT1080, and cells in which integration had occurred were selected by G418 resistance. Three independently integrated viruses were rescued. In each case, the C-terminal Ty3 IN sequences were maintained and short direct repeats of the genomic DNA flanked the integration site. Sequence analysis of the genomic DNA flanking the insertion did not identify a tRNA gene; therefore, these integration events did not have Ty3 position specificity. This study showed that IN sequences from the yeast retrovirus-like element Ty3 can substitute for M-MuLV IN sequences in the C-terminal domain and contribute to IN function in vivo. It is also one of the first in vivo demonstrations of activity of a retrovirus encoding an integrase chimera. Studies of chimeras between IN species with distinctive integration patterns should complement previous work by expanding our understanding of the roles of nonconserved domains.