Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray

The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein-coding transcriptome remains unknown. Expression profiling on whole-genome tiling microarrays applied to a mixed-stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction (11%) of the polyadenylated transcription is non-annotated and appears to consist of approximately 3200 missed or alternative exons and 7800 small transcripts of unknown function (TUFs). Almost half (44%) of the detected transcriptional output is non-polyadenylated and probably not protein coding, and of this, 70% overlaps the boundaries of protein-coding genes in a complex manner. Specific analysis of small non-polyadenylated transcripts verified 97% of all annotated small ncRNAs and suggested that the transcriptome contains approximately 1200 small (<500 nt) unannotated noncoding loci. After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed.

Functional diversification of the nematode mbd2/3 gene between Pristionchus pacificus and Caenorhabditis elegans

Background

Several members of the Methyl-Binding Domain protein family link DNA methylation with chromatin remodeling complexes in vertebrates. Amongst the four classes of MBD proteins, MBD2/3 is the most highly conserved and widespread in metazoans. We have previously reported that an mbd2/3 like gene (mbd-2) is encoded in the genomes of the nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae. RNAi knock-down of mbd-2 in the two Caenorhabditis species results in varying percentages of lethality.

Results

Here, we report that a general feature of nematode MBD2/3 proteins seems to be the lack of a bona fide methyl-binding domain. We isolated a null allele of mbd-2 in P. pacificus and show that Ppa-mbd-2 mutants are viable, fertile and display a fully penetrant egg laying defect. This egg laying defect is partially rescued by treatment with acetylcholine or nicotine suggesting a specific function of this protein in vulval neurons. Using Yeast-two-hybrid screens, Ppa-MBD-2 was found to associate with microtubule interacting and vesicle transfer proteins.

Conclusion

These results imply that MBD2/3 proteins in nematodes are more variable than their relatives in insects and vertebrates both in structure and function. Moreover, nematode MBD2/3 proteins assume functions independent of DNA methylation ranging from the indispensable to the non-essential.

Identification and analysis of internal promoters in Caenorhabditis elegans operons

The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoterGFP methodology, we have conducted the largest survey to date on the regulatory regions of annotated C. elegans operons and identified 65, over 25% of those studied, with internal promoters. We have termed these operons "hybrid operons." GFP expression patterns driven from internal promoters differ in tissue specificity from expression of operon promoters, and serial analysis of gene expression data reveals that there is a lack of expression correlation between genes in many hybrid operons. The average length of intergenic regions with putative promoter activity in hybrid operons is larger than previous estimates for operons as a whole. Genes with internal promoters are more commonly involved in gene duplications and have a significantly lower incidence of alternative splicing than genes without internal promoters, although we have observed almost all trans-splicing patterns in these two distinct groups. Finally, internal promoter constructs are able to rescue lethal knockout phenotypes, demonstrating their necessity in gene regulation and survival. Our work suggests that hybrid operons are common in the C. elegans genome and that internal promoters influence not only gene organization and expression but also operon evolution.

Meiotic recombination in Caenorhabditis elegans

The faithful segregation of homologous chromosomes during meiosis is dependent on the formation of physical connections (chiasma) that form following reciprocal exchange of DNA molecules during meiotic recombination. Here we review the current knowledge in the Caenorhabditis elegans meiotic recombination field. We discuss recent developments that have improved our understanding of the crucial steps that must precede the initiation and propagation of meiotic recombination. We summarize the pathways that impact on meiotic prophase entry and the current understanding of how chromosomes reorganize and interact to promote homologous chromosome pairing and subsequent synapsis. We pay particular attention to the mechanisms that contribute to meiotic DNA double-strand break (DSB) formation and strand exchange processes, and how the C. elegans system compares with other model organisms. Finally, we highlight current and future areas of research that are likely to further our understanding of the meiotic recombination process.

DNA probes for identifying chromosomes 5, 6, and 7 of Schistosoma mansoni

Schistosoma mansoni has a genome of 270 Mb contained on 8 pairs of chromosomes. C-banding has been a useful technique in identifying the 7 autosomal and sex chromosomes. However, even with C-banding, S. mansoni chromosomes 5, 6, and 7 are difficult to discriminate from each other, because of their small sizes, morphological similarity, and poor banding patterns. We have identified probes that specifically paint chromosomes 5, 6, and 7 of S. mansoni with the use of chromosome microdissection and the degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR). Exact chromosome identification is required for accurate chromosome mapping of genomic clones and genetic elements, which is an essential component of the schistosome genome project.

Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny

To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism-based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80-110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.

Characterization of the complete mitochondrial genome of Diphyllobothrium nihonkaiense (Diphyllobothriidae: Cestoda), and development of molecular markers for differentiating fish tapeworms

We sequenced and characterized the complete mitochondrial genome of the Japanese fish tapeworm D. nihonkaiense. The genome is a circular-DNA molecule of 13607 bp (one nucleotide shorter than that of D. latum mtDNA) containing 12 protein-coding genes (lacking atp8), 22 tRNA genes and two rRNA genes. Gene order and genome content are identical to those of the other cestodes reported thus far, including its congener D. latum. The only exception is Hymenolepis diminuta in which the positions of trnS2 and trnL1 are switched. We tested a PCR-based molecular assay designed to rapidly and accurately differentiate between D. nihonkaiense and D. latum using species-specific primers based on a comparison of their mtDNA sequences. We found the PCR-based system to be very reliable and specific, and suggest that PCR-based identification methods using mtDNA sequences could contribute to the study of the epidemiology and larval ecology of Diphyllobothrium species.

Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure

MOTIVATION

Correct gene predictions are crucial for most analyses of genomes. However, in the absence of transcript data, gene prediction is still challenging. One way to improve gene-finding accuracy in such genomes is to combine the exons predicted by several gene-finders, so that gene-finders that make uncorrelated errors can correct each other.

RESULTS

We present a method for combining gene-finders called Genomix. Genomix selects the predicted exons that are best conserved within and/or between species in terms of sequence and intron-exon structure, and combines them into a gene structure. Genomix was used to combine predictions from four gene-finders for Caenorhabditis elegans, by selecting the predicted exons that are best conserved with C.briggsae and C.remanei. On a set of approximately 1500 confirmed C.elegans genes, Genomix increased the exon-level specificity by 10.1% and sensitivity by 2.7% compared to the best input gene-finder.

AVAILABILITY

Scripts and Supplementary Material can be found at http://www.sanger.ac.uk/Software/analysis/genomix

Genetic regulation of arrested development in nematodes: are age-1 and daf-gene orthologs present in Dictyocaulus viviparus?

In opposite to the free-living soil nematode Caenorhabditis elegans, the genetic regulation of hypobiosis or inhibited or arrested development in parasitic nematodes is completely unknown. In C. elegans, the daf-genes or the age-1 gene are of major importance in signaling pathways regulating arrested development. To investigate if orthologs of these genes are present in the bovine lungworm Dictyocaulus viviparus, a PCR analysis with gene-specific primer combinations was performed. No orthologs of the age-1 or daf-genes could be identified in D. viviparus. The possible differences in the role of the daf-genes concerning arrested development in parasitic and free-living nematodes will be discussed.

Transcription factor NFY globally represses the expression of the C. elegans Hox gene Abdominal-B homolog egl-5

The C. elegans Hox gene egl-5 (ortholog of Drosophila Abdominal-B) is expressed in multiple tissues in the tail region and is involved in tail patterning. In this study, we identify and clone the corresponding C. elegans orthologs of the components of the heterotrimeric transcription factor NFY, nfya-1, nfyb-1 and nfyc-1 and demonstrate that mutations in these components result in the ectopic expression of egl-5 outside of its normal expression domains. The NFYA-1 protein forms a complex with NFYB-1 and NFYC-1, specifically recognizing the CCAAT box. Mutating a CCAAT box in the proximal promoter of egl-5 also leads to the derepression of egl-5, suggesting a direct role for the NFY complex in the regulation of egl-5. In addition, we show that the NFY complex interacts with the MES-2/MES-6 PcG complex in Hox gene regulation. Thus, our studies unravel a physiological function of NFY in establishing the spatially restricted expression pattern of egl-5.

Schistosome biology and proteomics: progress and challenges

The recent availability of schistosomal genome-sequence information allows protein identification in schistosome-derived samples by mass spectrometry (proteomics). Over the last few years, several proteome studies have been performed that addressed important questions in schistosome biology. This review summarizes the applied experimental approaches that have been used so far, it provides an overview of the most important conclusions that can be drawn from the performed studies and finally discusses future challenges in this research area.

Meiotic parthenogenesis in a root-knot nematode results in rapid genomic homozygosity

Many isolates of the plant-parasitic nematode Meloidogyne hapla reproduce by facultative meiotic parthenogenesis. Sexual crosses can occur, but, in the absence of males, the diploid state appears to be restored by reuniting sister chromosomes of a single meiosis. We have crossed inbred strains of M. hapla that differ in DNA markers and produced hybrids and F(2) lines. Here we show that heterozygous M. hapla females, upon parthenogenetic reproduction, produce progeny that segregate 1:1 for the presence or absence of dominant DNA markers, as would be expected if sister chromosomes are rejoined, rather than the 3:1 ratio typical of a Mendelian cross. Codominant markers also segregate 1:1 and heterozygotes are present at low frequency (<3%). Segregation patterns and recombinant analysis indicate that a homozygous condition is prevalent for markers flanking recombination events, suggesting that recombination occurs preferentially as four-strand exchanges at similar locations between both pairs of non-sister chromatids. With this mechanism, meiotic parthenogenesis would be expected to result in rapid genomic homozygosity. This type of high negative crossover interference coupled with positive chromatid interference has not been observed in fungal or other animal systems in which it is possible to examine the sister products of a single meiosis and may indicate that meiotic recombination in this nematode has novel features.

Dramatic age-related changes in nuclear and genome copy number in the nematode Caenorhabditis elegans

The nematode Caenorhabditis elegans has become one of the most widely used model systems for the study of aging, yet very little is known about how C. elegans age. The development of the worm, from egg to young adult has been completely mapped at the cellular level, but such detailed studies have not been extended throughout the adult lifespan. Numerous single gene mutations, drug treatments and environmental manipulations have been found to extend worm lifespan. To interpret the mechanism of action of such aging interventions, studies to characterize normal worm aging, similar to those used to study worm development are necessary. We have used 4',6'-diamidino-2-phenylindole hydrochloride staining and quantitative polymerase chain reaction to investigate the integrity of nuclei and quantify the nuclear genome copy number of C. elegans with age. We report both systematic loss of nuclei or nuclear DNA, as well as dramatic age-related changes in nuclear genome copy number. These changes are delayed or attenuated in long-lived daf-2 mutants. We propose that these changes are important pathobiological characteristics of aging nematodes.

Genetic manipulation of schistosomes

In contrast to the situations with model organisms and parasitic protozoa, progress with gene manipulation with schistosomes has been delayed by impediments that include our inability to maintain the life cycle in vitro, absence of immortalized cell lines, large genome sizes, unavailability of drug resistance markers and other difficulties. However, in the past few years, tangible progress has been reported towards development of tools for gene manipulation and transgenesis of schistosomes, and there is reason to believe that the field is on the verge of transformation into an era where genetic manipulation is routine. Recent reports dealing with approaches and tools to manipulate the genome and gene expression in schistosomes are reviewed here.

Integrating transcriptome, proteome and glycome analyses of Schistosoma biology

Publication of the transcriptomes of Schistosoma mansoni and Schistosoma japonicum, in conjunction with the sequencing and assembly of their genomes, has generated a comprehensive picture of Schistosoma transcriptional and genomic diversity. Subsequently, researchers who study conjugal and developmental biology, tegumental composition and larval or egg, secretory and excretory products have used these data, in combination with the latest '-omics' technologies, to extend large-scale screens of the schistosome transcriptome, proteome and glycome. In this article, we review these postgenomic investigations and contend that the generated datasets provide a plethora of novel drug, vaccine and immunomodulatory targets that might be useful for developing new antischistosome agents.

Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean

Global analysis of gene expression changes in soybean (Glycine max) and Heterodera glycines (soybean cyst nematode [SCN]) during the course of infection in a compatible interaction was performed using the Affymetrix GeneChip soybean genome array. Among 35,611 soybean transcripts monitored, we identified 429 genes that showed statistically significant differential expression between uninfected and nematode-infected root tissues. These included genes encoding enzymes involved in primary metabolism; biosynthesis of phenolic compounds, lignin, and flavonoids; genes related to stress and defense responses; cell wall modification; cellular signaling; and transcriptional regulation. Among 7,431 SCN transcripts monitored, 1,850 genes showed statistically significant differential expression across different stages of nematode parasitism and development. Differentially expressed SCN genes were grouped into nine different clusters based on their expression profiles during parasitism of soybean roots. The patterns of gene expression we observed in SCN suggest coordinated regulation of genes involved in parasitism. Quantitative real-time reverse-transcription polymerase chain reaction confirmed the results of our microarray analysis. The simultaneous genome-wide analysis of gene expression changes in the host and pathogen during a compatible interaction provides new insights into soybean responses to nematode infection and the first profile of transcript abundance changes occurring in the nematode as it infects and establishes a permanent feeding site within a host plant root.

A common origin of complex life cycles in parasitic flatworms: evidence from the complete mitochondrial genome of Microcotyle sebastis (Monogenea: Platyhelminthes)

BACKGROUND

The parasitic Platyhelminthes (Neodermata) contains three parasitic groups of flatworms, each having a unique morphology, and life style: Monogenea (primarily ectoparasitic), Trematoda (endoparasitic flukes), and Cestoda (endoparasitic tapeworms). The evolutionary origin of complex life cyles (multiple obligate hosts, as found in Trematoda and Cestoda) and of endo-/ecto-parasitism in these groups is still under debate and these questions can be resolved, only if the phylogenetic position of the Monogenea within the Neodermata clade is correctly estimated.

RESULTS

To test the interrelationships of the major parasitic flatworm groups, we estimated the phylogeny of the Neodermata using complete available mitochondrial genome sequences and a newly characterized sequence of a polyopisthocotylean monogenean Microcotyle sebastis. Comparisons of inferred amino acid sequences and gene arrangement patterns with other published flatworm mtDNAs indicate Monogenea are sister group to a clade of Trematoda+Cestoda.

CONCLUSION

Results confirm that vertebrates were the first host for stem group neodermatans and that the addition of a second, invertebrate, host was a single event occurring in the Trematoda+Cestoda lineage. In other words, the move from direct life cycles with one host to complex life cycles with multiple hosts was a single evolutionary event. In association with the evolution of life cycle patterns, our result supports the hypothesis that the most recent common ancestor of the Neodermata giving rise to the Monogenea adopted vertebrate ectoparasitism as its initial life cycle pattern and that the intermediate hosts of the Trematoda (molluscs) and Cestoda (crustaceans) were subsequently added into the endoparasitic life cycles of the Trematoda+Cestoda clade after the common ancestor of these branched off from the monogenean lineage. Complex life cycles, involving one or more intermediate hosts, arose through the addition of intermediate hosts and not the addition of a vertebrate definitive host. Additional evidence is required from monopisthocotylean monogeneans in order to confirm the monophyly of the group.

Mitochondrial genomes of the human broad tapeworms Diphyllobothrium latum and Diphyllobothrium nihonkaiense (Cestoda: Diphyllobothriidae)

Mitochondrial DNA (mtDNA) sequences of the human broad tapeworms Diphyllobothrium latum and Diphyllobothrium nihonkaiense have been totally determined. Both of them are closed circular molecules (total length, 13,720 bp in D. latum and 13,747 bp in D. nihonkaiense) containing genes for 12 proteins, 22 transfer RNAs, and two ribosomal RNAs. All the genes are coded on T-rich strand. The gene order of Diphyllobothrium mtDNAs is completely identical with that of Taenia and Echinococcus mtDNAs. The overall A + T contents of the genomes are 68.3% in D. latum and 67.8% in D. nihonkaiense. The pairwise divergence values of nucleotide sequences between these tapeworms ranged from 0.069 to 0.152 in protein-coding genes, demonstrating that D. nihonkaiense is a distinct species. The sequences determined in this study may provide useful marker systems for diagnostic, epidemiological, and phylogeographical studies of human diphyllobothriasis.

WormBase: new content and better access

WormBase (http://wormbase.org), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.elegans, including data on classical genetics, cell biology and functional genomics; expanded the annotation of closely related nematodes with a new genome browser for Caenorhabditis remanei; and deployed new hardware for stronger performance. Several existing datasets including phenotype descriptions and RNAi experiments have seen a large increase in new content. New datasets such as the C.remanei draft assembly and annotations, the Vancouver Fosmid library and TEC-RED 5' end sites are now available as well. Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google.

Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus

Comparative studies have been of invaluable importance to the understanding of evolutionary biology. The evolution of developmental programs can be studied in nematodes at a single cell resolution given their fixed cell lineage. We have established Pristionchus pacificus as a major satellite organism for evolutionary developmental biology relative to Caenorhabditis elegans, the model nematode. Online genomic information to support studies in this satellite system can be accessed at . Our web resource offers diverse content covering genome browsing, genetic and physical maps, similarity searches, a community platform and assembly details. Content will be continuously improved as we annotate the P.pacificus genome, and will be an indispensable resource for P.pacificus genomics.

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in a model genetic organism, Caenorhabditis elegans, we have carried out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores were liberated using an enzyme (micrococcal nuclease) with a strong preference for cleavage in non-nucleosomal regions. Sequence analysis of 284,091 putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As has previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale.

Detection of broadly expressed neuronal genes in C. elegans

The genes that are expressed in most or all types of neurons define generic neuronal features and provide a window into the developmental origin and function of the nervous system. Few such genes (sometimes referred to as pan-neuronal or broadly expressed neuronal genes) have been defined to date and the mechanisms controlling their regulation are not well understood. As a first step in investigating their regulation, we used a computational approach to detect sequences overrepresented in their promoter elements. We identified a ten-nucleotide cis-regulatory motif shared by many broadly expressed neuronal genes and demonstrated that it is involved in control of neuronal expression. Our results further suggest that global and cell-type-specific controls likely act in concert to establish pan-neuronal gene expression. Using the newly discovered motif and genome-level gene expression data, we identified a set of 234 candidate broadly expressed genes. The known involvement of many of these genes in neurogenesis and physiology of the nervous system supports the utility of this set for future targeted analyses.

The evolution of biased codon and amino acid usage in nematode genomes

Despite the degeneracy of the genetic code, whereby different codons encode the same amino acid, alternative codons and amino acids are utilized nonrandomly within and between genomes. Such biases in codon and amino acid usage have been demonstrated extensively in prokaryote genomes and likely reflect a balance between the action of mutation, selection, and genetic drift. Here, we quantify the effects of selection and mutation drift as causes of codon and amino acid-usage bias in a large collection of nematode partial genomes from 37 species spanning approximately 700 Myr of evolution, as inferred from expressed sequence tag (EST) measures of gene expression and from base composition variation. Average G + C content at silent sites among these taxa ranges from 10% to 63%, and EST counts range more than 100-fold, underlying marked differences between the identities of major codons and optimal codons for a given species as well as influencing patterns of amino acid abundance among taxa. Few species in our sample demonstrate a dominant role of selection in shaping intragenomic codon-usage biases, and these are principally free living rather than parasitic nematodes. This suggests that deviations in effective population size among species, with small effective sizes among parasites, are partly responsible for species differences in the extent to which selection shapes patterns of codon usage. Nevertheless, a consensus set of optimal codons emerges that is common to most taxa, indicating that, with some notable exceptions, selection for translational efficiency and accuracy favors similar sets of codons regardless of the major codon-usage trends defined by base compositional properties of individual nematode genomes.

The genome ofOscheius tipulae: determination of size, complexity, and structure by DNA reassociation using fluorescent dye

This work describes the physicochemical characterization of the genome and telomere structure from the nematode Oscheius tipulae CEW1. Oscheius tipulae is a free-living nematode belonging to the family Rhabditidae and has been used as a model system for comparative genetic studies. A new protocol that combines fluorescent detection of double-stranded DNA and S1 nuclease was used to determine the genome size of O. tipulae as 100.8 Mb (approximately 0.1 pg DNA/haploid nucleus). The genome of this nematode is made up of 83.4% unique copy sequences, 9.4% intermediate repetitive sequences, and 7.2% highly repetitive sequences, suggesting that its structure is similar to those of other nematodes of the genus Caenorhabditis. We also showed that O. tipulae has the same telomere repeats already found in Caenorhabditis elegans at the ends and in internal regions of the chromosomes. Using a cassette-ligation-mediated PCR protocol we were able to obtain 5 different putative subtelomeric sequences of O. tipulae, which show no similarity to C. elegans or C. briggsae subtelomeric regions. DAPI staining of hermaphrodite gonad cells show that, as detected in C. elegans and other rhabditids, O. tipulae have a haploid complement of 6 chromosomes.Key words: Oscheius tipulae, Caenorhabditis elegans, DNA reassociation, telomere, genome size, karyotype.