-
[
WormBook,
2005]
The C. elegans genome contains approximately 1300 genes that produce functional noncoding RNA (ncRNA) transcripts. Here we describe what is currently known about these ncRNA genes, from the perspective of the annotation of the finished genome sequence. We have collated a reference set of C. elegans ncRNA gene annotation relative to the WS130 version of the genome assembly, and made these data available in several formats.
-
[
WormBook,
2007]
Heterorhabditis bacteriophora is an entomopathogenic nematode (EPN) mutually associated with the enteric bacterium, Photorhabdus luminescens, used globally for the biological control of insects. Much of the previous research concerning H. bacteriophora has dealt with applied aspects related to biological control. However, H. bacteriophora is an excellent model to investigate fundamental processes such as parasitism and mutualism in addition to its comparative value to Caenorhabditis elegans. In June 2005, H. bacteriophora was targeted by NHGRI for a high quality genome sequence. This chapter summarizes the biology of H. bacteriophora in common and distinct from C. elegans, as well as the status of the genome project.
-
[
WormBook,
2006]
The completion of the C. elegans genome sequence permits the comprehensive examination of the expression and function of genes. Annotation of virtually every encoded gene in the genome allows systematic analysis of those genes using high-throughput assays, such as microarrays and RNAi. This chapter will center on the use of microarrays to comprehensively identify genes with enriched expression in the germ line during development. This knowledge provides a database for further studies that focus on gene function during germline development or early embryogenesis. Additionally, a comprehensive overview of germline gene expression can uncover striking biases in how genes expressed in the germ line are distributed in the genome, leading to new discoveries of global regulatory mechanisms in the germ line.
-
[
WormBook,
2006]
Transposons are discrete segments of DNA capable of moving through the genome of their host via an RNA intermediate in the case of class I retrotransposon or via a "cut-and-paste" mechanism for class II DNA transposons. Since transposons take advantage of their host''s cellular machinery to proliferate in the genome and enter new hosts, transposable elements can be viewed as parasitic or "selfish DNA". However, transposons may have been beneficial for their hosts as genome evolution drivers, thus providing an example of molecular mutualism. Interactions between transposon and C. elegans research were undoubtedly mutualistic, leading to the advent of needed genomic tools to drive C. elegans research while providing insights into the transposition field. Tc1, the first C. elegans transposon to be identified, turned out to be the founding member of a widespread family of mobile elements: the Tc1/ mariner superfamily. The investigation into transposition regulation in C. elegans has uncovered an unforeseen link between transposition, genome surveillance and RNA interference. Conversely, transposons were utilized soon after their identification to inactivate and clone genes, providing some of the first molecular identities of C. elegans genes. Recent results suggest that transposons might provide a means to engineer site-directed mutations into the C. elegans genome. This article describes the different transposons present in the C. elegans genome with a specific emphasis on the ones that proved to be mobile under laboratory conditions. Mechanisms and control of transposition are discussed briefly. Some tools based on the use of transposons for C. elegans research are presented at the end of this review.
-
[
WormBook,
2005]
Ion channels are the "transistors" (electronic switches) of the brain that generate and propagate electrical signals in the aqueous environment of the brain and nervous system. Potassium channels are particularly important because, not only do they shape dynamic electrical signaling, they also set the resting potentials of almost all animal cells. Without them, animal life as we know it would not exist, much less higher brain function. Until the completion of the C. elegans genome sequencing project the size and diversity of the potassium channel extended gene family was not fully appreciated. Sequence data eventually revealed a total of approximately 70 genes encoding potassium channels out of the more than 19,000 genes in the genome. This seemed to be an unexpectedly high number of genes encoding potassium channels for an animal with a small nervous system of only 302 neurons. However, it became clear that potassium channels are expressed in all cell types, not only neurons, and that many cells express a complex palette of multiple potassium channels. All types of potassium channels found in C. elegans are conserved in mammals. Clearly, C. elegans is "simple" only in having a limited number of cells dedicated to each organ system; it is certainly not simple with respect to its biochemistry and cell physiology.
-
[
WormBook,
2005]
The mitochondrial genome is vital for Caenorhabditis elegans metabolism, physiology, and development. The C. elegans mitochondrial DNA is typical of animal mitochondrial genomes in its size and gene content. It is 13,794 nucleotides in length and encodes 36 genes: 2 ribosomal RNAs, 22 transfer RNAs, and 12 protein subunits of the mitochondrial respiratory chain. Although it represents only a small number of genes, an elaborate cellular machinery comprised of over 200 nuclear genes is needed to replicate, transcribe, and maintain the mitochondrial chromosome and to assemble the translation machinery needed to express this dozen proteins. Mitochondrial genetics is peculiar and complex because mitochondrial DNA is maternally inherited and can be present at tens to tens of thousands of copies per cell. The mitochondrial genome content of the developing nematode is developmentally regulated; it increases about 30-fold between the L1 and the adult stages and blocking the increase leads to larval arrest. Energy metabolism is also intimately linked to aging and lifespan determination. The nematode model system offers numerous advantages for understanding the full importance and scope of the mitochondrial genome in animal life.
-
[
WormBook,
2006]
The DNA in eukaryotes is wrapped around a histone octamer core, together comprising the main subunit of chromatin, the nucleosome. Modifications of the nucleosomal histones in the genome correlate with the ability or inability of chromatin to form higher order structures, that in turn influence gene activity. The genome in primordial germ cells in early C. elegans germ cells carries a unique pattern of histone modifications that correlate with transcriptional repression in these cells, and aspects of this chromatin regulation are conserved in Drosophila. Loss of repression causes sterility in the adults, suggesting that chromatin-based repression is essential for germ line maintenance. The post-embryonic germ line also exhibits unique and dynamic aspects of chromatin regulation, with chromosome-wide regulation particularly evident on the X chromosome. Several properties of X-specific chromatin assembly are also sex-specific. These properties appear to be responding to the meiotic pairing status of the X chromosome, rather than the sex of the germ cells. Finally, gamete-specific chromatin regulation during gametogenesis impacts on X chromatin assembly in the offspring, leading to an apparent sperm-imprinted X inactivation in the early embryo. Other potential roles for germline-specific modes of chromatin assembly in genome regulation and protection are discussed.
-
[
WormBook,
2007]
The soil nematode Caenorhabditis briggsae is an attractive model system for studying evolution of both animal development and behavior. Being a close relative of C. elegans, C. briggsae is frequently used in comparative studies to infer species-specific function of the orthologous genes and also for studying the dynamics of chromosome evolution. The genome sequence of C. briggsae is valuable in reverse genetics and genome-wide comparative studies. This review discusses resources and tools, which are currently available, to facilitate study of C. briggsae in order to unravel mechanisms of gene function that confer morphological and behavioral diversity.
-
[
WormBook,
2006]
Throughout the C. elegans sequencing project Genefinder was the primary protein-coding gene prediction program. These initial predictions were manually reviewed by curators as part of a "first-pass annotation" and are actively curated by WormBase staff using a variety of data and information. In the WormBase data release WS133 there are 22,227 protein-coding gene, including 2,575 alternatively-spliced forms. Twenty-eight percent of these have every base of every exon confirmed by transcription evidence while an additional 51% have some bases confirmed. Most of the genes are relatively small covering a genomic region of about 3 kb. The average gene contains 6.4 coding exons accounting for about 26% of the genome. Most exons are small and separated by small introns. The median size of exons is 123 bases, while the most common size for introns is 47 bases. Protein-coding genes are denser on the autosomes than on chromosome X, and denser in the central region of the autosomes than on the arms. There are only 561 annotated pseudogenes but estimates but several estimates put this much higher.
-
[
Genetics,
2022]
The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.