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[
Curr Top Dev Biol,
2012]
Noncoding RNAs have emerged as an integral part of posttranscriptional gene regulation. Among that class of RNAs are the microRNAs (miRNAs), which posttranscriptionally regulate target mRNAs containing complementary sequences. The broad presence of miRNAs in lower eukaryotes, plants, and mammals highlights their importance throughout evolution. MiRNAs have been shown to regulate many pathways, including development, and disruption of miRNA function can lead to disease (Ivey and Srivastava, 2010; Jiang et al., 2009). Although the first miRNA genes were discovered in the nematode, Caenorhabditis elegans, almost 20 years ago, the field of miRNA research began when they were found in multiple organisms a little over a decade ago (Lagos-Quintana et al., 2001; Lau et al., 2001; Lee and Ambros, 2001; Lee et al., 1993; Pasquinelli et al., 2000; Wightman et al., 1993). Here, we review one of the first characterized miRNAs,
let-7, and describe its role in development and the intricacies of its biogenesis and function.
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[
2005]
RNA interference (RNAi) is a recently discovered phenomenon in which doublestranded RNA (dsRNA) silences endogenous gene expression in a sequencespecific manner (Fire et al., 1998). Since its discovery, the use of RNAi has become widely employed in many organisms to specifically knock down gene function. RNAi shares a remarkable degree of similarity with silencing phenomena in other organisms (Cogoni et al., 1999a; Sharp, 1999). For instance, RNAi, posttranscriptional gene silencing in plants and cosuppression in fungi can all be activated by the presence of aberrant RNAs (Maine, 2000; Tijsterman et al., 2002a). Additionally, plant, worm, and fly cells or extracts undergoing RNA-mediated interference all contain small dsRNAs, around 25 nucleotides in length, identical to the sequences present in the silenced gene (Baulcombe, 1996; Hammond et al., 2000; Zamore et al., 2000; Catalanotto et al., 2000). The high degree of similarity between these RNA-mediated silencing phenomena supports the notion that they were derived from an ancient and conserved pathway used to regulate gene expression, presumably to eliminate defective RNAs and to defend against viral infections and transposons. (Zamore, 2002). Components of RNAi have also been implicated in developmental processes, suggesting that RNAi may play a broader role in regulating gene expression (Smardon et al., 2000; Knight et al., 2001; et al., Ketting et al., 2001). Although we have learned much about the general mechanisms underlying RNAi, a detailed understanding of how RNAi works remains to be elucidated. In this chapter we will discuss first the biology of RNAi, then the genes required for its function, and we will end with a discussion on recent findings that have implicated chromatin silencing in the mechanism of RNAi.
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[
Methods Cell Biol,
1995]
DNA transformation assays in a whole organism provide experimental links between molecular structure and phenotype. Experiments with transgenic Caenorhabditis elegans start in general with the injection of DNA into the adult gonad. Effects on phenotype or gene expression patterns can be analyzed either in F1 progeny derived from the injected animals or in derived transgenic lines. Microinjection of C. elegans was first carried out by Kimble et al. (1982). Stinchcomb et al. (1985) then showed that injected DNA could be maintained for several generations in transgenic lines. The first selective methods for producing and maintaining transgenic lines were reported in 1986 (Fire, 1986). These methods have been considerably improved since then (Mello et al., 1991) , so that assays involving DNA transformation are now a standard part of the experimental repertoire for C. elegans.
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[
2017]
Since their discovery in late 1970, transient receptor potential (TRP) channels have been implicated in a variety of cellular and physiological functions (Minke, 2010). The superfamily of TRP channels consists of nearly 30 members that are organized into seven major subgroups based on their specific function and sequence similarities (Owsianik et al., 2006; Ramsey et al., 2006). With the exception of TRPN channels that are only found in invertebrates and fish, mammalian genomes contain representatives of all six subfamilies: (1) TRPV (vanilloid); (2) TRPC (canonical); (3) TRPM (melastatin); (4) TRPA (ankyrin); (5) TRPML (mucolipin); and (6) TRPP (polycystin). TRP channels play crucial regulatory roles in many physiological processes, including those associated with reproductive tissues. As calcium-permeable cation channels that respond to a variety of signals (Clapham et al., 2003; Wu et al., 2010), TRP channels exert their role as sensory detectors in both male and female gametes, and play regulatory functions in germ cell development and maturation. Recent evidence obtained from Caenorhabditis elegans studies point to the importance of these proteins during fertilization where certain sperm TRP channels could migrate from a spermatozoon into an egg to ensure successful fertilization and embryo development. In this chapter we discuss how TRP channels can regulate both female and male fertility in different species and their specific roles.
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[
1969]
In order to study properly the nutrition and culture of nematodes, it is desirable to establish the organisms in axenic culture. Only in this way can the metabolic abilities of the nematodes be separated from those of coexisting and interacting organisms. One may settle for a mono-axenic culture, but the best way to attain this is to obtain axenic nematodes and then add the second organism or tissue, for example, alfalfa callus tissue for plant parasitic nematodes (Krusberg, 1961). This chapter will devote itself, in the main, to recent work on the culture and nutrition of nematodes, free-living and parasitic, and will refer only in passing to work already thoroughly reviewed (Dougherty et al., 1959; Nicholas, et al., 1959; Dougherty, 1960).
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[
Methods Cell Biol,
1995]
Complementary DNA libraries are useful tools for uncovering genes of interest in C. elegans and finding specific homologies to genes in other organisms (Waterston et al., 1992; McCombie et al., 1992). When working with existing cDNA libraries, be sure to carefully choose which libraries would be most beneficial to the type of research being done. Some libraries may be specific for genes that are present in lower copy numbers, whereas others may be of a more general nature. It is important to fully understand the source and construction of the library you will be working with. Once an appropriate library has been chosen, work may begin to isolate a specific cDNA and sequence it completely or to survey many cDNAs by single-pass DNA sequencing. Whatever the project, it is important to develop a specific strategy for both the sequencing and the organization of the clones being characterized. The strategies and procedures we have outlined in this chapter have proven effective for rapid and comprehensive cDNA characterization.
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[
Methods Cell Biol,
1995]
Sequence analysis of cosmids from C. elegans and other organisms currently is best done using the random or "shotgun" strategy (Wilson et al., 1994). After shearing by sonication, DNA is used to prepare M13 subclone libraries which provide good coverage and high-quality sequence data. The subclones are assembled and the data edited using software tools developed especially for C. elegans genomic sequencing. These same tools facilitate much of the subsequent work to complete both strands of the sequence and resolve any remaining ambiguities. Analysis of the finished sequence is then accomplished using several additional computer tools including Genefinder and ACeDB. Taken together, these methods and tools provide a powerful means for genome analysis in the nematode.
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[
1979]
We have isolated temperature sensitive maternal effect mutants in the free-living nematode Caenorhabditis elegans. We use C. elegans for several basic reasons. It is easy to culture in the laboratory and it has a rapid life cycle. The genetics of C. elegans have been elucidated by Brenner and more recently have been refined by the lethal analysis of Herman et. al. Both embryonic and postembryonic development can be observed directly and conveniently on the living worm with Nomarski differential interference optics because egg shell and worm cuticle are transparent. The precise embryonic cell lineages of C. elegans are known from fertilization to the 200 blastomere stage. All of the postembryonic somatic cell lineages are precisely known. It ...
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[
1990]
Sex determination in the C. elegans germ line addresses two major problems of biological control. First, any regulation that directs male or female development in all tissues must rely on tissue-specific controls to specify a particular pathway of differentiation (e.g., sperm or oocyte) in a single tissue. The C. elegans germ line provides several technical advantages for analyzing sex determination in a single tissue, including powerful genetic selections (Kimble, 1988) and ease of micro-injection (Kimble et al., 1982). Second, the self-fertility of the C. elegans hermaphrodite depends upon its transient production of sperm in an otherwise female animal. Analysis of sex determination in the hermaphrodite germ line should therefore shed light on the evolution of hermaphrodites from females. Here, we review our efforts towards identifying the regulatory elements that control the C. elegans hermaphrodite germ line to produce sperm and
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[
Methods Cell Biol,
1995]
ACeDB (A Caenorhabditis elegans Data Base) is a data management and display system that contains a wide range of genomic and other information about C. elegans. This chapter provides an overview of ACeDB for the C. elegans user, focusing in particular on the Macintosh version Macace. Previous reviews of AceDB include those of Thierry-Mieg and Durbin (1992) and Durbin and Thierry-Mieg (1994), which describe the general properties of the whole system, and that by Dunham et al. (1994), which discussed the use of AceDB for physical map data collection and assembly. ACeDB was developed by Jean Thierry-Mieg and Richard Durbin primarily for the C. elegans project, when the genomic sequencing project was just beginning in 1990. The original aim was to create a single database that integrated the genetic and physical maps with both genomic sequence data and the literature references. The forerunner of ACeDB was the program CONTIG9 (Sulston et al., 1988), which was developed to maintain and edit the physical map. CONTIG9 served researchers around the world by providing critical on-line access to the current physical map as it was being constructed (Coulson et al., 1986). This policy of immediate access allowed members of the worm community to see the same data as the people making the map, and proved very successful in maximizing use of the map. The same approach was adopted as a template for ACeDB. These two principles, developing a comprehensive database for all types of genomic and related data and providing public access to the data in the same form as used by the data-collecting laboratories, have continued to underlie developments of ACeDB. Over the last 5 years, a wide range of genome projects relating to other organisms have taken the ACeDB program and used it to develop databases for their own data. ACeDB has been used both in public projects designed to redistribute public data in a coordinated fashion and laboratory-based projects for collecting new data. Others, such as the C. elegans ACeDB, have used the database for both purposes. The reason it has been possible to adapt ACeDB so widely is that its flexible data structure allows new types of objects and new types of information about these objects to be added easily. This chapter describes (1) how to obtain ACeDB and documentation for it, (2) how to access and use the information in ACeDB, and (3) how to use ACeDB as a laboratory-based data managing system. Some of what we discuss is specific to the nematode database, but other information applies to the basic computer software program and, hence, to any database using the ACeDB program.