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[
WormBook,
2005]
The regulation of transcription in C. elegans shares many similarities to transcription in other organisms. The details of how specific transcription factors bind to target promoters and act as either activators or repressors are still being examined in many cases, but an increasing number of factors and their binding sites are being characterized. This chapter reviews the general concepts that have emerged with regards to promoter function in C. elegans. Included are the methods that have been successfully employed as well as limitations encountered to date. Specific cis-acting promoter elements from
myo-2 ,
hlh-1 and
lin-26 are discussed as examples of complex promoters regulated by multiple sequence elements. In addition, examples of organ-, tissue-, and cell type-specific mechanisms for generating spatial specificity in gene expression are discussed.
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[
Methods Cell Biol,
1995]
The genetics of Caenorhabditis elegans provides a convenient experimental entry point into many developmental processes and a powerful tool that can be exploited to characterize interactions among a set of genes regulating a particular pathway. Eventually, though, the study of developmental processes becomes a molecular study of gene regulation. At this level, the determination of the on/off state of a gene requires an understanding of not only its transcriptional state, but also post-transcriptional, translational, and post-translational control mechanisms. Although the vertebrate literature is rich in details of factors that influence these regulatory processes, relatively few of the factors responsible for gene expression in the nematode C. elegans have been characterized. This lag in knowledge reflects both the relatively recent arrival of C. elegans on the list of experimental systems, as well as its general unsuitability for biochemistry. There are no tissue culture cell lines established from C. elegans, and it is difficult to isolate, in large amounts, any homogeneous cell type. Moreover, the impermeable eggshell encasing the embryo and the cuticle encasing the worm make pharmacological studies in intact animals difficult and tedious. Grim as this sounds, progress has been made in C. elegans in the field of gene expression. The sensitivity of techniques has improved and the available molecular tool kit has expanded. The study of individual genes has provided descriptions of several regulatory processes, some general and some gene specific. Our current level of understanding of gene regulation is sufficient to say that C. elegans appears, in general, to be a typical eukaryote. As such, C. elegans is amenable to many of the standard analytical approaches used in other developmental systems. The purpose of this chapter is to review our current state of knowledge of transcription and translation in C. elegans (for a review
-
[
Methods Cell Biol,
1995]
This chapter is devoted to providing information on techniques applicable to studying transcription and translation in Caenorhabditis elegans. These techniques are constantly evolving and being passed among workers, each making improvements or adaptations. None of the techniques discussed below are original, but, rather, have emerged from a variety of sources over the years, making it difficult to trace their origin or give credit to the originators. Although each technique has been used successfully, for each there are alternative methods available in the literature that work equally well. In fact, depending on the available resources, you might find that an alternative technique suits your needs and facilities better than the one described below. For this reason, the procedures discussed below are usually accompanied by one or more references that will allow you to look at other, related methods. Where appropriate, there will also be a discussion of factors to consider when
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[
2013]
C. elegans germline stem cells are a particularly simple system for analysis of stem cell regulation. Their well-defined mesenchymal niche consists of a single cell, the Distal Tip Cell, which uses Notch signaling to maintain a pool of germline stem cells. Downstream of Notch signaling a post-transcriptional regulatory network dictates self-renewal or differentiation. The major self-renewal hub of that network is FBF, a conserved RNA-binding protein and conserved stem cell regulator. FBF represses mRNAs encoding key regulators of germline differentiation (entry into the meiotic cell cycle, sperm or oocyte specification) as well as established regulators of somatic differentiation. Transcriptional and post-transcriptional mechanisms also control totipotency in the C. elegans germline. The key C. elegans GSC regulators are conserved broadly, making this system a paradigm for stem cell regulation.
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[
WormBook,
2005]
In C. elegans, the germ line is set apart from the soma early in embryogenesis. Several important themes have emerged in specifying and guiding the development of the nascent germ line. At early stages, the germline blastomeres are maintained in a transcriptionally silent state by the transcriptional repressor PIE-1 . When this silencing is lifted, it is postulated that correct patterns of germline gene expression are controlled, at least in part, by MES-mediated regulation of chromatin state. Accompanying transcriptional regulation by PIE-1 and the MES proteins, RNA metabolism in germ cells is likely to be regulated by perinuclear RNA-rich cytoplasmic granules, termed P granules. This chapter discusses the molecular nature and possible roles of these various germline regulators, and describes a recently discovered mechanism to protect somatic cells from following a germline fate.
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[
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.
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[
WormBook,
2007]
The intestine is one of the major organs in C. elegans and is largely responsible for food digestion and assimilation as well as the synthesis and storage of macromolecules. In addition, the intestine is emerging as a powerful experimental system in which to study such universal biological phenomena as vesicular trafficking, biochemical clocks, stress responses and aging. The present chapter describes some of these many and varied properties of the C. elegans intestine: the embryonic cell lineage, intestine morphogenesis, structure and physiology of the intestinal cell and, finally, the transcription factor network controlling intestine development and function.
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[
Methods Cell Biol,
2008]
The nuclear lamina is found between the inner nuclear membrane and the peripheral chromatin. Lamins are the main components of the nuclear lamina, where they form protein complexes with integral proteins of the inner nuclear membrane, transcriptional regulators, histones and chromatin modifiers. Lamins are required for mechanical stability, chromatin organization, Pol II transcription, DNA replication, nuclear assembly, and nuclear positioning. Mutations in human lamins cause at least 13 distinct human diseases, collectively termed laminopathies, affecting muscle, adipose, bone, nerve and skin cells, and range from muscular dystrophies to accelerated aging. Caenorhabditis elegans has unique advantages in studying lamins and nuclear lamina genes including low complexity of lamina genes and the unique ability of bacterially expressed C. elegans lamin protein to form stable 10 nm fibers. In addition, transgenic techniques, simple application of RNA interference, sophisticated genetic analyses, and the production of a large collection of mutant lines, all make C. elegans especially attractive for studying the functions of its nuclear lamina genes. In this chapter we will include a short review of our current knowledge of nuclear lamina in C. elegans and will describe electron microscopy techniques used for their analyses.
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[
WormBook,
2005]
Cell-cell interactions mediated by the Notch signaling pathway occur throughout C. elegans embryogenesis. These interactions have major roles in specifying cell fates and in tissue morphogenesis. The network of Notch interactions is linked in part through the Notch-regulated expression of components of the pathway, allowing one interaction to pattern subsequent ones. The Notch signal transduction pathway is highly conserved in animal embryogenesis. The REF-1 family of bHLH transcription factors are major targets of Notch signaling in the C. elegans embryo, and are distantly related to HES proteins that are targets of Notch signaling in Drosophila and vertebrates.