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[
1996]
At fertilization, the calm of oogenesis is broken, and the egg abruptly begins a flurry of activity. Many crucial steps - decisions concerning when and where to divide, specification of cell fates, and establishment of body axes - rely on materials the egg contains at that moment. In many animals, the first few hours of life proceed with little or no transcription. As a result, developmental regulation at these early stages is dependent on maternal cytoplasm, rather than the zygotic nucleus. The regulatory molecules accumulated during oogenesis might, in principle, be of any type, including RNA and protein. It is now clear that messenger RNAs present in the egg before fertilization (so-called maternal mRNAs) have a prominent role in early decisions. Viewed from this perspective, it is not surprising that oocytes and early embryos display an impressive array of posttrancriptional regulatory mechanisms, controlling mRNA stability, localization, and translation.
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[
2000]
At fertilization, the calm of oogenesis ends and the egg abruptly begins a flurry of activity. Many crucial steps - decisions concerning when and where to divide, specification of cell fates, and establishment of body axes - rely on materials the egg contains at that moment. In many animals, the first few hours of life proceed with little or no transcription. As a result, developmental regulation at these early stages is dependent on maternal cytoplasm rather than the zygotic nucleus. The regulatory molecules accumulated during oogenesis might, in principle, be of any type, including RNA and protein. It is clear that mRNAs present in the egg before fertilization - so-called maternal mRNAs - play a particularly prominent role in early decisions. Viewed from this perspective, it is not surprising that oocytes and early embryos display an impressive array of posttranscriptional regulatory mechanisms, controlling mRNA stability, localization, and translation.
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Each year hundreds of students and practicing scientists join in the study of the soil nematode Caenorhabditis elegans. Their reasons for doing so are varied, but at the core these individuals are uniformly impressed by the cohesiveness and generosity of the C. elegans research community, the focused effort to understand every aspect of C. elegans biology, the power and flexibility of the...
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[
Chromosomes Today,
2004]
C. elegans meiotic chromosomes do not require meiotic double-stranded DNAbreaks for synaptonemal complex formation. However, homologues must share a cisactingregion, the so-called HRR, to become synapsed. To achive orderly segregation at thefirst and second meiotic divisions, C. elegans chromosomes must transform from theirmitotic holocentric to monocentric organization. Here we address issues concerning thenature of the HRR and the selection of the meiotic kinetochore site.
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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 most abundant synapses in the central nervous system of vertebrates are inhibitory synapses that use the neurotransmitter gamma-aminobutyric acid (GABA). GABA is also an important neurotransmitter in C. elegans; however, in contrast to vertebrates where GABA acts at synapses of the central nervous system, in nematodes GABA acts primarily at neuromuscular synapses. Specifically, GABA acts to relax the body muscles during locomotion and foraging and to contract the enteric muscles during defecation. The importance of this neurotransmitter for basic motor functions of the worm has facilitated the genetic analysis of proteins required for GABA function. Genetic screens have identified the GABA biosynthetic enzyme, the vesicular transporter, inhibitory and excitatory receptors, and a transcription factor required for the differentiation of GABA cell identity. The plasma membrane transporter and other GABA receptors have been identified by molecular criteria.
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[
1985]
Expression of the vitellogenin genes is restricted to the intestine of adult hermaphrodite C. elegans. In order to identify potential cis-acting elements involved in this developmental regualtion, we have sequenced the regions surrounding the 5' ends of five of the six members of this gene family. In addition, we have sequenced several of the promoters from the homologous genes from the related species C. briggsae. Although the various promoters are largely diverged from one another, we have discovered two potential regulatory sequences within the first 250 bp upstream of each of the genes. The first, TGTCAAT, occurs eight times as a perfect heptamer upstream of the five C. elegans genes, at least once per promoter. Allowing a 1 bp mismatch, the element is found in both orientations a total of 27 times, four to six timer per promoter. It is present preferentially at two locations: just upstream of the TATA box and, in the opposite orientation, at position -180. The second sequence, CTGATAA, is also present as a perfect heptamer in a restricted region of each promoter: near position -135. Remarkably, this sequence is also found upstream of the vitellogenin genes of vertebrates. Both sequences have been conserved in the C. briggsae promoters. We hypothesize that these two sequences are involved in the sex-, tissue-, and stage-specific expression of the vitellogenin genes.
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[
WormBook,
2005]
This chapter reviews analytical tools currently in use for protein classification, and gives an overview of the C. elegans proteome. Computational analysis of proteins relies heavily on hidden Markov models of protein families. Proteins can also be classified by predicted secondary or tertiary structures, hydrophobic profiles, compositional biases, or size ranges. Strictly orthologous protein families remain difficult to identify, except by skilled human labor. The InterPro and NCBI KOG classifications encompass 79% of C. elegans protein-coding genes; in both classifications, a small number of protein families account for a disproportionately large number of genes. C. elegans protein-coding genes include at least ~12,000 orthologs of C. briggsae genes, and at least ~4,400 orthologs of non-nematode eukaryotic genes. Some metazoan proteins conserved in other nematodes are absent from C. elegans. Conversely, 9% of C. elegans protein-coding genes are conserved among all metazoa or eukaryotes, yet have no known functions.
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[
Cellular and Molecular Biology,
1989]
Myosin is assembled into thick filaments of distinct lengths and substructures in phylogenetically and histologically diverse muscles. In these different muscles, specific proteins are associated with myosin in the assembled filaments. In the nematode Caenorhabditis elegans, the major protein component is paramyosin which assembles with two myosin isoforms about a separate core structure. At least six non-myosin proteins are associated with the core structures. Previous models of myosin assembly have emphasized a linear sequence of steps in which myosin molecules themselves are involved in nucleation, elongation and termination of individual filaments. Nematode muscle mutants accumulate assemblages of multiple thich filaments which also appear at low levels in wild-type. The effects of various alterations of myosin myosin levels upon the assembly of the two myosins and the existence of these multi-filament assemblages suggest a possible alternative model for myosin assembly. In this model, a cycle in which multiple thick filaments nucleate from a common structure is driven by synthesis of a
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[
Methods Mol Biol,
2016]
The development of genomics and next generation sequencing platforms has dramatically improved our insight into chromatin structure and organization and its fine interplay with gene expression. The nuclear envelope has emerged as a key component in nuclear organization via extensive contacts between the genome and numerous proteins at the nuclear periphery. These contacts may have profound effects on gene expression as well as cell proliferation and differentiation. Indeed, their perturbations are associated with several human pathologies known as laminopathies or nuclear envelopathies. However, due to their dynamic behavior the contacts between nuclear envelope proteins and chromatin are challenging to identify, in particular in intact tissues. Here, we propose the DamID technique as an attractive method to globally characterize chromatin organization in the popular model organism Caenorhabditis elegans. DamID is based on the in vivo expression of a chromatin-associated protein of interest fused to the Escherichia coli DNA adenine methyltransferase, which produces unique identification tags at binding site in the genome. This marking is simple, highly specific and can be mapped by sensitive enzymatic and next generation sequencing approaches.