Alan M. Zahler (2005) WormBook "Alternative splicing in C. elegans."

Alan M. Zahler

[WormBook, 2005]

Alternative splicing is a common mechanism for the generation of multiple isoforms of proteins. It can function to expand the proteome of an organism and can serve as a way to turn off gene expression post-transcriptionally. This review focuses on splicing and its regulation in C. elegans. The fully-sequenced C. elegans genome combined with its elegant genetics offers unique advantages for exploring alternative splicing regulation in metazoans. The topics covered in this review include constitutive splicing factors, identification of alternatively spliced genes, examples of alternative splicing in C. elegans, and alternative splicing regulation. Key genes whose regulated alternative splicing are reviewed include let-2 , unc-32 , unc-52 , egl-15 and xol-1 . Factors involved in alternative splicing that are discussed include mec-8 , smu-1 , smu-2 , fox-1 , exc-7 and unc-75 .

Nelson GA et al. "Nematode radiobiology and development in space. Results from IML-1."

Benton ER, Henke R, Benton EV, Kazarians GA, Nelson GA, Richards DG, Schubert WW

The International Microgravity Laboratory #1 Spacelab mission was launched on 22-Jan-1992 for an 8-day mission. The Radiat experiment was one of 17 investigations which used the ESA Biorack on IML-1 and it had two objectives. The first objective was to isolate and characterize mutations induced by cosmic rays; the second was to assess the fidelity of development in 0-gravity over two consecutive generations. Two strategies were used to isolate mutations in a set of essential genes or a specific gene and to correlate the genetic events with the passage of charged particles. The results were isolation of 60 lethal mutations whose phenotypes are related to the local pattern of energy deposition. 12 mutations in the unc-22 gene include large deletions as characterized by DNA hybridization studies. Development of nematodes proceeded through two consecutive generations with no obvious defects. Cytoplasmic determinants in embryos, nuclear location and symmetry of cellular anatomy were normal as were Mendelian segregation and recombination of

Ishii N et al. "Oxygen sensitive mutants of the nematode Caenorhabditis elegans and aging."

Ishii N, Suzuki K

It has been proposed that free radicals, especially those of molecular oxygen, may accelerate aging in animals. To investigate the possible role of oxygen free radicals in aging, mutants of the nematode Caenorhabditis elegans were isolated which are hypersensitive to methyl viologen (paraquat) and oxygen. The free-living nematode is an attractive model system for aging research on metazoans. The nematode offers the great advantages of genetic manipulability, short life span, cellular simplicity, and easy cultivation. Investigation of two genes in C. elegans should serve to illuminate the relationship between oxidative damage and aging. A mutation in one of these genes, mev-1, has been shown to reduce Cu/Zn superoxide dismutase activity by 30 to 50% relative to wild-type animals. The life spans of this mutant and a second mutant, rad-8, are significantly shortened in the presence of high oxygen concentration. We suggest that oxygen radicals may be involved in the normal aging in C. elegans.

Moerman DG et al. (1989) "Mobile elements in Caenorhabditis elegans and other nematodes."

Moerman DG, Waterston RH

[1989]

Transposable elements have recently been described in several species: Caenorhabditis elegans, Caenorhabditis briggsae, Ascaris lumbricoides, and Panagrellus redivivus. Because of the intense interest in C. elegans as an experimental organism for developmental genetic studies and the availability of sophisticated genetics, most is know about transposons in this species. This review focuses principally on Tc1 (Tc=transposon) of C. elegans, the best understood element in nematodes. Other elements in C. elegans and also elements in other species of nematodes will be briefly surveyed. The interested reader should also see two recent related reviews. The genome of C. elegans is 8 x 10(7) base pairs (bp) in extent, the smallest known for any metazoan. There are six chromosomes per haploid set, and about 83% of C. elegans DNA behaves as single-copy sequence in renaturation experiments. The repeated sequences are of several types, including functional genes, inverted or "foldback" sequences, and short repeated sequences of a few hundred nucleotides. The global arrangment of these short repeats is of the "short-period-interspersion" or "Xenopus" pattern. Some of the repetitive sequences consist of transposable elements, and at least five distinct families have been identified in C. elegans, Tc1 through Tc5. The sequence of one Tc1 element has been determined and shows that Tc1 resembles bacterial insertion sequence elements with terminal inverted repeats and a central open reading frame. The complete sequences for any members of the other transposon families have not been determined, but the data suggest that Tc2, Tc3, and Tc5 are also insertion sequence-like in structure and that Tc4 is foldbacklike in structure. No "retrotransposon-like" elements have been identified in C. elegans, although such elements have been described in A.

Thomas Blumenthal (2005) WormBook "Trans-splicing and operons."

Thomas Blumenthal

[WormBook, 2005]

About 70% of C. elegans mRNAs are trans-spliced to one of two 22 nucleotide spliced leaders. SL1 is used to trim off the 5'' ends of pre-mRNAs and replace them with the SL1 sequence. This processing event is very closely related to cis-splicing, or intron removal. The SL1 sequence is donated by a 100 nt small nuclear ribonucleoprotein particle (snRNP). This snRNP is structurally and functionally related to the U snRNAs (U1, U2, U4, U5 and U6) that play key roles in intron removal and trans-splicing, except that it is consumed in the process of splicing. More than half of C. elegans pre-mRNAs are subject to SL1 trans-splicing. About 30% are not trans-spliced at all. The remaining genes are trans-spliced by SL2. These genes are all downstream genes in closely spaced gene clusters similar to bacterial operons. They are transcribed from a promoter at the 5'' end of the cluster of between 2 and 8 genes. This transcription makes a polycistronic pre-mRNA that is co-transcriptionally processed by cleavage and polyadenylation at the 3'' end of each gene, and this event is closely coupled to the SL2 trans-splicing event that occurs only ~100 nt further downstream. Recent studies on the mechanism of SL2 trans-splicing have revealed that one of the 3'' end formation proteins, CstF, interacts with the only protein known to be specific to the SL2 snRNP. The operons contain primarily genes whose products are needed for mitochondrial function and the basic machinery of gene expression: transcription, splicing and translation. Many operons contain genes whose products are known to function together. This presumably provides co-regulation of these proteins by producing a single RNA that encodes both.

Driscoll MA (1995) Methods Cell Biol "Methods for the study of cell death in the nematode Caenorhabditis elegans."

Driscoll MA

[Methods Cell Biol, 1995]

The nematode Caenorhabditis elegans seems so well suited to investigation of genetically specified cell death that one might also suspect that it was designed for this purpose. The complete cell lineage of this nematode has been recorded. Thus, it is well established that of 1090 somatic cells generated during hermaphrodite development, 131 identified cells undergo programmed cell death (PCD) at characteristic times. Because the cuticle of the animal is transparent and individual cells are easily identified, cell deaths can be observed while they occur in the living animal. The ease of observation of specific cells, coupled with the fact that C. elegans is readily amenable to genetic analysis, has allowed mutations to be identified that either disrupt the normal pattern of PCD or cause inappropriate cell death. Molecular analysis of the identified genes is facilitated by the fact that the genetic map has been aligned with the physical map of the C. elegans genome so each chromosome is now nearly completely represented by an overlapping collection of cosmid or YAC clones that include defined genetic loci. In addition, significant progress toward sequencing the genome has been accomplished. Finally, it is possible to construct transgenic animals so the activities of engineered genes can be assayed in vivo. Two types of cell death have been studied in C. elegans. One type is PCD, which occurs as a component of normal development. Genetic studies have led to the elaboration of a genetic pathway for PCD that includes a negative regulator, ced-9 (cell death abnormal), that acts to prevent PCD and two genes, ced-3 and ced-4, that are involved in the execution of the death program. A third group of genes (ced-1, ced-2, ced-5, ced-5, ced-7, ced-8, ced-10) is required for efficient removal of corpses of dead cells. Cells undergoing PCD exhibit stereotypic morphological changes. A second type of cell death studied in C. elegans resembles necrosis and is characterized by swelling and lysis of specific groups of neurons. This pathological cell death can be induced by mutations in a family of genes including deg-1, mec-4 and mec-10 (degeneration and mechanosensory abnormal, respectively). These genes, called degenerin genes, encode subunits of a newly identified class of ion channels. Degeneration appears to occur as a consequence

Paul W. Sternberg (2005) WormBook "Vulval development."

Paul W. Sternberg

[WormBook, 2005]

C. elegans vulval development is an intensively studied example of animal organogenesis. A network of intercellular signaling, signal transduction, and transcriptional regulation underlies the precise formation of this organ, which is the connection between the hermaphrodite uterus and the outside of the nematode. A single cell of the somatic gonad, the anchor cell, organizes the development of the vulva from epidermal precursors as well as the physical connection of the epidermis with the uterus. WNT signaling acting via the HOX gene lin-39 renders six epidermal precursor cells competent to respond to other developmental signals. The anchor cell induces nearby epidermal precursor cells to generate vulval cells via an epidermal growth factor (EGF) signaling pathway. The precise pattern of vulval precursor cell fates involves the graded action of the EGF signaling and LIN-12 (Notch) mediated lateral signaling. EGF promotes the 1 fate while LIN-12 promotes the 2 fate. Both EGF and LIN-12 prevent precursor cells from adopting the 3 fate, which generates non-specialized epidermis. EGF-receptor and Notch signaling are antagonistic: EGF-receptor signaling leads to down-regulation of the Notch-like receptor LIN-12 , while LIN-12 signaling induces negative regulators of EGF-receptor signaling such as MAP kinase phosphatase LIP-1 and the tyrosine kinase ARK-1. The 1 precursor cell generates vulE and vulF mature vulval cells; the pattern of vulE and vulF cells requires an additional signal from the anchor cell as well as WNT signaling. The two 2 precursor cells generate vulA, vulB1, vulB2, vulC and vulD cells but in mirror symmetric polar patterns: ABCD and DCBA. The reversed polarity of the posterior 2 precursor cell lineage requires WNT signaling mediated by both Frizzled class and Ryk class WNT-receptors LIN-17 and LIN-18 , respectively. A network of transcription factors controls the seven mature adult cell types; these include the LIM domain protein LIN-11 , the Pax2/5/8 protein EGL-38 , the zinc finger protein LIN-29 , and the Nkx6.1/6.2 protein COG-1. The anchor cell also patterns nearby uterine cells, via the DSL ligand LAG-2 and LIN-12 , to generate the four uv1 cells that form the tight connection with the vulva. This connection is initiated by the anchor cell, which invades between the vulF cells in a process analogous to invasive behavior of metastatic tumor cells. During this invasion process, the basement membranes between the gonad and body wall are degraded. The extensive information about vulval development in C. elegans has helped it become a paradigmatic case for identifying and studying a variety of regulatory pathways.