The linkage mapping of cloned restriction fragment length differences in Caenorabditis elegans

Genomic organization in Caenorhabditis elegans: deficiency mapping on linkage group V(left)

In this study we genetically analyse a large autosomal region (23 map units) in Caenorhabditis elegans. The region comprises the left half of linkage group V [LGV(left)] and is recombinationally balanced by the translocation eT1(III; V). We have used rearrangement breakpoints to subdivide the region from the left end of LGV to daf-11 into a set of 23 major zones. Twenty of these zones are balanced by eT1. To establish the zones we examined a total of 110 recessive lethal mutations derived from a variety of screening protocols. The mutations identified 12 deficiencies, 1 duplication, as well as 98 mutations that fell into 59 complementation groups, significantly increasing the number of available genetic sites on LGV. Twenty-six of the latter had more than 1 mutant allele. Significant differences were observed among the alleles of only 6 genes, 3 of which have at least one ‘visible’ allele. Several deficiencies and 3 alleles of let-336 were demonstrated to affect recombination. The duplication identified in this study is sDp30(V;X). Lethal mutations covered by sDp30 were not suppressed uniformly in hermaphrodites. The basis for this non-uniformity may be related to the mechanism of X chromosome dosage compensation in C. elegans.

Use of genomic DNA restriction fragment length differences to identify nematode species

Restriction endonuclease digestion of genomic DNA generates DNA fragments of unique size, dependent upon the particular base sequence. Following fractionation by agarose gel electrophoresis, repetitive DNA can be visualized as distinct bands in stained gels and the restriction fragment length of such bands used as diagnostic characters. Restriction fragment length differences were detected between species within the genera Trichinella, Caenorhabditis, Romanomermis, Steinernema (syn. Neoaplectana) and Meloidogyne. This technique provides a new tool for the taxonomist, which is independent of phenotypic variation and it enables the rapid and reliable separation of closely related species.

Evolution of the Caenorhabditis elegans genome

A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.

Towards a mutation in every gene in Caenorhabditis elegans

The combined efforts of the Caenorhabditis elegans Knockout Consortium and individuals within the worm community are moving us closer to the goal of identifying mutations in every gene in the nematode C. elegans. At present, we count about 7000 deletion alleles that fall within 5500 genes. The principal method used to detect deletion mutations in the nematode utilizes polymerase chain reaction (PCR). More recently, the Moerman group has incorporated array comparative genome hybridization (aCGH) to detect deletions across the entire coding genome. Other methods used to detect mutant alleles in C. elegans include targeting induced local lesion in genomes (TILLING), transposon tagging, using either Tc1 or Mos1 and resequencing. These combined strategies have improved the overall throughput of the gene-knockout labs, and have broadened the types of mutations that we, and others, can identify. In this review, we will discuss these different approaches.

The lin-15 locus encodes two negative regulators of Caenorhabditis elegans vulval development

During Caenorhabditis elegans vulval development, an inductive signal from the anchor cell stimulates three of the six vulval precursor cells (VPCs) to adopt vulval rather than nonvulval epidermal fates. Genes necessary for this induction include the lin-3 growth factor, the let-23 receptor tyrosine kinase, and let-60 ras. lin-15 is a negative regulator of this inductive pathway. In lin-15 mutant animals, all six VPCs adopt vulval fates, even in the absence of inductive signal. Previous genetic studies suggested that lin-15 is a complex locus with two independently mutable activities, A and B. We have cloned the lin-15 locus by germline transformation and find that it encodes two nonoverlapping transcripts that are transcribed in the same direction. The downstream transcript encodes the lin-15A function; the upstream transcript encodes the lin-15B function. The predicted lin-15A and lin-15B proteins are novel and hydrophilic. We have identified a molecular null allele of lin-15 and have used it to analyze the role of lin-15 in the signaling pathway. We find that lin-15 acts upstream of let-23 and in parallel to the inductive signal.

Genetic and molecular analysis of the dpy-14 region in Caenorhabditis elegans

Essential genes have been identified in the 1.5 map unit (m.u.) dpy-14-unc-29 region of chromosome 1 in Caenorhabditis elegans. Previous work defined nine genes with visible mutant phenotypes and nine genes with lethal mutant phenotypes. In this study, we have identified an additional 28 essential genes with 97 lethal mutations. The mutations were mapped using eleven duplication breakpoints, eight deficiencies and three-factor recombination experiments. Genes required for the early stages of development were common, with 24 of the 37 essential genes having mutant phenotypes arresting at an early larval stage. Most mutants of a gene have the same time of arrest; only four of the 20 essential genes with multiple alleles have alleles with different phenotypes. From the analysis of complementing alleles of let-389, alleles with the same time-of-arrest phenotype were classified as either hypomorphic or amorphic. Mutants of let-605, let-534 and unc-37 have both uncoordinated and lethal phenotypes, suggesting that these genes are required for the coordination of movement and for viability. The physical and genetic maps in the dpy-14 region were linked by positioning two N2/BO polymorphisms with respect to duplications in the region, and by localizing the right breakpoint of the deficiency hDf8 on the physical map. Using cross-species hybridization to C. briggsae, ten regions of homology have been identified, eight of which are known to be coding regions, based on Northern analysis and/or the isolation of cDNA clones.

Isolation and sequence analysis of Caenorhabditis briggsae repetitive elements related to the Caenorhabditis elegans transposon Tc1

We have identified two repetitive element families in the genome of the nematode Caenorhabditis briggsae with extensive sequence identity to the Caenorhabditis elegans transposable element Tc1. Five members each of the TCb1 (previously known as Barney) and TCb2 families were isolated by hybridization to a Tc1 probe. Tc1-hybridizing repetitive elements were grouped into either the TCb1 or TCb2 family based on cross-hybridization intensities among the C. briggsae elements. The genomic copy number of the TCb1 family is 15 and the TCb2 family copy number is 33 in the C. briggsae strain G16. The two transposable element families show numerous genomic hybridization pattern differences between two C. briggsae strains, suggestive of transpositional activity. Two members of the TCb1 family, TCb1#5 and TCb1#10, were sequenced. Each of these two elements had suffered an independent single large deletion. TCb1#5 had a 627-bp internal deletion and TCb1#10 had lost 316 bp of one end. The two sequenced TCb1 elements were highly conserved over the sequences they shared. A 1616-bp composite TCb1 element was constructed from TCb1#5 and TCb1#10. The composite TCb1 element has 80-bp terminal inverted repeats with three nucleotide mismatches and two open reading frames (ORFs) on opposite strands. TCb1 and the 1610-bp Tc1 share 58% overall nucleotide sequence identity, and the greatest similarity occurs in their ORF1 and inverted repeat termini.

Structural analysis of Tc1 elements in Caenorhabditis elegans var. Bristol (strain N2)

The transposable element Tc1 in the genome of Caenorhabditis elegans var. Bristol strain N2 is very stable. In order to investigate possible causes of Tc1 immobility in this strain 17 individual isolates have been cloned and characterized with regard to their structure and genomic environment. Ten of 16 elements examined had identical restriction maps, and at least 1 of these (#7) showed a high level of somatic excision. Two of the elements had altered restriction sites, 2 had different internal deletions of about 700 bp, 1 had an 89-bp terminal deletion, and 1 a 54-bp insertion. When DNA sequences flanking the N2 Tc1 elements were used as probes in genomic hybridizations, it was found that most N2 elements are located in regions of repetitive DNA. Furthermore when hybridizations to DNA from N2 and var. Bergerac strain B0 were performed, a major band of the same size was observed in both strains. Two flanking sequences identified strain polymorphic sites hP2(IV) and hP3(IV). In at least one of these cases, a rearranged Tc1 was present in the B0 strain at the same location. The fact that all or most of the Tc1 elements are in the same location in N2 and B0 adds support to the hypothesis that the high copy number B0 strain arose from amplification of Tc1 copies in a N2-like strain. The N2 Tc1 elements are highly conserved; however, intact elements had fewer nucleotide changes than the rearranged elements. These results may indicate that the intact Tc1 elements in N2 are functionally active and subject to selective pressure.

Initiator tRNAMet genes from the nematode Caenorhabditis elegans

Five different members of the initiator tRNAMet gene family have been isolated and characterized from the nematode Caenorhabditis elegans. All five show identical tRNA coding sequences, followed by a block of T residues associated with termination by RNA polymerase III. Nucleotide sequences flanking the tDNAs are completely divergent, except for two distinct members with identical flanking sequences, which may have arisen from a recent gene duplication event. Each tDNA is also flanked by middle-repetitive DNA, but the lack of cross-hybridization to each other suggests that these repetitive sequences have no common functional significance. The tRNAMeti genes do not appear to be closely linked to each other, although in vitro transcription reveals a putative tDNA adjacent to one member. Finally, there are large differences in the extent to which the five genes are transcribed by a homologous C. elegans cell-free extract, suggesting that flanking sequences have a significant effect on transcription by RNA polymerase III.

The Caenorhabditis elegans hsp70 gene family: a molecular genetic characterization

We have isolated genomic clones representing six distinct members of the Caenorhabditis elegans 70-kDa heat-shock protein gene (hsp70) family. Each member exists as a single copy element in the C. elegans genome. Transcripts of four of the hsp70 genes have been detected by Northern-blot analysis. One member, hsp70C, appears to be a heat-shock-cognate hsp70 gene (hsc70) since its transcription is developmentally regulated and is not increased in response to heat shock. Transcripts of another gene, hsp70A, are abundant in control worms and are also increased (two- to six-fold) upon heat shock. Nucleotide sequencing of genomic and cDNA clones of hsp70A reveals that it is highly homologous to Drosophila and yeast heat-shock-inducible and heat-shock-cognate hsp70 genes. Three DNA elements homologous to the heat-shock promoter, 5'-C--GAA--TTC--G-3' are located upstream from the Hsp70A-coding region. We find that hsp70A contains three introns, one of which is in a similar position with an intron in the Drosophila hsc1 and hsc2 genes. Finally, utilizing strain-specific restriction fragment length differences, we have mapped the chromosomal position of hsp70A to the far right of chromosome IV.

Correlation of the physical and genetic maps in the lin-12 region of Caenorhabditis elegans

We describe the assembly of a set of overlapping clones from the lin-12 III chromosomal region that spans approximately 600 kb, and the identification of two restriction fragment length polymorphisms, eP6 and eP7, that flank the lin-12 locus. A comparison of the physical map and the genetic map yields approximate measurements of 930 kb/map unit for the eP6--lin-12 interval and 830 kb/map unit for the lin-12--eP7 interval. We interpret these values as supporting the proposal that the apparent clustering of genes observed for C. elegans autosomes results from decreased recombination frequency in clusters and not from nonrandom distribution of genes on the physical map.

Somatic excision of transposable element Tc1 from the Bristol genome of Caenorhabditis elegans

We investigated the ability of the transposable element Tc1 to excise from the genome of the nematode Caenorhabditis elegans var. Bristol N2. Our results show that in the standard lab strain (Bristol), Tc1 excision occurred at a high frequency, comparable to that seen in the closely related Bergerac strain BO. We examined excision in the following way. We used a unique sequence flanking probe (pCeh29) to investigate the excision of Tc1s situated in the same location in both strains. Evidence of high-frequency excision from the genomes of both strains was observed. The Tc1s used in the first approach, although present in the same location in both genomes, were not known to be identical. Thus, a second approach was taken, which involved the genetic manipulation of a BO variant, Tc1(Hin). The ability of this BO Tc1(Hin) to excise was retained after its introduction into the N2 genome. Thus, we conclude that excision of Tc1 from the Bristol genome occurs at a high frequency and is comparable to that of Tc1 excision from the Bergerac genome. We showed that many Tc1 elements in N2 were apparently functionally intact and were capable of somatic excision. Even so, N2 Tc1s were prevented from exhibiting the high level of heritable transposition displayed by BO elements. We suggest that Bristol Tc1 elements have the ability to transpose but that transposition is heavily repressed in the gonadal tissue.

Somatic excision of transposable element Tc1 from the Bristol genome of Caenorhabditis elegans

We investigated the ability of the transposable element Tc1 to excise from the genome of the nematode Caenorhabditis elegans var. Bristol N2. Our results show that in the standard lab strain (Bristol), Tc1 excision occurred at a high frequency, comparable to that seen in the closely related Bergerac strain BO. We examined excision in the following way. We used a unique sequence flanking probe (pCeh29) to investigate the excision of Tc1s situated in the same location in both strains. Evidence of high-frequency excision from the genomes of both strains was observed. The Tc1s used in the first approach, although present in the same location in both genomes, were not known to be identical. Thus, a second approach was taken, which involved the genetic manipulation of a BO variant, Tc1(Hin). The ability of this BO Tc1(Hin) to excise was retained after its introduction into the N2 genome. Thus, we conclude that excision of Tc1 from the Bristol genome occurs at a high frequency and is comparable to that of Tc1 excision from the Bergerac genome. We showed that many Tc1 elements in N2 were apparently functionally intact and were capable of somatic excision. Even so, N2 Tc1s were prevented from exhibiting the high level of heritable transposition displayed by BO elements. We suggest that Bristol Tc1 elements have the ability to transpose but that transposition is heavily repressed in the gonadal tissue.

Transcription of class III genes in cell-free extracts from the nematode Caenorhabditis elegans

Using the nematode Caenorhabditis elegans as a model organism, we have prepared cell-free extracts which accurately transcribe cloned homologous 5S RNA genes in vitro. These extracts also transcribe cloned tRNA genes, and actively process the resulting products. Unlike tRNA genes, transcription of 5S DNA shows some species specificity: C. elegans extracts do not transcribe Xenopus 5S RNA genes, nor does a Xenopus extract efficiently transcribe the heterologous nematode 5S DNA. However, addition of limiting amounts of C. elegans fractions permits Xenopus extracts to transcribe nematode 5S RNA genes. This apparent biochemical "complementation" may provide an assay to purify 5S RNA gene-specific factors from C. elegans.

The application of recombinant DNA technology to problems of helminth identification

During the past decade, enormous technological developments have occurred in biology that have led to significant and revolutionary advances. New techniques of DNA cloning, restriction-enzyme analyses and nucleotide sequencing are providing a mass of data concerning the genomes of a wide variety of organisms. Such insights are having a great impact upon many areas of biological investigation, and would seem to be of considerable potential value for studies of taxonomy and population biology. The application of these new approaches to the characterization and identification of parasitic helminths has only recently begun, but they promise to become powerful additional tools for this purpose. Better methods of characterization are required for more precise definition of the parasites of man and domestic animals and for determining vectors and intermediate hosts as well as possible animal reservoir hosts. Moreover, a greater understanding of the genetic diversity of parasitic organisms is required since many helminths, which are morphologically similar, show marked differences in epidemiologically significant factors such as infectivity, pathogenicity, immunogenicity and drug sensitivity.

Genes coding for 5S ribosomal RNA of the nematode Caenorhabditis elegans

We have identified a 1-kb genomic sequence that represents the major class of 5S rRNA genes in the nematode Caenorhabditis elegans. This 1-kb sequence is tandemly repeated 110 times in the haploid genome forming a single homogeneous gene family. Other nematode genomic sequences, distinct from the major 1-kb repeat class but homologous to it, may represent dispersed 5S rRNA genes or the ends of a gene cluster. One such fragment shows a restriction fragment length difference between two C. elegans strains. This should allow the genetic analysis of 5S rRNA-coding DNA (5S X rDNA) and its flanking regions in C. elegans.

Isolation of the closed circular form of the transposable element Tc1 in Caenorhabditis elegans

The mobilization of Tc1, a transposable element in the genome of the roundworm Caenorhabditis elegans, has been investigated. Genomic blot hybridization has shown that Tc1 exists in very different numbers in the genomes of two closely related strains of C. elegans: there are approximately 30 copies of Tc1 in the Bristol strain, whereas in the Bergerac strain there are 200-300. Most of these Tc1 elements are structurally highly conserved although there exists a second form which contains a HindIII restriction site (Tc1 (Hin) form) and comprises approximately 10% of the population. Excision of Tc1 from its chromosomal location in the Bergerac strain is indicated by the presence, on genomic blots, of a minor band corresponding to the size of the uninserted restriction fragment. Here we describe the recovery of extrachromosomal linear and closed circular copies of Tc1 from the Bergerac strain, presumably a result of Tc1 excision.

Meiotic pairing behavior of two free duplications of linkage group I in Caenorhabditis elegans

In this paper we describe the meiotic pairing behavior of two free duplications in Caenorhabditis elegans. sDp1 is a duplication of approximately 30 map units of the right portion of linkage group I including unc-74 to unc-54. This duplication pairs, recombines, and apparently segregates from one of the normal homologues. A second duplication, sDp2, is a duplication of approximately 15 map units of the left portion of the linkage group. sDp2 was not observed to recombine with the normal homologue but did suppress exchange between the two normal homologues in a sDp2/ ++/ dpy-5 unc-35 heterozygote. Although a number of free duplications have been described previously in Caenorhabditis elegans, none of these have been shown to pair with normal homologues. The meiotic behavior of the duplications described in this paper can be understood assuming the existence in C. elegans chromosomes of pairing sites of the type described in D. melanogaster chromosomes (I. Sandler 1956; Hawley 1980).

A high degree of DNA strain polymorphism associated with the major heat shock gene in Caenorhabditis elegans

We have searched for sequence variation between the Bristol and Bergerac strains of C. elegans in regions flanking three members of the 70 kilodalton (kd) heat shock peptide (hsp) gene family. No sequence variation was detected in 40 kb of DNA flanking two 70 kd hsp genes which are not stimulated by heat shock. In contrast, analysis of DNA flanking the heat shock inducible 70 kd hsp gene showed an unusually high amount of sequence variation between the two strains. Isolation and restriction map analysis of this gene from both strains revealed that the 5' and 3' flanking regions have diverged by 8.1 and 7.0% in nucleotide sequence, respectively. We have shown that these alterations are not due to large DNA rearrangements and conclude that the majority of sequence difference is the result of point mutations. Our results suggest that the heat shock inducible 70 kd hsp gene region accumulates mutations at a rate 10 to 20 fold higher than other regions of the genome. We propose that the anomalously high accumulation of mutational events is a direct consequence of the special status of the 70 kd hsp gene and its surrounding chromatin domain in the germline of C. elegans.

High-frequency excision of transposable element Tc 1 in the nematode Caenorhabditis elegans is limited to somatic cells

Tc 1 transposable elements in the nematode Caenorhabditis elegans undergo excision at high frequency. We show here that this excision occurs primarily or entirely in the somatic tissues of the organism. Absence of germ-line excision is demonstrated by showing that Tc 1 elements are genetically stable; elements at particular genomic sites, as well as the overall number of elements in the genome, were stably maintained during a year of continuous, nonselective propagation. Somatic excision is demonstrated by showing that empty Tc 1 sites arise during a single generation of growth of a synchronous population and are not inherited by the next generation. These results suggest that excision of Tc 1 elements is under the control of tissue-specific factors.