Elegans Gene Research Articles

Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

BackgroundCaenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form.ResultsWe describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO). The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor.ConclusionsWe provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and interoperability across the different Model Organism Databases (MODs) and other biological databases. This standardized phenotype ontology will therefore allow for more complex data queries and enhance bioinformatic analyses.

Chapter 10 - Gene-Centered Regulatory Network Mapping

The Caenorhabditis elegans hermaphrodite is a complex multicellular animal that is composed of 959 somatic cells. The C. elegans genome contains ∼20,000 protein-coding genes, 940 of which encode regulatory transcription factors (TFs). In addition, the worm genome encodes more than 100 microRNAs and many other regulatory RNA and protein molecules. Most C. elegans genes are subject to regulatory control, most likely by multiple regulators, and combined, this dictates the activation or repression of the gene and corresponding protein in the relevant cells and under the appropriate conditions. A major goal in C. elegans research is to determine the spatiotemporal expression pattern of each gene throughout development and in response to different signals, and to determine how this expression pattern is accomplished. Gene regulatory networks describe physical and/or functional interactions between genes and their regulators that result in specific spatiotemporal gene expression. Such regulators can act at transcriptional or post-transcriptional levels. Here, I will discuss the methods that can be used to delineate gene regulatory networks in C. elegans. I will mostly focus on gene-centered yeast one-hybrid (Y1H) assays that are used to map interactions between non-coding genic regions, such as promoters, and regulatory TFs. The approaches discussed here are not only relevant to C. elegans biology, but can also be applied to other model organisms and humans.

A global analysis of C. elegans trans-splicing

Trans-splicing of one of two short leader RNAs, SL1 or SL2, occurs at the 5' ends of pre-mRNAs of many C. elegans genes. We have exploited RNA-sequencing data from the modENCODE project to analyze the transcriptome of C. elegans for patterns of trans-splicing. Transcripts of ∼70% of genes are trans-spliced, similar to earlier estimates based on analysis of far fewer genes. The mRNAs of most trans-spliced genes are spliced to either SL1 or SL2, but most genes are not trans-spliced to both, indicating that SL1 and SL2 trans-splicing use different underlying mechanisms. SL2 trans-splicing occurs in order to separate the products of genes in operons genome wide. Shorter intercistronic distance is associated with greater use of SL2. Finally, increased use of SL1 trans-splicing to downstream operon genes can indicate the presence of an extra promoter in the intercistronic region, creating what has been termed a "hybrid" operon. Within hybrid operons the presence of the two promoters results in the use of the two SL classes: Transcription that originates at the promoter upstream of another gene creates a polycistronic pre-mRNA that receives SL2, whereas transcription that originates at the internal promoter creates transcripts that receive SL1. Overall, our data demonstrate that >17% of all C. elegans genes are in operons.

A response to Rome: lessons from pre- and post-publication data-sharing in the C. elegans research community

BackgroundIn recent years numerous studies have undertaken to measure the impact of patents, material transfer agreements, data-withholding and commercialization pressures on biomedical researchers. Of particular concern is the theory that such pressures may have negative effects on academic and other upstream researchers. In response to these concerns, commentators in some research communities have called for an increased level of access to, and sharing of, data and research materials. We have been studying how data and materials are shared in the community of researchers who use the nematode Caenorhabditis elegans (C. elegans) as a model organism for biological research. Specifically, we conducted a textual analysis of academic articles referencing C. elegans, reviewed C. elegans repository request lists, scanned patents that reference C. elegans and conducted a broad survey of C. elegans researchers. Of particular importance in our research was the role of the C. elegans Gene Knockout Consortium in the facilitation of sharing in this community.ResultsOur research suggests that a culture of sharing exists within the C. elegans research community. Furthermore, our research provides insight into how this sharing operates and the role of the culture that underpins it.ConclusionsThe greater scientific community is likely to benefit from understanding the factors that motivate C. elegans researchers to share. In this sense, our research is a 'response' to calls for a greater amount of sharing in other research communities, such as the mouse community, specifically, the call for increased investment and support of centralized resource sharing infrastructure, grant-based funding of data-sharing, clarity of third party recommendations regarding sharing, third party insistence of post-publication data sharing, a decrease in patenting and restrictive material transfer agreements, and increased attribution and reward.

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

Posttranscriptional gene regulation frequently occurs through elements in mRNA 3′ untranslated regions (UTRs)1,2. Although crucial roles for 3′UTR-mediated gene regulation have been found in Caenorhabditis elegans3,4,5, most C. elegans genes have lacked annotated 3′UTRs6,7. Here we describe a high-throughput method to reliably identify polyadenylated RNA termini, and we apply this method, called poly(A)-position profiling by sequencing (3P-Seq), to determine C. elegans 3′UTRs. Compared to standard methods also recently applied to C. elegans UTRs8, 3P-Seq identified 8,581 additional UTRs while excluding thousands of shorter UTR isoforms that do not appear to be authentic. Analysis of this expanded and corrected dataset suggested that the high A/U content of C. elegans 3′UTRs facilitated genome compaction, since the elements specifying cleavage and polyadenylation, which are A/U-rich, can more readily emerge in A/U rich regions. Indeed, 30% of the protein-coding genes have mRNAs with alternative, partially overlapping end regions that generate another 10,498 cleavage and polyadenylation sites that had gone largely unnoticed and represent potential evolutionary intermediates of progressive UTR shortening. Moreover, a third of the convergently transcribed genes utilize palindromic arrangements of bidirectional elements to specify UTRs with convergent overlap, which also contributes to genome compaction by eliminating regions between genes. Although nematode 3′UTRs have median length only one-sixth that of mammalian 3′UTRs, they have twice the density of conserved microRNA sites, in part because additional types of seed-complementary sites are preferentially conserved. These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying posttranscriptional gene regulation.

Regulation of longevity by genes required for the functions of AIY interneuron in nematode Caenorhabditis elegans

In Caenorhabditis elegans, functional ttx-3, sra-11, ceh-10, and ceh-23 genes are required for the functions of AIY interneuron. Compared to wild-type N2, mutations in ttx-3 and ceh-10 significantly decreased lifespan, whereas mutations in sra-11 and ceh-23 did not obviously influence nematode lifespan. Mutations in ttx-3 and ceh-10 were associated closely with lower pumping rates at adult day 8 and caused a more rapid accumulated intestinal autofluorescence than wild-type N2. Mutations in ceh-10 remarkably affected fertility and egg number in the uterus. The regulation of ttx-3 and ceh-10 on longevity was not temperature-dependent, and ttx-3, and ceh-10 mutants all formed very few dauers at 27 °C. The shortened lifespan of the ttx-3 or ceh-10 mutants was completely or largely rescued by expression of TTX-3 or CEH-10 in AIY interneurons. Moreover, the long-lived phenotype of the daf-2 mutant could be suppressed by both the ttx-3 and the ceh-10 mutations. Furthermore, ablation of AIY interneurons shortened the longevity of wild-type and the daf-2 mutant. Therefore, ttx-3 and ceh-10 regulate the longevity through influencing the insulin/IGF signaling pathway in C. elegans.

A New Look at Old Data

Although the full genome of Caenorhabditis elegans has been available for over 10 years, only a portion of the full-length messenger RNAs (mRNAs) and their expression through development has been analyzed. By combining multiple methods, involving a careful reannotation of existing data sets, sequencing of poly-A captured RNAs from multiple developmental stages, as well as cloning and deep sequencing of a subset of genes, Mangone et al. (p. [432][1], published online 3 June) defined ∼26,000 distinct mRNA three-prime untranslated regions (3′UTRs) for ∼85% of the protein-coding genes. Most C. elegans genes have more than one 3′UTR, arising through different mechanisms including trans-splicing–coupled cleavage and polyadenylation. The work highlights the importance of the 3'UTRs in the regulation of mRNA stability and translation. [1]: /lookup/doi/10.1126/science.1191244

Post-transcriptional gene silencing of root-knot nematode in transformed soybean roots

RNAi constructs targeted to four different genes were examined to determine their efficacy to reduce galls formed by Meloidogyne incognita in soybean roots. These genes have high similarity with essential soybean cyst nematode ( Heterodera glycines) and Caenorhabditis elegans genes. Transformed roots were challenged with M. incognita. Two constructs, targeted to genes encoding tyrosine phosphatase (TP) and mitochondrial stress-70 protein precursor (MSP), respectively, strongly interfered with M. incognita gall formation. The number of galls formed on roots transformed with constructs targeting the M. incognita TP and MSP genes was reduced by 92% and 94.7%, respectively. The diameter of M. incognita inside these transformed roots was 5.4 and 6.5 times less than the diameter of M. incognita found inside control plants transformed with the empty vector. These results indicate that silencing the genes encoding TP and MSP can greatly decrease gall formation and shows a promising solution for broadening resistance of plants against this plant-parasitic nematode.

Distinct pathogenesis and host responses during infection of C. elegans by P. aeruginosa and S. aureus.

The genetically tractable model host Caenorhabditis elegans provides a valuable tool to dissect host-microbe interactions in vivo. Pseudomonas aeruginosa and Staphylococcus aureus utilize virulence factors involved in human disease to infect and kill C. elegans. Despite much progress, virtually nothing is known regarding the cytopathology of infection and the proximate causes of nematode death. Using light and electron microscopy, we found that P. aeruginosa infection entails intestinal distention, accumulation of an unidentified extracellular matrix and P. aeruginosa-synthesized outer membrane vesicles in the gut lumen and on the apical surface of intestinal cells, the appearance of abnormal autophagosomes inside intestinal cells, and P. aeruginosa intracellular invasion of C. elegans. Importantly, heat-killed P. aeruginosa fails to elicit a significant host response, suggesting that the C. elegans response to P. aeruginosa is activated either by heat-labile signals or pathogen-induced damage. In contrast, S. aureus infection causes enterocyte effacement, intestinal epithelium destruction, and complete degradation of internal organs. S. aureus activates a strong transcriptional response in C. elegans intestinal epithelial cells, which aids host survival during infection and shares elements with human innate responses. The C. elegans genes induced in response to S. aureus are mostly distinct from those induced by P. aeruginosa. In contrast to P. aeruginosa, heat-killed S. aureus activates a similar response as live S. aureus, which appears to be independent of the single C. elegans Toll-Like Receptor (TLR) protein. These data suggest that the host response to S. aureus is possibly mediated by pathogen-associated molecular patterns (PAMPs). Because our data suggest that neither the P. aeruginosa nor the S. aureus–triggered response requires canonical TLR signaling, they imply the existence of unidentified mechanisms for pathogen detection in C. elegans, with potentially conserved roles also in mammals.

Structure and Properties of a Bis-Histidyl Ligated Globin from Caenorhabditis elegans,

Globins are heme-containing proteins that are best known for their roles in oxygen (O(2)) transport and storage. However, more diverse roles of globins in biology are being revealed, including gas and redox sensing. In the nematode Caenorhabditis elegans, 33 globin or globin-like genes were recently identified, some of which are known to be expressed in the sensory neurons of the worm and linked to O(2) sensing behavior. Here, we describe GLB-6, a novel globin-like protein expressed in the neurons of C. elegans. Recombinantly expressed full-length GLB-6 contains a heme site with spectral features that are similar to those of other bis-histidyl ligated globins, such as neuroglobin and cytoglobin. In contrast to these globins, however, ligands such as CO, NO, and CN(-) do not bind to the heme in GLB-6, demonstrating that the endogenous histidine ligands are likely very tightly coordinated. Additionally, GLB-6 exhibits rapid two-state autoxidation kinetics in the presence of physiological O(2) levels as well as a low redox potential (-193 +/- 2 mV). A high-resolution (1.40 A) crystal structure of the ferric form of the heme domain of GLB-6 confirms both the putative globin fold and bis-histidyl ligation and also demonstrates key structural features that can be correlated with the unusual ligand binding and redox properties exhibited by the full-length protein. Taken together, the biochemical properties of GLB-6 suggest that this neural protein would most likely serve as a physiological sensor for O(2) in C. elegans via redox signaling and/or electron transfer.

Comparative Characterization of Three D‐Aspartate Oxidases and One D‐Amino Acid Oxidase from Caenorhabditis elegans

Previously, we cloned cDNAs for four Caenorhabditis elegans genes (F20 Hp, C47Ap, F18Ep, and Y69Ap genes) that were annotated in the database as encoding D-amino acid oxidase (DAO) or D-aspartate oxidase (DDO) proteins. These genes were expressed in Escherichia coli, and the recombinant C47Ap and F18Ep were shown to have functional DDO activities, while Y69Ap had functional DAO activity. In this study, we improved the E. coli culture conditions for the production of recombinant F20 Hp and, following purification of the protein, revealed that it has functional DDO activity. The kinetic properties of recombinant C47Ap (DDO-1), F18Ep (DDO-2), F20 Hp (DDO-3), and Y69Ap (DAO) were also determined and compared with recombinant human DDO and DAO. In contrast to the low catalytic efficiency of human DDO for D-Glu, all three C. elegans DDOs showed higher catalytic efficiencies for D-Glu than D-Asp or N-methyl-D-Asp. The catalytic efficiency of C. elegans DAO for D-Ser was substantially lower than that of human DAO, while the C. elegans DAO was more efficient at deamination of basic D-amino acids (D-Arg and D-His) than human DAO. Collectively, our results indicate that C. elegans contains at least three genes that encode functional DDOs, and one gene encoding a functional DAO, and that these enzymes have different and distinctive properties.

Knockout of the folate transporter folt-1 causes germline and somatic defects in C. elegans.

BackgroundThe C. elegans gene folt-1 is an ortholog of the human reduced folate carrier gene. The FOLT-1 protein has been shown to transport folate and to be involved in uptake of exogenous folate by worms. A knockout mutation of the gene, folt-1(ok1460), was shown to cause sterility, and here we investigate the source of the sterility and the effect of the folt-1 knockout on somatic function.ResultsOur results show that folt-1(ok1460) knockout hermaphrodites have a substantially reduced germline, generate a small number of functional sperm, and only rarely produce a functional oocyte. We found no evidence of increased apoptosis in the germline of folt-1 knockout mutants, suggesting that germline proliferation is defective. While folt-1 knockout males are fertile, their rate of spermatogenesis was severely diminished, and the males were very poor maters. The mating defect is likely due to compromised metabolism and/or other somatic functions, as folt-1 knockout hermaphrodites displayed a shortened lifespan and elongated defecation intervals.ConclusionsThe FOLT-1 protein function affects both the soma and the germline. folt-1(ok1460) hermaphrodites suffer severely diminished lifespan and germline defects that result in sterility. Germline defects associated with folate deficiency appear widespread in animals, being found in humans, mice, fruit flies, and here, nematodes.

APC16 is a conserved subunit of the anaphase-promoting complex/cyclosome

Error-free chromosome segregation depends on timely activation of the multi-subunit E3 ubiquitin ligase APC/C. Activation of the APC/C initiates chromosome segregation and mitotic exit by targeting critical cell-cycle regulators for destruction. The APC/C is the principle target of the mitotic checkpoint, which prevents segregation while chromosomes are unattached to spindle microtubules. We now report the identification and characterization of APC16, a conserved subunit of the APC/C. APC16 was found in association with tandem-affinity-purified mitotic checkpoint complex protein complexes. APC16 is a bona fide subunit of human APC/C: it is present in APC/C complexes throughout the cell cycle, the phenotype of APC16-depleted cells copies depletion of other APC/C subunits, and APC16 is important for APC/C activity towards mitotic substrates. APC16 sequence homologues can be identified in metazoans, but not fungi, by four conserved primary sequence stretches. We provide evidence that the C. elegans gene K10D2.4 and the D. rerio gene zgc:110659 are functional equivalents of human APC16. Our findings show that APC/C is composed of previously undescribed subunits, and raise the question of why metazoan APC/C is molecularly different from unicellular APC/C.

Transcript analysis of parasitic females of the sedentary semi-endoparasitic nematode Rotylenchulus reniformis

Rotylenchulus reniformis, the reniform nematode, is a sedentary semi-endoparasitic nematode capable of infecting >300 plant species, including a large number of crops such as cotton, soybean, and pineapple. In contrast to other economically important plant-parasitic nematodes, molecular genetic data regarding the R. reniformis transcriptome is virtually nonexistant. Herein, we present a survey of R. reniformis ESTs that were sequenced from a sedentary parasitic female cDNA library. Cluster analysis of 2004 high quality ESTs produced 123 contigs and 508 singletons for a total of 631 R. reniformis unigenes. BLASTX analyses revealed that 39% of all unigenes showed similarity to known proteins (E≤1.0e−04). R. reniformis genes homologous to known parasitism genes were identified and included β-1,4-endoglucanase, fatty acid- and retinol-binding proteins, and an esophageal gland cell-specific gene from Heterodera glycines. Furthermore, a putative ortholog of an enzyme involved in thiamin biosynthesis, thought to exist solely in prokaryotes, fungi, and plants, was identified. Lastly, 114 R. reniformis unigenes orthologous to RNAi-lethal Caenorhabditis elegans genes were discovered. The work described here offers a glimpse into the transcriptome of a sedentary semi-endoparasitic nematode which (i) provides the transcript sequence data necessary for investigating engineered resistance against R. reniformis and (ii) hints at the existance of a thiamin biosynthesis pathway in an animal.

Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo

BackgroundImage analysis is an essential component in many biological experiments that study gene expression, cell cycle progression, and protein localization. A protocol for tracking the expression of individual C. elegans genes was developed that collects image samples of a developing embryo by 3-D time lapse microscopy. In this protocol, a program called StarryNite performs the automatic recognition of fluorescently labeled cells and traces their lineage. However, due to the amount of noise present in the data and due to the challenges introduced by increasing number of cells in later stages of development, this program is not error free. In the current version, the error correction (i.e., editing) is performed manually using a graphical interface tool named AceTree, which is specifically developed for this task. For a single experiment, this manual annotation task takes several hours.ResultsIn this paper, we reduce the time required to correct errors made by StarryNite. We target one of the most frequent error types (movements annotated as divisions) and train a support vector machine (SVM) classifier to decide whether a division call made by StarryNite is correct or not. We show, via cross-validation experiments on several benchmark data sets, that the SVM successfully identifies this type of error significantly. A new version of StarryNite that includes the trained SVM classifier is available at http://starrynite.sourceforge.net.ConclusionsWe demonstrate the utility of a machine learning approach to error annotation for StarryNite. In the process, we also provide some general methodologies for developing and validating a classifier with respect to a given pattern recognition task.

Two Very Long Chain Fatty Acid Acyl-CoA Synthetase Genes, acs-20 and acs-22, Have Roles in the Cuticle Surface Barrier in Caenorhabditis elegans

In multicellular organisms, the surface barrier is essential for maintaining the internal environment. In mammals, the barrier is the stratum corneum. Fatty acid transport protein 4 (FATP4) is a key factor involved in forming the stratum corneum barrier. Mice lacking Fatp4 display early neonatal lethality with features such as tight, thick, and shiny skin, and a defective skin barrier. These symptoms are strikingly similar to those of a human skin disease called restrictive dermopathy. FATP4 is a member of the FATP family that possesses acyl-CoA synthetase activity for very long chain fatty acids. How Fatp4 contributes to skin barrier function, however, remains to be elucidated. In the present study, we characterized two Caenorhabditis elegans genes, acs-20 and acs-22, that are homologous to mammalian FATPs. Animals with mutant acs-20 exhibited defects in the cuticle barrier, which normally prevents the penetration of small molecules. acs-20 mutant animals also exhibited abnormalities in the cuticle structure, but not in epidermal cell fate or cell integrity. The acs-22 mutants rarely showed a barrier defect, whereas acs-20;acs-22 double mutants had severely disrupted barrier function. Moreover, the barrier defects of acs-20 and acs-20;acs-22 mutants were rescued by acs-20, acs-22, or human Fatp4 transgenes. We further demonstrated that the incorporation of exogenous very long chain fatty acids into sphingomyelin was reduced in acs-20 and acs-22 mutants. These findings indicate that C. elegans Fatp4 homologue(s) have a crucial role in the surface barrier function and this model might be useful for studying the fundamental molecular mechanisms underlying human skin barrier and relevant diseases.

A study of ascertaining the exact gene location where C. elegans form abnormal habituation using SNPs methods

Objective To determine the enact gene location hab-1 ( en308) which effects C elagans abnormal habituation using SNPs methods. Methods (1) To retrieve the SNP markers of Y71A12B which chained at the first autosome the CB4856 (22. 330MU) and SNP markers of C37A5 (22. 330MU) in C. elegans gene bank,its genotype was set to YC/YC,the genotypes of hab-1 (cn308) was set to h/h. (2) By means of Synchronized processing, the size of worms was unified. (3) Wild-type CB4856 male was three-factor hybridized with her-maphroditism cn308. F1 generation were tested by Tap test, recording the distance of response of the worms, statistical processing, screening habituation and retaining the Normal Heterozygote (YC/h) , suboulturing to F2. (4) Then F2 generation were tested by Tap test,C. elegans with slow habitualion were selected, processed by PCR, digested by restriction enzyme , separated target fragment with 2% agarose gel electrophoresis. Results After the first Tap test, the formation of habituation of the wild-type was significantly faster than the cn308. (the average of habituation for Tap stimulation( Moving distance, unit;mm) ,the wild-type' s was (0.414 ±0. 049)mm,cn308 was (0.777 ±0.062)mm, ( = 10.08, P<0.001) ,in the habituation retention test 1 hour later,the habituation of wild-type was found that it retained significantly longer than cn308 (the average of habituation retention, wild-type was (0.307 ±0.041)mm,cn308 was (0. 815 ±0. 054) mm, : = 11.54, P< 0.001). (2) SNP fragments were analyzed, the genetic recombination number between SNP marker of Y71A12B and hab-1 and the genetic recombination number between SNP marker of C37A5 and hab-1 were gathered, observing the phenotype of H non C-type, namely, Ch/h:20, Yh/h:6 ,by reckoning the restructuring proportion it was determined that the distance between hab-1 and SNP marker of Y71A12B was 0. 831MU. The distance between hab-1 and SNP marker of C37A5 was 0. 249MU. So it could be ascertained that hab-1 located between the SNP marker of Y71A12B and SNP marker of C37A5. Conclusion The gene location of hab-1 which influence C. elegans abnormal habituation by harmless mechanical tap stimulation is 23. 161MU. Key words: Tap stimulation; Habitualion; SNPs; Hab-1

Whole genomic expression analysis of octachlorostyrene-induced chronic toxicity in Caenorhabditis elegans

In recent years, microarray technology has enabled the investigation of possible mechanisms the expression of genes related to toxic compounds. We used a C. elegans whole genome microarray to observe and evaluate the chronic toxicity of the free-living nematode Caenorhabditis elegans (C. elegans) after exposure to octachlorostyrene, (OCS), a by-product in the manufacture of many chlorinated hydrocarbons. In this study, we examined sublethal toxicity, egg hatching, and movement of octachlorostyrene over three generations using a nematode growth medium (NGM) agar plate. In the third generation, OCS affected the fecundity rate of C. elegans. Specifically, the number of worm and eggs decreased significantly to about 50% of control (p < 0.05). In microarray experiments, total RNA was isolated at 0, 2 and 3 generations following treatment of OCS, and hybridized to the microarray containing about 22,000 C. elegans genes. Dye swaps were performed. After data analysis, we identified a total of 1,294 genes that were differentially expressed through generations.

Ubiquitin ligases join the field of dietary restriction in C.elegans

Ubiquitin ligases join the field of dietary restriction in C.elegans

Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning

We have characterized two post-translational histone modifications in Caenorhabditis elegans on a genomic scale. Micrococcal nuclease digestion and immunoprecipitation were used to obtain distinct populations of single nucleosome cores, which were analyzed using massively parallel DNA sequencing to obtain positional and coverage maps. Two methylated histone H3 populations were chosen for comparison: H3K4 histone methylation (associated with active chromosomal regions) and H3K9 histone methylation (associated with inactivity). From analysis of the sequence data, we found nucleosome cores with these modifications to be enriched in two distinct partitions of the genome; H3K4 methylation was particularly prevalent in promoter regions of widely expressed genes, while H3K9 methylation was enriched on specific chromosomal arms. For each of the six chromosomes, the highest level of H3K9 methylation corresponds to the pairing center responsible for chromosome alignment during meiosis. Enrichment of H3K9 methylation at pairing centers appears to be an early mark in meiotic chromosome sorting, occurring in the absence of components required for proper pairing of homologous chromosomes. H3K9 methylation shows an intricate pattern within the chromosome arms with a particular anticorrelation to regions that display a strong approximately 10.5 bp periodicity of AA/TT dinucleotides that is known to associate with germline transcription. By contrast to the global features observed with H3K9 methylation, H3K4 methylation profiles were most striking in their local characteristics around promoters, providing a unique promoter-central landmark for 3,903 C. elegans genes and allowing a precise analysis of nucleosome positioning in the context of transcriptional initiation.