Andreas H Ludewig et al. (2001) International C. elegans Meeting "DIN-1, a putative DAF-12 cofactor that regulates the C.elegans dauer diapause"

Alexander Stein, Andreas H Ludewig, Adam Antebi

[International C. elegans Meeting, 2001]

The nuclear receptor daf-12 acts as a control gene at the intersection of heterochronic and dauer pathways. To further understand the molecular mechanisms of DAF-12 regulated pathways, we screened for DAF-12 interacting proteins by the Yeast-Two Hybrid method. Three candidate interactors were identified. One of these, called DIN-1 (DAF-12 interacting Protein 1) is predicted to be a nuclear protein of 2328 amino acids, containing several nuclear localisation sites, an RNA recognition motif, and regions of homology to the mammalian Msx-2 interacting target protein (MINT). In the C-terminus, there are several motifs characteristic of nuclear receptor corepressors in the region that interacts with DAF-12. These structural data suggest that DIN-1 might be a DAF-12 cofactor. din-1 was shown to have clear effects in functional knock out assays done by RNAi feeding experiments. din-1 partly or completely suppressed the dauer constitutive (Daf-c) phenotypes of mutants that act upstream of daf-12 in the dauer pathway, including insulin-like ( daf-2 ), TGF-beta ( daf-7 ), cGMP ( daf-11 ) and hormonal ( daf-9 ) signaling. Moreover, din-1 dramatically suppressed the delayed heterochronic and Daf-c phenotypes of daf-12 gain-of-function alleles, but had no effect on daf-12 null mutants. Consistent with two-hybrid interaction, these genetic data strongly suggest that DAF-12 and DIN-1act at the same step. We think that DIN-1could function in a transcriptional complex with DAF-12, perhaps as a corepressor or coactivator controlling developmental arrest and dauer formation.

Andreas H Ludewig et al. (2002) European Worm Meeting "DIN-1, a putative DAF-12 coregulator important for the C.elegans dauer diapause"

Andreas H Ludewig, Alexander Stein, Adam Antebi, Corinna Kober-Eisermann, Cindy Weitzel

[European Worm Meeting, 2002]

The C. elegans orphan nuclear receptor DAF-12 acts as key control gene at the intersection of heterochronic, dauer and aging pathways. A putative steroid hormone, metabolized by DAF-9/ cytochrome P450 likely regulates DAF-12. In addition, distinct transcriptional ensembles could mediate DAF-12 functional complexity. Some vertebrate nuclear receptors activate gene expression in the presence of cognate hormone, and repress in its absence, by assembling coactivator and corepressor complexes, respectively. This mechanism allows nuclear receptors to act as ligand-inducible logic switches. To define such transcriptional complexes, we screened for DAF-12 interacting proteins by the Yeast-Two Hybrid method. Eight candidate interactors were identified. One of these, DIN-1 (DAF-12 Interacting Protein 1) is predicted to encode two large nuclear proteins of 2713 and 2784 amino acids based on cDNAs isolated by RT-PCR. DIN-1 contains several nuclear localization sites and three RNA recognition motifs. It also has several motifs typical of nuclear receptor corepressors, and most of these are located within the receptor interaction domain (RID). Recently, the human homolog, SHARP, was shown to act as a corepressor with a number of nuclear receptors. In C. elegans, DIN-1(+) is important for the dauer diapause. A knockdown of DIN-1(+) activity by RNAi or conventional mutations produces no evident phenotype in an otherwise wild type background. However, din-1 partly or completelv suppresses the dauer constitutive phenotypes (Daf-c) of various dauer pathway mutants, e.g. insulin like receptor daf-2 (class I) alleles. It also suppresses the delayed heterochronic and Daf-c phenotypes of certain daf-12 alleles. Interestingly, all din-1 alleles identified to date map within the RID. din-1 does not affect the expression or localization of daf-12::GFP. Taken together, these structural and functional data strongly suggest that DIN-1 is a DAF-12 coregulator. We propose that in the absence of reproductive hormone, DAF-12 assembles a corepressor complex containing DIN-1 and other components to mediate developmental arrest and diapause. Moreover, these complexes must be functionally redundant because DIN-1(+)is not essential for diapause under dauer inducing conditions.

Donlin MJ (2007) Curr Protoc Bioinformatics "Using the Generic Genome Browser (GBrowse)."

Donlin MJ

[Curr Protoc Bioinformatics, 2007]

A genome browser is software that allows users to visualize DNA, protein, or other sequence features within the context of a reference sequence, such as a chromosome or contig. The Generic Genome Browser (GBrowse) is an open-source browser developed as part of the Generic Model Organism Database project (Stein et al., 2002). GBrowse can be configured to display genomic sequence features for any organism and is the browser used for the model organisms Drosophila melanogaster (Grumbling and Strelets, 2006) and Caenorhabditis elegans (Schwarz et al., 2006), among others. The software package can be downloaded from the web and run on a Windows, Mac OS X, or Unix-type system. Version 1.64, as described in this protocol, was released in November 2005, but the software is under active development and new versions are released about every six months.

Donlin MJ (2009) Curr Protoc Bioinformatics "Using the Generic Genome Browser (GBrowse)."

Donlin MJ

[Curr Protoc Bioinformatics, 2009]

A genome browser is software that allows users to visualize DNA, protein, or other sequence features within the context of a reference sequence, such as a chromosome or contig. The Generic Genome Browser (GBrowse) is an open-source browser developed as part of the Generic Model Organism Database project (Stein et al., 2002). GBrowse can be configured to display genomic sequence features for any organism and is the browser used for the model organisms Drosophila melanogaster (Grumbling and Strelets, 2006) and Caenorhabditis elegans (Schwarz et al., 2006), among others. The software package can be downloaded from the Web and run on a Windows, Mac OS X, or Unix-type system. Version 1.64, as described in the original protocol, was released in November 2005, but the software is under active development and new versions are released about every six months. This update includes instructions on updating existing data sources with new files from NCBI.

Memar N et al. (2018) Dev Biol "Twenty million years of evolution: The embryogenesis of four Caenorhabditis species are indistinguishable despite extensive genome divergence."

Conradt B, Schiemann S, Memar N, Findeis D, Hennig C, Schnabel R

[Dev Biol, 2018]

The four Caenorhabditis species C. elegans, C. briggsae, C. remanei and C. brenneri show more divergence at the genomic level than humans compared to mice (Stein et al., 2003; Cutter et al., 2006; Cutter et al., 2008). However, the behavior and anatomy of these nematodes are very similar. We present a detailed analysis of the embryonic development of these species using 4D-microscopic analyses of embryos including lineage analysis, terminal differentiation patterns and bioinformatical quantifications of cell behavior. Further functional experiments support the notion that the early development of all four species depends on identical induction patterns. Based on our results, the embryonic development of all four Caenorhabditis species are nearly identical, suggesting that an apparently optimal program to construct the body plan of nematodes has been conserved for at least 20 million years. This contrasts the levels of divergence between the genomes and the protein orthologs of the Caenorhabditis species, which is comparable to the level of divergence between mouse and human. This indicates an intricate relationship between the structure of genomes and the morphology of animals.

Consortium Wormbase et al. (2000) West Coast Worm Meeting "From ACeDB to a more complete and usable database"

Consortium Wormbase, Foltz NL, Schwarz EM, Sternberg PW

[West Coast Worm Meeting, 2000]

We briefly describe the current status and plans for WormBase, initially an extension of the existing ACeDB database with a new user interface. The WormBase consortium includes the team that developed ACeDB (Richard Durbin and colleagues at the Sanger Centre; Jean Thierry-Mieg and colleagues at Montpellier); Lincoln Stein and colleagues at Cold Spring Harbor, who developed the current web interface for WormBase; and John Spieth and colleagues at the Genome Sequencing Center at Washington University, who along with the Sanger Centre team, continue to annotate the genomic sequence. The Caltech group will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level, and gene interactions. Data will be extracted from the literature, as well as by community submission. We look forward to providing the C. elegans and broader research community easy access to vast quantities of high quality data on C. elegans. Also, we welcome your suggestions and criticism at any time. WormBase can be accessed at www.wormbase.org.

Sheldon J McKay et al. (2005) International Worm Meeting "Genome organization and colinearity in three Caenorhabditis species"

Sheldon J McKay, Lincoln D Stein

[International Worm Meeting, 2005]

C. elegans and C. briggsae are morphologically similar but their genomes have had about 100 million years to diverge. Examples of ways in which the two genomes have diverged include not only nucleotide substitutions but also species-specific expansion of gene families and many inter- and intra-chromosomal rearrangements (1). In addition to coding DNA and other functional sequences, higher order chromosome structure is also under selective constraints, for example against loss of genetic material due to non-reciprocal chromosome rearrangements. Conservation of regions of colinearity between divergent genomes suggests that gene order is also important. A striking example of this is the high degree inter-species conservation of gene order and composition of operons. We are building on the previously described comparison of the C. elegans and C. briggsae genomes using a global analysis of conservation of syntenic blocks in the genomes of these two species as well as that of C. remanei. The foundation of these comparisons is sequence similarity-based genome alignments performed by WABA(2) and blastz(3). Although conservation at the nucleotide sequence level is helpful in understanding genome evolution, global application of DNA sequence alignments in divergent genomes can be confounded by multiple rearrangements affecting the same region of the chromosome. Disruption in alignable sequences caused by a complex history of local rearrangements can mask larger blocks of colinearity that may be functionally significant. To identify such regions in these three species and, hopefully, unravel some of the complexity of nested chromosome rearrangements, we are applying a method based on the dynamic programming algorithm described in Stein et al. (1) and comparing it to the approach developed by Kent et al. (4) for the mouse and human genomes. We will discuss our findings in relation to the existing body of knowledge on C. elegans and C. briggsae genome organization and the impact of adding an additional species on our understanding of Caenorhabditis genome evolution. 1. Stein, L. D. et al., PLoS Biology 1:166-192 2. Kent, W. J. and A. M. Zahler, Genome Res 10:1115-1125 3. Schwartz, S. et al., Genome Res 13:103-107 4. Kent, W. J. et al., PNAS 100:11484-11489

Shakes, Diane et al. (2009) International Worm Meeting "EMB-1 is a novel protein involved in the metaphase-to-anaphase transition."

Golden, Andy, Shakes, Diane

[International Worm Meeting, 2009]

The Anaphase Promoting Complex (APC) is a multi-subunit E3 ubiquitin ligase that promotes the metaphase-to-anaphase transition during meiotic and mitotic divisions. Temperature-sensitive (ts) mutants in mat-1, mat-2, mat-3, emb-27, and emb-30 arrest as 1-cell embryos, stuck in metaphase of meiosis I. These five genes code for five subunits of the APC. The ts alleles of emb-1 have grabbed our attention because their arrest phenotype is indistinguishable from the APC mutants. Furthermore, genetic doubles constructed between emb-1(hc62) and the APC mutants cannot be maintained at the permissive temperature, a common feature of any APC double mutant. Additionally, suppressors that suppress the APC mutants (Stein et al., 2007) also suppress emb-1. What is EMB-1 you may ask? We mapped emb-1 to a tiny interval on LG III and used RNAi to phenocopy the 1-cell arrest phenotype. Rescue and sequencing confirmed that emb-1 codes for a novel protein with no known homologies outside of Caenorhabditis species. Localization studies are underway. We propose that EMB-1 is a novel subunit or regulator of the APC in C. elegans.

Bhaskar Reddy Gavinolla et al. (2007) International Worm Meeting "Interactions between the microtubule severing protein MEI-2 and spindle checkpoints."

Bhaskar Reddy Gavinolla, Paul E. Mains

[International Worm Meeting, 2007]

The spindle checkpoint protein, SAN-1/MDF-3 is expressed on mitotic centromeres. During anoxia, mutants fail to arrest the cell cycle, leading to chromosome mis-segregation and reduced viability (Nystul et. al 2003). Checkpoint proteins arrest the cell cycle by inhibiting the Anaphase Promoting Complex (APC) and san-1/mdf-3 mutants suppress APC mutants (Stein et al. 2007). We have uncovered a possible link between the microtubule severing complex MEI-1/MEI-2 and the meiotic spindle checkpoint. Like SAN-1/MDF-3, MEI-1 and MEI-2 localize to chromatin and genetically interact with APC mutants. Furthermore, yeast two hybrid data (Li et al. 2004) shows that MEI-2 and SAN-1 interact physically. Both the similar expression patterns and the yeast two-hybrid binding suggested possible genetic interaction between them, so we made double mutants of san-1 and mei-2. This resulted in increased lethality, low brood sizes and spontaneous males, indications of meiotic failure. While enhancement of mei-2 spindle formation defects might be expected by the presence of a compromised spindle checkpoint, the physical interaction and colocalization might indicate a more specific role for MEI-1/MEI-2 in monitoring spindle quality.

Nansheng Chen et al. (2005) International Worm Meeting "Conservation and Functional Significance of Overlapping Genes in Caenorhabditis elegan"

Nansheng Chen, Lincoln Stein

[International Worm Meeting, 2005]

We have systematically examined the overlapping genes in the Caenorhabditis elegans genome. There exist over one thousand such gene pairs in the entire C. elegans genome and can be subdivided into six major categories based on the overlap topology. We demonstrate that some categories of overlapping genes are bipolarized in terms of gene evolution. Some types of overlapping genes are strongly and significantly more conserved than the genome as a whole when compared to Caenorhabditis briggsae, a nematode that split from C. elegans about 100 million years ago (1), while other types of overlapping genes, the nested genes that reside within introns of other genes in particular, are significantly less conserved compared with other genes in the genome. We have also found that although overlapping gene pairs tend not to share common functional motifs, they are enriched with essential genes and genes that cause various defined phenotypes revealed by RNAi trials, indicating the functional significance of these genes. Tissue-specific SAGE library datasets analysis suggests that the flanking genes and their corresponding nested genes are not as strongly positively correlated in gene expression pattern as tandem gene pairs, suggesting that the flanking / nested gene pair arrangement interferes with coexpression among the members of the gene pairs. 1. L. D. Stein et al., PLoS Biol 1, E45 (Nov, 2003).