WormBase 2014: new views of curated biology

Harris, Todd W.; Baran, Joachim; Bieri, Tamberlyn; Cabunoc, Abigail; Chan, Juancarlos; Chen, Wen J.; Davis, Paul A.; Done, James; Grove, Christian A.; Howe, Kevin; Kishore, Ranjana; Lee, Raymond Y. N.; Li, Yuling; Müller, Hans‐Michael; Nakamura, Cecilia; Ozersky, Philip; Paulini, Michael; Raciti, Daniela; Schindelman, Gary; Tuli, Mary Ann; Auken, Kimberly Van; Wang, Daniel; Wang, Xiaodong; Williams, Gary W.; Wong, Joseph; Yook, Karen; Schedl, Tim; Hodgkin, Jonathan; Berriman, Matthew; Kersey, Paul J.; Strouboulis, John; Stein, Lincoln; Sternberg, Paul W.

doi:10.1093/nar/gkt1063

Cited by 155 publications

(154 citation statements)

References 18 publications

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“…We produced around 8 million reads for each sample with three replicates each. All RNA reads were mapped against annotated coding sequences in C. briggsae (AF16) (Harris et al 2014). The reads were also de novo assembled into transcripts using Trinity (Haas et al 2013) for the purpose of small RNA mapping as detailed below.…”

Section: Resultsmentioning

confidence: 99%

Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression

Ren

et al. 2016

Genome Res.

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Hybrid incompatibility (HI) prevents gene flow between species, thus lying at the heart of speciation genetics. One of the most common HIs is male sterility. Two superficially contradictory observations exist for hybrid male sterility. First, an introgression on the X Chromosome is more likely to produce male sterility than on autosome (so-called large-X theory); second, spermatogenesis genes are enriched on the autosomes but depleted on the X Chromosome (demasculinization of X Chromosome). Analysis of gene expression in Drosophila hybrids suggests a genetic interaction between the X Chromosome and autosomes that is essential for male fertility. However, the prevalence of such an interaction and its underlying mechanism remain largely unknown. Here we examine the interaction in nematode species by contrasting the expression of both coding genes and transposable elements (TEs) between hybrid sterile males and its parental nematode males. We use two lines of hybrid sterile males, each carrying an independent introgression fragment from Caenorhabditis briggsae X Chromosome in an otherwise Caenorhabditis nigoni background, which demonstrate similar defects in spermatogenesis. We observe a similar pattern of down-regulated genes that are specific for spermatogenesis between the two hybrids. Importantly, the down-regulated genes caused by the X Chromosome introgressions show a significant enrichment on the autosomes, supporting an epistatic interaction between the X Chromosome and autosomes. We investigate the underlying mechanism of the interaction by measuring small RNAs and find that a subset of 22G RNAs specifically targeting the down-regulated spermatogenesis genes is significantly up-regulated in hybrids, suggesting that perturbation of small RNA-mediated regulation may contribute to the X-autosome interaction.

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Section: Resultsmentioning

confidence: 99%

Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression

Ren

et al. 2016

Genome Res.

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“…Functional annotation and other information about C. elegans genes can be found on Wormbase, the leading database for genome data in C. elegans. 5 Wormbase has a gene-centric main user interface but lacks a simple search interface that allows the user to display information about a large number of genes on a single results page. GExplore provides such an interface.…”

Section: Gexplore In Comparison To Other Nematode Databasesmentioning

confidence: 99%

“…For C. elegans these data are available through Wormbase, 5 the major database for C. elegans genes.…”

Section: Introductionmentioning

confidence: 99%

GExplore 1.4: An expanded web interface for queries onCaenorhabditis elegansprotein and gene function

Hutter

Suh

2016

Worm

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Genetic high-throughput experiments often result in hundreds or thousands of genes satisfying certain experimental conditions. Grouping and prioritizing a large number of genes for further analysis can be a time-consuming challenge. In 2009 we developed a web-based user interface, GExplore, to assist with large-scale data-mining related to gene function in Caenorhabditis elegans. The underlying database contained information about Caenorhabditis elegans genes and proteins including domain organization of the proteins, phenotypic descriptions, expression data and Gene Ontology Consortium annotations. These data enable users to quickly obtain an overview of biological and biochemical functions of a large number of genes at once. Since its inception the underlying database has been updated and expanded significantly. Here we describe the current version of GExplore 1.4, documenting the changes since the original release. GExplore 1.4 now contains information about the domain organization of the proteomes of 9 nematode species, can display the location of Caenorhabditis elegans mutations with respect to the domain organization of the proteins, and includes stage-specific RNAseq gene expression data generated by the modENCODE project. The underlying database has been reorganized to facilitate independent updates of the different parts of the database and to allow the addition of novel data sets in the future. The web interface is available under http://genome.sfu.ca/gexplore.

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“…17 Three major categories were identified: information storage and processing (23 proteins, 27% of all proteins), including proteins involved in chromosome segregation, nucleic acid metabolism, and protein synthesis; cellular processes and signaling (34 proteins, 40%), including proteins involved in membrane transport and cytoskeletal structure; and metabolism (24 proteins, 28%), including mitochondrial proteins. Five proteins (6%) are "poorly characterized."…”

Section: Resultsmentioning

confidence: 99%

Proteomic identification of germline proteins inCaenorhabditis elegans

Turner

Basecke

Bazan

et al. 2015

Worm

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Abbreviations: 2DGE, 2D gel electrophoresis; MALDI-TOF/TOF MS, matrix-assisted laser desorption ionization tandem time of flight mass spectrometry; SAGE, serial analysis of gene expression; RNAi, RNA interference; GO, gene ontology; COG, clusters of orthologous groupsSexual reproduction involves fusion of 2 haploid gametes to form diploid offspring with genetic contributions from both parents. Gamete formation represents a unique developmental program involving the action of numerous germline-specific proteins. In an attempt to identify novel proteins involved in reproduction and embryonic development, we have carried out a proteomic characterization of the process in Caenorhabditis elegans. To identify candidate proteins, we used 2D gel electrophoresis (2DGE) to compare protein abundance in nucleus-enriched extracts from wild-type C. elegans, and in extracts from mutant worms with greatly reduced gonads (glp-4(bn2) worms reared at 25 C); 84 proteins whose abundance correlated with germline presence were identified. To validate candidates, we used feeding RNAi to deplete candidate proteins, and looked for reduction in fertility and/or germline cytological defects. Of 20 candidates so screened for involvement in fertility, depletion of 13 (65%) caused a significant reduction in fertility, and 6 (30%) resulted in sterility (<5 % of wild-type fertility). Five of the 13 proteins with demonstrated roles in fertility have not previously been implicated in germline function. The high frequency of defects observed after RNAi depletion of candidate proteins suggests that this approach is effective at identifying germline proteins, thus contributing to our understanding of this complex organ.

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WormBase 2014: new views of curated biology

Cited by 155 publications

References 18 publications

Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression

Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression

GExplore 1.4: An expanded web interface for queries onCaenorhabditis elegansprotein and gene function

Proteomic identification of germline proteins inCaenorhabditis elegans

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