Faerberg, Denis et al. (2021) International Worm Meeting "Discerning the temporal organization of development"

Faerberg, Denis, Gurarie, Victor, Ruvinsky, Ilya

[International Worm Meeting, 2021]

Understanding temporal regulation of development remains an important challenge. Whereas average, species-typical timing of many developmental processes has been established, less is known about inter-individual variability and correlations in timing of specific events. We are studying these questions in the context of development in Caenorhabditis elegans. In one study, based on patterns of locomotor activity of freely moving animals, we inferred durations of four larval stages (L1-L4) in over 100 individuals. Analysis of these data supports several conclusions. Individuals have consistently faster or slower rates of development because durations of L1 through L3 stages are positively correlated. The last larval stage, the L4, is less variable than the earlier stages and its duration is largely independent of the rate of early larval development, implying existence of two distinct larval epochs. Interestingly, stage durations tend to scale relative to total developmental time. Fractional stage durations (calculated as L1 duration/total time to adulthood, etc.) are indistinguishable across several independent studies that relied on different methodologies and were conducted at different temperatures. This scaling relationship suggests that each larval stage is not limited by an absolute duration, but is instead terminated when a subset of events that must occur prior to adulthood have been completed. Comparing these results to our more recent studies of developmental timing allows the inference of general principles of temporal organization of development.

Jane Shingles et al. (2006) European Worm Meeting "Progress of the Localization of Expression Mapping Project"

Jane Shingles, Denis Dupuy, Marc Vidal, Ian Hope, John Reece-Hoyes

[European Worm Meeting, 2006]

Jane Shingles1, John Reece-Hoyes1, Denis Dupuy2, Marc Vidal2 and Ian Hope1. The Promoterome library containing 6500 Caenorhabditis elegans promoter fragments has previously been generated and used to construct promoter ::GFP fusions to allow determination of gene expression patterns in C. elegans. Optimization of the C. elegans micro-particle bombardment transformation technique, to give a medium through-put system, allowed the generation of expression patterns for over 300 C. elegans promoter::GFP fusions. Promoter fusion constructs of transcription factors genes and genes with homology to human genes with no assigned function were selected for the initial analysis and the results are shown. Initial analysis of the results highlights several significant differences between the two sets of genes. Promoters from C. elegans homologues of human genes with no known function were far more likely to yield either no GFP expression (35% vs. 6%) or ubiquitous GFP expression (23% vs. 8%) under the standard laboratory conditions utilized. In contrast, promoters from C. elegans transcription factor genes were far more likely to drive neuronal expression (62% vs.16%).. Full results are presented on the Hope Laboratory Expression Pattern database URL:http://bgypc059.leeds.ac.uk /~web

John Reece-Hoyes et al. (2006) European Worm Meeting "wTF2.0: A Fundamental First Step for Mapping the Caenorhabditis elegans Transcription Factor Localizome"

Jane Shingles, A.J. Marian Walhout, Denis Dupuy, Bart Deplancke, Ian Hope, John Reece-Hoyes, Marc Vidal, Christian Grove

[European Worm Meeting, 2006]

John Reece-Hoyes1, Bart Deplancke2, Jane Shingles1, Christian Grove2, Denis Dupuy3, A.J. Marian Walhout2, Marc Vidal3 and Ian Hope1. The Localization of Expression Mapping Project (LEMP) aims to use cloned C.elegans promoter fragments to generate a genome-wide set of expression patterns termed the Localizome. The Promoterome currently contains promoter fragments of up to 2kb from about 6,500 of the approximately 20,000 identified genes in the C.elegans genome. Using the Multisite Gateway system these promoter fragments are re-cloned upstream of GFP within an unc-119 rescue vector and the resulting constructs used to transform unc-119 mutant nematodes by a modified ballistic DNA transfer technique. The current focus of the LEMP is on C.elegans transcription factor genes with the view that these expression pattern data will be essential for mapping transcription regulatory networks. While C.elegans gene models have undergone continuous refinement, the extant lists of predicted C.elegans transcription factors (collectively referred to as wTF1.0) were in need of updating. We have identified a compendium of 934 transcription factor genes (referred to as wTF2.0) by interrogating Wormbase version 140 for proteins with appropriate Gene Ontology (GO) terms and then manually removed false positives (369) and added false negatives (373). The results of various bioinformatic analyses using wTF2.0 as well as how the list can be used to investigate regulatory networks will be discussed. We expect wTF2.0 to be a dynamic resource due to regular updating of the C.elegans genome annotation as well as changes in the functional annotations of protein domains. wTF2.0 will be accessible to the scientific community via an online interface where input is possible. wTF2.0 provides a starting point to decipher the transcription regulatory networks that control metazoan development and function.