consortium, modERN et al. (2015) International Worm Meeting "Comprehensive identification of worm and fly transcription factor binding sites."

Gerstein, M, White, KP, consortium, modERN, Celnicker, S, Reinke, V, Waterston, RH

[International Worm Meeting, 2015]

Studies of the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster have vastly increased our understanding of metazoan biology. Both organisms have provided test beds for genome sequencing strategies, and since the publication of their genome sequences at the turn of the century, efforts at understanding the information content of these key genomes have been at the forefront. As members of modENCODE, we established ChIP-seq pipelines and identified binding sites for about 100 transcription factors or chromatin modifiers in each organism. We have now combined efforts and work together as the modERN (model organism encyclopedia of regulatory networks) consortium. We have created a merged, more efficient pipeline to systematically and comprehensively identify binding sites for the remaining ~600 transcription factors (TFs) in each organism. Since the project began in Sept 2013, we have analyzed about 100 additional factors for each organism. We are also embarked on efforts to assign TF binding sites to regulated genes using RNA-seq to monitor gene expression changes in TF loss-of-function animals. We will map these results to a network framework to provide functional validation. In addition, we will perform targeted bioinformatic analyses to examine the association of binding sites between factors, their distribution in the genome, and how they are linked with changes in gene expression from the RNAi experiments. All strains are being deposited in the stock centers. All data are being incorporated in the ENCODE database (www.encodeproject.org) and will be made available through WormBase and FlyBase.

Mark Edgley et al. (2007) International Worm Meeting "At least a yeast genome's worth of KO's: report on the number of genes with mutations in C. elegans."

Don Moerman, Jeff Holmes, Gary Moulder, Mark Edgley, John Rummage, Others To Be Named, Bob Barstead, Stephane Flibotte, Jason Maydan

[International Worm Meeting, 2007]

The C. elegans Gene Knockout Consortium (http://www.celeganskoconsortium.omrf.org/) pursues systematic targeted gene disruption in the nematode, both upon request from the research community and in the larger context of the whole set of genes for which human orthologs exist (more than 7,000 genes). We are also now working on nematode specific genes. Previously our work was solely based on a reverse-genetics PCR method to generate single-gene deletions. More recently we have incorporated array Comparative Genome Hybridization (array-CGH) for efficient generation of deletion mutations (see abstract by Maydan et al). The combined strategies of directed and non-directed approaches are improving our throughput and broadening the types of mutations we can identify. All deletions isolated by the consortium are stabilized as homozygous or balanced heterozygous strains, deletion breakpoints are sequenced, and the strains and data are placed immediately into the public domain through our collaborators at the Caenorhabditis Genetics Center and WormBase. Distribution of Consortium strains accounts for a significant proportion of distributions from the CGC and has stood at 20% for the past two calendar years. To date the Consortium has generated deletions in more than 2,300 genes, and most of these have been stabilized and archived at the CGC. In addition, using CGH methodology we have identified over 700 genes missing in either the Hawaiian or Madeiran strains and consequently these genes will not be targeted for deletion by the consortium. Obtaining deletions in all genes in this nematode is the goal of the consortium and the general worm community. The combined efforts of the consortium, the Mitani lab and individuals within the worm community are moving us closer to this goal - analysis of 7205 mutations yields a very conservative estimate of about 5,000 genes with associated deletions. To put this in perspective the nematode community has now matched the yeast community whole genome effort of 5,500 KO''s.

Mark Edgley et al. (2008) European Worm Meeting "The C. elegans Gene Knockout Consortium"

John Rummage, Jeff Holmes, Jason Maydan, Bob Barstead,, Gary Moulder, Stephane Flibotte, Mark Edgley, Don Moerman

[European Worm Meeting, 2008]

The C. elegans Gene Knockout Consortium. (http://www.celeganskoconsortium.omrf.org/ ) pursues systematic targeted. gene disruption in the nematode, both upon request from the research. community and in the larger context of the whole set of genes for which. human orthologs exist (more than 7,000 genes). We have expanded our target. set to include nematode specific genes. Most of our work has been based on. PCR detection of single-gene deletions after random mutagenesis. More. recently we have incorporated array Comparative Genome Hybridization (array-. CGH) for efficient generation of deletion mutations. The combined strategy. of directed and non-directed approaches are improving our throughput and. broadening the types of mutations we can identify.. All deletions isolated by the consortium are stabilized as homozygous. or balanced heterozygous strains, deletion breakpoints are sequenced, and. the strains and data are placed immediately into the public domain through. our collaborators at the Caenorhabditis Genetics Center and WormBase.. Distribution of Consortium strains accounts for a significant proportion of. distributions from the CGC and has stood at 20% for the past two calendar. years. To date the Consortium has generated deletions in more than 2,600. genes, and most of these have been stabilized and archived at the CGC. In. addition, using CGH methodology we have identified nearly 800 genes missing. in either the Hawaiian or Madeiran strains. Since these genes are not. required by the N2 strain, they will not be targeted for deletion by the. consortium.. Obtaining deletions in all genes in this nematode is the goal of the. consortium and the general worm community. The combined efforts of the. consortium, the Mitani lab and individuals within the worm community are. moving us closer to this goal, with the result that approximately one. quarter of the C. elegans genome is represented among the aggregate set of. knockout mutations.. Do not add objects such as pictures, boxes, headers, footers, footnotes,. etc.

Schierenberg E (1995) International C. elegans Meeting "A SEVENTEEN YEARS OLD WORM.."

Schierenberg E

[International C. elegans Meeting, 1995]

... Meeting appears to be a good occasion to look back to the early days of the C. elegans research, when the bald and bearded bandmasters of today were handsome, slender lads, when the modern matrons of mutants were rosy and shy maidens. Some so far undisclosed photo documents of the First International C. elegans Meeting 1977 in Woods Hole have been rediscovered under mysterious circumstances and will be proudly presented to the general public for the first (and last) time.

Cain, S. et al. (2019) International Worm Meeting "Genome Browsing at WormBase."

Gao, S., Grove, C., Nuin, P., Stein, L., Harris, T., Wright, A., Cain, S.

[International Worm Meeting, 2019]

Here we present recent updates to the genome browser at WormBase, JBrowse. Since it's introduction three years ago, JBrowse's presence in WormBase has grown, as has its functionality. JBrowse updates include the addition of new datasets, display improvements and increased functionality. Dataset changes include the addition of common and rare predicted introns from RNAseq data as well as the ability to add modERN and other public datasets. Visualization changes include improvements to how modENCODE tracks are displayed as well as the addition of new and improved glyphs throughout the app.

Reinke, V et al. (2017) International Worm Meeting "Model organism Encyclopedia of Regulatory Networks (modERN)."

Xu, J, Celniker, SE, Weiszmann, R, White, KP, Gewirtzman, L, Ma, L, Vafeados, D, Gerstein, M, Samanta, S, Fisher, WW, Yan, KK, Reinke, V, Patton, J, Victorsen, A, Hammonds, AS, Higdon, A, Han, M, Waterston, RH, Kudron, M

[International Worm Meeting, 2017]

The goal of the modERN consortium is to create comprehensive maps of transcription factor (TF) binding sites in C. elegans and D. melanogaster. We have developed an effective high throughput pipeline to create strains of flies and worms with GFP-tagged TFs, which we use to perform ChIP-seq experiments. We are targeting 691 sequence-specific TF genes in the worm and 708 TF genes in the fly. The modERN project has generated 420 worm strains and 330 fly strains to date. A subset of worm strains had tagged TFs that localized to the cytoplasm (54), were poorly expressed (23), or did not pass quality control measures for ChIP (37). Thus, including data generated previously for the modENCODE project, we have completed ~900 ChIP-seq experiments for 235 factors (219 TFs and 16 other regulatory proteins) in the worm and 287 TFs in the fly. We processed all data sets with a uniform peak-calling pipeline for worm and fly. The resultant inferred binding sites can be useful to predict gene expression, particularly using combinations of TF binding profiles. In the worm, for example, combinatorial TF binding patterns can suggest expression in muscle, intestine, hypodermis, pharynx and neurons. For a limited number of transcription factors, we are conducting RNA-seq of strains with knock down of specific transcription factors by deletion or RNAi to identify potential target genes of the given TF and to validate targets identified by the ChIP-seq experiments. To date, we have collected RNA-seq data from 30 worm TF knockdown lines and 12 TF fly knock down lines. RNA-seq data and ChIP-seq data are deposited to the ENCODE DCC for access by the research community through the ENCODE DCC (https://www.encodeproject.org), as well as through the UCSC genome browser. A dedicated track hub for the worm data at UCSC is available as well. TF tagged lines are available through the Caenorhabditis Genetics Center and Bloomington Drosophila Stock Center. Here, we will summarize progress, present future plans, and demonstrate how to access and use the data.

Gary L Moulder et al. (2003) International Worm Meeting "Methods for High-Throughput Production of Deletion Mutants"

Jeff Holmes, Gary L Moulder, Robert Barstead, Beth Rogers

[International Worm Meeting, 2003]

In collaboration with our colleagues at the University of British Columbia, we have undertaken the development of a high-throughput platform for the targeted production of C. elegans deletion mutants. This has given rise to the C. elegans Gene Knockout Consortium. The Consortium operates under a generally agreed standard. Nevertheless, each of the consortium groups maintains an independent production line using management and production strategies that are unique to the group. With the goal to scale up production at the Oklahoma Medical Research Foundation, we have undertaken a thorough review of our particular internal methods. As a result, we have made a large number of seemingly simple modifications to our production line that, added up, have greatly improved the consistency and quality of our operation. These modifications touch on every aspect of the production line and, in part, involve improvements in existing technology so that the methods better fit a high-throughput operation. A partial list of the areas of our operation that have received special attention includes the following: acquisition of a bacterial food source to feed the worm cultures, DNA production, worm culture in microtitre wells, PCR quality, sib selection, assessment of homozygosity, communications with our colleagues at UBC, computer data basing and data sharing with the worm community. Here we describe in detail our latest protocols and operating procedures.

Kelly Kraus et al. (2004) East Coast Worm Meeting "Attempts to develop molecular genetic tools to study parasitic nematodes"

Meera Sundaram, Kelly Kraus

[East Coast Worm Meeting, 2004]

Parasitic nematodes have a tremendous negative impact on human and animal health. Modern molecular genetic tools for studying the biology of these parasites are currently lacking. We are collaborating with several parasitic helminthologists to try to develop transgenic, RNAi and/or morpholino-based approaches to study gene function in these parasites. So far our efforts have focused on the parasitic nematode Strongyloides stercoralis. These nematodes can survive for one generation outside of the host animal, and we can manipulate this free-living generation in ways similar to C. elegans. We are experimenting with DNA microinjections and bombardment with various GFP reporter transgenes, as well as testing morpholinos, and will report on our progress at the meeting.

Marra MA et al. (1995) International C. elegans Meeting "AN UPDATE FROM THE C. ELEGANS GENOME SEQUENCING CONSORTIUM"

Consortium TCeGS, Marra MA

[International C. elegans Meeting, 1995]

We present here an update on our efforts to obtain the complete nucleotide sequence of the worm genome. Following an initial pilot phase sequencing project of a 2.2 Mb region on chromosome III, the Consortium labs in both Cambridge and St. Louis have scaled up their respective operations with the goal of obtaining the sequence of the genome by 1998. Progress toward this goal has been substantial. The Consortium has concentrated its efforts on those genomic regions that are richest in physical map resources and genes. Sequences have been obtained from 455 cosmids, resulting in 14 Mb of finished sequence, primarily from the central regions of chromosomes II, III and X. Analysis of the sequence data by the program GENEFINDER and other tools has shown that predicted genes occur at an average density of one per five kb. Approximately 40% of these predicted genes show significant similarity to other sequences in the public domain databases.

Bhagwati P Gupta et al. (2002) West Coast Worm Meeting "Genetic analysis of the vulval mutants in C. briggsae"

Shahla Gharib, Bhagwati P Gupta, Paul W Sternberg, Jennifer X Li

[West Coast Worm Meeting, 2002]

To understand the evolution of developmental mechanisms, we are doing a comparative analysis of vulval patterning in C. elegans and C. briggsae. C. briggsae is closely related to C. elegans and has identical looking vulval morphology. However, recent studies have indicated subtle differences in the underlying mechanisms of development. The recent completion of C. briggsae genome sequence by the C. elegans Sequencing Consortium is extremely valuable in identifying the conserved genes between C. elegans and C. briggsae.