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[
WormBook,
2006]
The completion of the C. elegans genome sequence permits the comprehensive examination of the expression and function of genes. Annotation of virtually every encoded gene in the genome allows systematic analysis of those genes using high-throughput assays, such as microarrays and RNAi. This chapter will center on the use of microarrays to comprehensively identify genes with enriched expression in the germ line during development. This knowledge provides a database for further studies that focus on gene function during germline development or early embryogenesis. Additionally, a comprehensive overview of germline gene expression can uncover striking biases in how genes expressed in the germ line are distributed in the genome, leading to new discoveries of global regulatory mechanisms in the germ line.
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[
Nat Genet,
2007]
In the nematode Caenorhabditis elegans, dosage compensation is mediated by a subtle twofold downregulation of both X chromosomes. A new study provides a significant advance in our understanding of how the X is targeted for dosage compensation and how this global regulation is integrated with regulation of the expression of each gene.
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Leng, J, Gerstein, Mark, Miller, III, David M, Reinke, Valerie, Robilotto, Rebecca, Slack, Frank J, Spencer, W Clay, Kato, Masaomi, Strasbourger, Pnina, Wang, Guilin, Green, Phil, High, Amber, MacCoss, Michael, Hillier, LaDeana, Thompson, Owen, Ratsch, Gunnar, Zeller, Georg, Ewing, Brent, Waterston, Robert H, Merrihew, Gennifer, Henz, S
[
International Worm Meeting,
2011]
As part of the modENCODE consortium, we are characterizing the C. elegans transcriptome using tiling arrays, RNA-seq, RT-PCR and mass spectrometry. Our earlier studies on whole animals of various stages and conditions and on specific cells and tissues led to a much improved set of protein coding genes covering greater than 95% of all genes including more than 12,413 trans-spliced leaders, 20,515 different trans-spliced transcript start sites, 28,199 polyA sites, 111,786 confirmed splice junctions, >7,000 inferred non-coding (nc) RNAs, and over 50 new miRNAs (1-5). More recently, we have (1) analyzed biological replicates with RNA-seq for different stages and conditions, validating the observed expression levels; (2) closed gaps in RNA-seq coverage of weakly expressed genes with RT-PCR; (3) characterized the RNA content of more finely staged embryos with RNA-seq; (4) tested methods that deplete rRNA to allow direct analysis by RNA-seq of ncRNAs and smaller samples, such as specific embryonic cells and tissues; (5) analyzed polyA+ RNA from selected stages of C. briggsae, C. remanei, C. brenneri and C. japonica; (6) analyzed miRNAs under additional stresses and conditions; and (7) characterized the proteins present in 12 size fractions from 16 different stages and conditions. All of the data are available through the modENCODE Data Coordinating Center and increasingly through WormBase. Our goal is to provide the community with a comprehensive description of the transcripts of the C. elegans genome, providing information about their specific utilization where possible. References 1. Hillier et al. Genome Research PMID: 19181841 2. Gerstein et al Science PMID: 21177976 3. Lu et al. Genome Reseaarch PMID: 21177971 4. Allen et al. Genome Research PMID: 21177958 5. Spencer et al. Genome Research PMID: 21177967.
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[
Curr Biol,
2008]
Gene regulation often plays by different rules in the germline compared to the soma. In Caenorhabditis elegans, the spatial and temporal expression of germline genes is controlled post-transcriptionally via the 3'' UTR rather than transcriptionally via the promoter.
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[
WormBook,
2013]
Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.
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[
Genetics,
2009]
Operons are found across multiple kingdoms and phyla, from prokaryotes to chordates. In the nematode Caenorhabditis elegans, the genome contains over 1000 operons that comprise roughly 15% of the protein-coding genes. However, determination of the force(s) promoting the origin and maintenance of operons in C. elegans has proved elusive. Compared to bacterial operons, genes within a C. elegans operon often show poor co-expression and only sometimes encode proteins with related functions. Using analysis of microarray and large-scale in situ hybridization data, we demonstrate that almost all operon-encoded genes are expressed in germline tissue. However, genes expressed during spermatogenesis are excluded from operons. Operons group together along chromosomes in local clusters that also contain monocistronic germline-expressed genes. Additionally, germline expression of genes in operons is largely independent of the molecular function of the encoded proteins. These analyses demonstrate that mechanisms governing germline gene expression influence operon origination and/or maintenance. Thus, gene expression in a specific tissue can have profound effects on the evolution of genome organization.
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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.
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[
Nat Genet,
2002]
Global changes in gene expression underlie developmental processes such as organogenesis, embryogenesis and aging in Caenorhabditis elegans. Recently developed methods allow gene expression profiles to be determined selectively for individual tissues and cell types. Results from both whole-animal and tissue-specific expression profiling have provided an unprecedented view into genome organization and gene function. Integration of these results with other types of functional genomics data gathered from RNA-mediated interference and yeast two-hybrid analyses will allow rapid identification and exploration of the complex functional gene networks that govern C. elegans development.