title: The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis.
abstract: Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Hench
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Henriksson
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Akram M
authors.initials: AM
authors.lastname: Abou-Zied
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Martin
authors.initials: M
authors.lastname: Lüppert
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Dethlefsen
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Krishanu
authors.initials: K
authors.lastname: Mukherjee
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Yong Guang
authors.initials: YG
authors.lastname: Tong
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Lois
authors.initials: L
authors.lastname: Tang
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden.
authors.forename: Umesh
authors.initials: U
authors.lastname: Gangishetti
authors.affiliation: Dept. of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
authors.forename: David L
authors.initials: DL
authors.lastname: Baillie
authors.affiliation: Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden; School of Life Sciences, Södertörns Högskola, Huddinge, Sweden.
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Bürglin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017173:Caenorhabditis elegans / Q000196:embryology / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000235:genetics* / Q000502:physiology; D047108:Embryonic Development / Q000235:genetics; D020869:Gene Expression Profiling; D005801:Genes, Homeobox; D008969:Molecular Sequence Data; D030781:Organisms, Genetically Modified / Q000196:embryology; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D009626:Terminology as Topic
chemical_list: D029742:Caenorhabditis elegans Proteins