TITLE

Comprehensive analysis of gene expression patterns of hedgehog-related genes

AUTHOR(S)
Hao, Limin; Johnsen, Robert; Lauter, Gilbert; Baillie, David; Burglin, Thomas R
PUB. DATE
January 2006
SOURCE
BMC Genomics;2006, Vol. 7, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: The Caenorhabditis elegans genome encodes ten proteins that share sequence similarity with the Hedgehog signaling molecule through their C-terminal autoprocessing Hint/Hog domain. These proteins contain novel N-terminal domains, and C. elegans encodes dozens of additional proteins containing only these N-terminal domains. These gene families are called warthog, groundhog, ground-like and quahog, collectively called hedgehog (hh)-related genes. Previously, the expression pattern of seventeen genes was examined, which showed that they are primarily expressed in the ectoderm. Results: With the completion of the C. elegans genome sequence in November 2002, we reexamined and identified 61 hh-related ORFs. Further, we identified 49 hh-related ORFs in C. briggsae. ORF analysis revealed that 30% of the genes still had errors in their predictions and we improved these predictions here. We performed a comprehensive expression analysis using GFP fusions of the putative intergenic regulatory sequence with one or two transgenic lines for most genes. The hh-related genes are expressed in one or a few of the following tissues: hypodermis, seam cells, excretory duct and pore cells, vulval epithelial cells, rectal epithelial cells, pharyngeal muscle or marginal cells, arcade cells, support cells of sensory organs, and neuronal cells. Using time-lapse recordings, we discovered that some hh-related genes are expressed in a cyclical fashion in phase with molting during larval development. We also generated several translational GFP fusions, but they did not show any subcellular localization. In addition, we also studied the expression patterns of two genes with similarity to Drosophila frizzled, T23D8.1 and F27E11.3A, and the ortholog of the Drosophila gene dally-like, gpn-1, which is a heparan sulfate proteoglycan. The two frizzled homologs are expressed in a few neurons in the head, and gpn-1 is expressed in the pharynx. Finally, we compare the efficacy of our GFP expression effort with EST, OST and SAGE data. Conclusion: No bona-fide Hh signaling pathway is present in C. elegans. Given that the hh-related gene products have a predicted signal peptide for secretion, it is possible that they constitute components of the extracellular matrix (ECM). They might be associated with the cuticle or be present in soluble form in the body cavity. They might interact with the Patched or the Patched-related proteins in a manner similar to the interaction of Hedgehog with its receptor Patched.
ACCESSION #
28858726

 

Related Articles

  • Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Kamath, Ravi S.; Fraser, Andrew G.; Dong, Yan; Poulin, Gino; Durbin, Richard; Gotta, Monica; Kanapin, Alexander; Le Bot, Nathalie; Moreno, Sergio; Sohrmann, Marc; Welchman, David P.; Zipperlen, Peder; Ahringer, Julie // Nature;1/16/2003, Vol. 421 Issue 6920, p231 

    A principal challenge currently facing biologists is how to connect the complete DNA sequence of an organism to its development and behaviour. Large-scale targeted-deletions have been successful in defining gene functions in the single-celled yeast Saccharomyces cerevisiae, but comparable...

  • Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16. Yu, Ron X.; Jie Liu; True, Nick; Wei Wang // PLoS ONE;2008, Vol. 3 Issue 3, p1 

    A major challenge in the post-genome era is to reconstruct regulatory networks from the biological knowledge accumulated up to date. The development of tools for identifying direct target genes of transcription factors (TFs) is critical to this endeavor. Given a set of microarray experiments, a...

  • Macoilin, a Conserved Nervous System-Specific ER Membrane Protein That Regulates Neuronal Excitability. Arellano-Carbajal, Fausto; Briseño-Roa, Luis; Couto, Africa; Cheung, Benny H. H.; Labouesse, Michel; de Bono, Mario // PLoS Genetics;Mar2011, Vol. 7 Issue 3, preceding p1 

    No abstract available.

  • Generation of an external guide sequence library for a reverse genetic screen in Caenorhabditis elegans. Qitao Yan; Rui Zhao; Wenlin Zheng; Changxin Yin; Bao Zhang; Wenli Ma // BMC Biotechnology;2009, Vol. 9, Special section p1 

    Background: A method for inhibiting the expression of particular genes using external guide sequences (EGSs) has been developed in bacteria, mammalian cells and maize cells. Results: To examine whether EGS technology can be used to down-regulate gene expression in Caenorhabditis elegans (C....

  • High-Throughput In Vivo Analysis of Gene Expression in Caenorhabditis elegans. Hunt-Newbury, Rebecca; Viveiros, Ryan; Johnsen, Robert; Mah, Allan; Anastas, Dina; Fang, Lily; Halfnight, Erin; Lee, David; Lin, John; Lorch, Adam; McKay, Sheldon; Okada, H. Mark; Jie Pan; Schulz, Ana K.; Tu, Domena; Wong, Kim; Zhao, Z.; Alexeyenko, Andrey; Burglin, Thomas; Sonnhammer, Eric // PLoS Biology;Sep2007, Vol. 5 Issue 9, pe237 

    Using DNA sequences 5' to open reading frames, the authors construct green fluorescent protein fusions and generate spatial and temporal tissue expression profiles for 10% of all genes in the nematode Caenorhabditis elegans.

  • Caenorhabditis elegans Operons Contain a Higher Proportion of Genes with Multiple Transcripts and Use 3' Splice Sites Differentially. Fei Wang; Shi Huang; Long Ma // PLoS ONE;2010, Vol. 5 Issue 8, p1 

    RNA splicing generates multiple transcript isoforms from a single gene and enhances the complexity of eukaryotic gene expression. In some eukaryotes, operon exists as an ancient regulatory mechanism of gene expression that requires strict positional and regulatory relationships among its genes....

  • Caenorhabditis elegans: An Old Genetic Model Can Learn New Epigenetic Tricks. Padilla, Pamela A.; Garcia, Anastacia M.; Ladage, Mary L.; Toni, Lee S. // Integrative & Comparative Biology;Jul2014, Vol. 54 Issue 1, p52 

    Gamete cells pass on information to the next generation via DNA sequence and also through epigenetic mechanisms such as small RNAs, DNA methylation, or chromatin modifications. Caenorhabditis elegans is a genetic model system that an enormous number of talented researchers have used to...

  • A Functional Nuclear Localization Sequence in the C. elegans TRPV Channel OCR-2. Ezak, Meredith J.; Ferkey, Denise M. // PLoS ONE;2011, Vol. 6 Issue 9, p1 

    The ability to modulate gene expression in response to sensory experience is critical to the normal development and function of the nervous system. Calcium is a key activator of the signal transduction cascades that mediate the process of translating a cellular stimulus into transcriptional...

  • Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element. Barrière, Antoine; Gordon, Kacy L.; Ruvinsky, Ilya // PLoS Genetics;Jun2011, Vol. 7 Issue 6, Special section p1 

    Different functional constraints contribute to different evolutionary rates across genomes. To understand why some sequences evolve faster than others in a single cis-regulatory locus, we investigated function and evolutionary dynamics of the promoter of the Caenorhabditis elegans unc-47 gene....

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics