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Identification of DVA Interneuron Regulatory Sequences in Caenorhabditis elegans

Robinson, Carmie Puckett and Schwarz, Erich M. and Sternberg, Paul W. (2013) Identification of DVA Interneuron Regulatory Sequences in Caenorhabditis elegans. PLoS ONE, 8 (1). Art. No. e54971. ISSN 1932-6203. PMCID PMC3557239. doi:10.1371/journal.pone.0054971. https://resolver.caltech.edu/CaltechAUTHORS:20130325-134216106

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Abstract

Background: The identity of each neuron is determined by the expression of a distinct group of genes comprising its terminal gene battery. The regulatory sequences that control the expression of such terminal gene batteries in individual neurons is largely unknown. The existence of a complete genome sequence for C. elegans and draft genomes of other nematodes let us use comparative genomics to identify regulatory sequences directing expression in the DVA interneuron. Methodology/Principal Findings: Using phylogenetic comparisons of multiple Caenorhabditis species, we identified conserved non-coding sequences in 3 of 10 genes (fax-1, nmr-1, and twk-16) that direct expression of reporter transgenes in DVA and other neurons. The conserved region and flanking sequences in an 85-bp intronic region of the twk-16 gene directs highly restricted expression in DVA. Mutagenesis of this 85 bp region shows that it has at least four regions. The central 53 bp region contains a 29 bp region that represses expression and a 24 bp region that drives broad neuronal expression. Two short flanking regions restrict expression of the twk-16 gene to DVA. A shared GA-rich motif was identified in three of these genes but had opposite effects on expression when mutated in the nmr-1 and twk-16 DVA regulatory elements. Conclusions/Significance: We identified by multi-species conservation regulatory regions within three genes that direct expression in the DVA neuron. We identified four contiguous regions of sequence of the twk-16 gene enhancer with positive and negative effects on expression, which combined to restrict expression to the DVA neuron. For this neuron a single binding site may thus not achieve sufficient specificity for cell specific expression. One of the positive elements, an 8-bp sequence required for expression was identified in silico by sequence comparisons of seven nematode species, demonstrating the potential resolution of expanded multi-species phylogenetic comparisons.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.pone.0054971DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557239/PubMed CentralArticle
ORCID:
AuthorORCID
Schwarz, Erich M.0000-0003-3151-4381
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:© 2013 Puckett Robinson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received August 12, 2010; Accepted December 21, 2012; Published January 28, 2013. Funding: Howard Hughes Medical Institute, with which PWS is an investigator; National Institutes of Health GM084389 (to PWS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank L. Ryan Baugh for his constructs and methods of PCR fusion and ballistics; Steven Kuntz for help with MUSSA; Cheryl Van Buskirk for identification of RID; Jagan Srinivasan, Amir Sapir, Adler Dillman and Christopher Cronin for technical help with illustration; and anonymous reviewers for comments. We thank L. Salkoff for the twk-16 construct A3 (pRxn4) for WT2000, and Bruce Wightman for the MU1147 line expressing fax-1::GFP. Author Contributions: Conceived and designed the experiments: CPR PWS. Performed the experiments: CPR. Analyzed the data: CPR EMS. Wrote the paper: CPR EMS PWS. Conceived and designed the experiments: CPR, EMS, PWS. Performed the experiments: CPR. Analyzed the data: CPR, EMS, PWS. Contributed reagents/materials/analysis tools: EMS. Wrote the paper: CPR, EMS, PWS.
Funders:
Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
NIHGM084389
Issue or Number:1
PubMed Central ID:PMC3557239
DOI:10.1371/journal.pone.0054971
Record Number:CaltechAUTHORS:20130325-134216106
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20130325-134216106
Official Citation:Puckett Robinson C, Schwarz EM, Sternberg PW (2013) Identification of DVA Interneuron Regulatory Sequences in Caenorhabditis elegans. PLoS ONE 8(1): e54971. doi:10.1371/journal.pone.0054971
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:37611
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:15 May 2013 19:55
Last Modified:09 Nov 2021 23:30

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