<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <HTML><HEAD><TITLE>UAB Whole body D.m. mRNA Lead control (Oct09) RMA</TITLE> <META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> <LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> <LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> <link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" /> <SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> <SCRIPT SRC="/javascript/dhtml.js"></SCRIPT> <script src="/javascript/tabbed_pages.js" type="text/javascript"></script> </HEAD> <BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff > <TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> <TBODY> <TR> <script language="JavaScript" src="/javascript/header.js"></script> </TR> <TR> <TD bgColor=#eeeeee class="solidBorder"> <Table width= "100%" cellSpacing=0 cellPadding=5> <TR> <!-- split from Here --> <!-- Body Start from Here --> <P class="title">UAB Whole body D.m. mRNA Lead control (Oct09) RMA (accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=249">GN249</A>) <A HREF="/webqtl/main.py?FormID=editHtml"> <img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> <blockquote> <p class="subtitle">Summary:</p> <p>The genetics of gene expression in recombinant inbred lines (RILs) can be mapped as expression quantitative trait loci (eQTLs). So-called ‘‘genetical genomics’’ studies have identified locally acting eQTLs (cis-eQTLs) for genes that show differences in steady-state RNA levels. These studies have also identified distantly acting master-modulatory trans-eQTLs that regulate tens or hundreds of transcripts (hotspots or transbands). We expand on these studies by performing genetical genomics experiments in two environments in order to identify trans-eQTL thatmight be regulated by developmental exposure to the neurotoxin lead. Flies from each of 75 RIL were raised from eggs to adults on either control food (made with 250 mM sodium acetate), or lead-treated food (made with 250 mM lead acetate, PbAc). RNA expression analyses of whole adult male flies (5–10 days old) were performed with Affymetrix DrosII whole genome arrays (18,952 probesets). Among the 1389 genes with cis-eQTL, there were 405 genes unique to control flies and 544 genes unique to lead-treated ones (440 genes had the same cis-eQTLs in both samples). There are 2396 genes with trans-eQTL which mapped to 12major transbands with greater than 95 genes. Permutation analyses of the strain labels but not the expression data suggests that the total number of eQTL and the number of transbands are more important criteria for validation than the size of the transband. Two transbands, one located on the 2nd chromosome and one on the 3rd chromosome, co-regulate 33 lead-induced genes, many of which are involved in neurodevelopmental processes. For these 33 genes, rather than allelic variation at one locus exerting differential effects in two environments, we found that variation at two different loci are required for optimal effects on leadinduced expression.</p> <p class="subtitle">Materials and Methods:</p> <p>The 75 Drosophila roo lines were obtained from Trudy Mackay. To avoid batch effects (Zakharkin et al., 2005), the growth of the flies, the RNA extraction and the order of running the arrays, and the fluidics well used for each array was completely randomized for the 75 lines in two treatments. Control food consisted of standard cornmeal, agar, sugar, yeast, and 250 mM NaAc (Ashburner, 1989). Lead-contaminated food consisted of standard food plus 250 mM PbAc (lead exposure at this concentration has been shown to affect locomotion in adults; Hirsch et al., 2003). Flies from each of the 75 roo lines (20 males and 20 females) were placed in a vial with 10 ml of food (control or PbAc) for 3 days at 25 8C and allowed to lay eggs; the adults were subsequently discarded. Newly enclosed adult males were placed on the same medium (control or PbAc) as had been present during pre-adult development for 5–10 days before being used as subjects. Male progeny were pooled from each vial (65 males per vial) and frozen at 80 8C. RNA samples were extracted in groups of 24 and arrays hybridization run in groups of 4 with 3 groups run per day. Effects of RNA extraction and array hybridizations day were examined by ANOVA and Support Vector approaches and no obvious day effects were observed.</p> <p class="subtitle">Data Source Acknowledgements:</p> <p> <p>This work was supported by the Environmental Health Sciences Center in Molecular and Cellular Toxicology with Human Applications Grant P30 ES06639 at Wayne State University, NIH R01 grants ES012933 and CA105349 to D.M.R., DK071073 to X.L., and UAB-CNGI grant to M.D.G. We thank H. Ghiradella for critical comments on the manuscript. The microarray data is freely available to the public, in the MIAME format in 150 CEL files, in the GEO database under GSE 11695.<p>Please cite this article in press as: Ruden DM, et al. Genetical toxicogenomics in Drosophila identifies master-modulatory loci that are regulated by developmental exposure to lead, Neurotoxicology (2009), doi:10.1016/j.neuro.2009.08.011<p><a href="http://www.genenetwork.org/dbdoc/Neurotox_2009_eQTL.pdf">Full Article</a></p> </blockquote> </TR></TABLE> </TD> </TR> <TR> <TD align=center bgColor=#ddddff class="solidBorder"> <!--Start of footer--> <TABLE width="90%"> <script language='JavaScript' src='/javascript/footer.js'></script> <TR> <TD colspan=3 class="fs12"> <UL> </UL> </TD> </TR> </TABLE> <!--End of footer--> </TD> </TR> </TABLE> <!-- /Footer --> <!-- menu script itself. you should not modify this file --> <script language="JavaScript" src="/javascript/menu_new.js"></script> <!-- items structure. menu hierarchy and links are stored there --> <script language="JavaScript" src="/javascript/menu_items.js"></script> <!-- files with geometry and styles structures --> <script language="JavaScript" src="/javascript/menu_tpl.js"></script> <script language="JavaScript"> <!--// // Note where menu initialization block is located in HTML document. // Don't try to position menu locating menu initialization block in // some table cell or other HTML element. 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