clusters of functionally related loci and genes [89]. At this stage we are also unable to discern whether there is a single or multiple QTLs within Qrr1d. While it is likely that a single QTL modulates the expression of the ARS, there may be additional gene variants in Qrr1d that modulate other transcripts involved in translation and RNA metabolism. With increased resolving power it may be possible to further subdivide transcripts that map to Qrr1p and Qrr1d into smaller functional modules. There may be multiple loci in Qrr1 that modulate different stages of protein metabolism in the CNS. Maintenance of cellular protein homeostasis requires finely tuned cross talk between transcription and RNA processing, the translation machinery, and protein degradation [90–92], gene functions highly overrepresent- ed among the transcripts that map to Qrr1. While these are generic cellular processes, there are unique demands on protein metabolism in the nervous system. Neurons are highly polarized cells and specialized mechanisms are in place to manage local protein synthesis and degradation in dendrites and axons [93]. The nervous system is also particularly sensitive to imbalances in protein homeostasis [94,95], a possible reason why the trans-effects of Qrr1 are detected only in neural tissues. Candidates in Qrr1d and Possible Links with Local Protein Synthesis Transfer RNAs are direct biological partners of the ARS, and the cluster of tRNAs in the highly polymorphic intergenic region of Qrr1d (figure 6) is an enticing candidate. In addition to their role in shuttling amino acids, tRNAs also act as sensors of cellular amino acid levels and regulate transcription of genes involved in amino acid metabolism and the ARS [66]. There is tissue specificity in the expression of different tRNA isoforms [96], and we speculate that the tRNA cluster in Qrr1d is specifically functional in neural tissues. Rgs7, a member of the RGS (regulator of G-protein signaling) family, is another high-ranking candidate in Qrr1d. RGS proteins are important regulators of G-protein mediated signal transduction. Rgs7 is predominantly expressed in the brain and has been implicated in regulation of neuronal excitability and synaptic transmission [97,98]. Although RGS proteins are usually localized in the plasma membrane, RGS7 has been found to shuttle between the membrane and the nucleus [99]. This implies a role for RGS7 in gene expression regulation in response to external stimuli. Our final high-ranking candidate in Qrr1d is Fmn2. It codes for an actin binding protein exclusively expressed in the CNS and oocytes, and is involved in the establishment of cell polarity [70,71]. In Drosophila, the formin homolog, cappuccino, has a role in RNA transport and in localizing the staufen protein to oocyte poles [100–102]. It is possible that FMN2 has parallel functions in mammalian neurons. Interestingly, Staufen 2 (Stau2), a gene involved in RNA transport to dendrites [62], maps to Qrr1d in BXD CNS datasets. Furthermore, deletion of formin homologs in yeast results in inhibition of protein translation [103], compelling evidence for an interaction between the protein translation system and formins. Evidence for a role for Fmn2 in dendrites also comes from our immunocytochemical analysis that clearly demonstrates the expression of FMN2 protein in dendrites. Taken together, Fmn2 is a functionally relevant candidate gene in Qrr1d and may be related to RNA transport and protein synthesis in the CNS. Methods Microarray Datasets The microarray datasets used in this study (table 2) were generated by collaborative efforts [46,47,49–52]. All datasets can QTL Hotspot on Mouse Distal Chromosome 1 be accessed from www.genenetwork.org. They provide estimates of global mRNA abundance in neural and non-neural tissues in the BXD, LXS, and CXB RI strains, B6D2F2 intercrosses, and B6C3HF2 intercrosses. Detailed description of each set, tissue acquisition, RNA extraction and array hybridization methods, and data processing and normalization methods are provided in the ‘‘Info’’ page linked to each dataset. In brief, the datasets are: 1) 2) 3) 4) 5) BXD CNS transcriptomes: The BXD CNS datasets measure gene expression in the forebrain and midbrain (INIA Forebrain), striatum (HBP/Rosen Striatum and HQF Striatum), hippocampus (Hippocampus Consortium and UMUTAffy Hippocampus), cerebellum (SJUT Cerebellum mRNA), and eye (Hamilton Eye) of BXD RI strains (table 2). The INIA Brain and HBP/Rosen Striatum datasets have been described in Peirce et al. [47]. The Hippocampus Consortium dataset measures gene expression in the adult hippocampus of 69 BXD RI strains, the parental B6 and D2 strains, and F1 hybrids. The SJUT Cerebellum dataset measures gene expression in the adult cerebellum of 45 BXD RI strains, parental strains, and F1 hybrids. The Eye dataset measures gene expression in the eyes of 64 BXD RI strains, parental strains, and F1 hybrids. The HQF BXD Striatum is one of the newest datasets and was generated on Illumina Sentrix Mouse–6.1 arrays. It is similar to the HBP/ Rosen Striatum and measures gene expression in the striatum of 54 BXD RI strains, parental strains, and F1 hybrids. BXD non-neural transcriptomes: The non-neural BXD array sets measure gene expression in the liver (UNC Liver) of 40 BXD strains, kidney (Kidney Consortium) of 53 BXD strains, and hematopoietic stem cells (GNF Hematopoietic Cells) of 30 BXD strains [49,50]. LXS hippocampus transcriptome: The LXS Hippocampus dataset measures gene expression in the adult hippocampus of 75 LXS RI strains and the parental ILS and ISS strains. B6D2F2 CNS transcriptomes: The B6D2F2 datasets measure gene expression in the whole brain (OHSU/VA Brain), and striatum (OHSU/VA Striatum) of B66D2 F2 intercrosses [47,52]. The whole brain dataset comprises of samples from 56 F2 animals, and the striatum dataset comprises of samples from 58 F2 animals. B6C3HF2 transcriptomes: These datasets were generated from large numbers of B66C3H F2 intercross progeny and assayed using Agilent arrays [51]. These datasets have been described in Yang et al [51]. Mouse Strains and Genotype Data The conventional BXD RI strains were derived from the B6 and D2 inbred mice [104,105]. The newer sets of advanced RI strains were derived by inbreeding intercrosses of the RI strains [57]. The parental B6 and D2 strains differ significantly in sequence and have approximately 2 million informative SNP. A subset of 14,000 SNPs and microsatellite markers have been used to genotype the BXD strains [106,107]. We used 3,795 informative markers for QTL mapping. Thirty such informative markers are in Qrr1 and we queried these markers to identify strains with recombinations in Qrr1; genes with strong cis-QTLs (Sdhc, Atp1a2, Dfy, and Fmn2) were used as additional markers. Smaller sub-sets of markers were used to genotype the two F2 panels (total of 306 markers for the whole brain, and 75 markers for the striatum F2 datasets). PLoS Genetics | www.plosgenetics.org 13 November 2008 | Volume 4 | Issue 11 | e1000260