Figure 3. QTL mapping precision in Qrr1. Mapping precision was empirically determined by measuring the distance between a cis-QTL peak and location of parent gene. Cis-QTLs in BXD Hippocampus Consortium, UMUTAffy Hippocampus, and Hamilton Eye datasets were used for this purpose. Mean gene-to-QTL peak distance (y-axis) was plotted as a function of LOD score (LOD score range on x-axis). Number of probe sets in each LOD range is shown. Mapping precision increases with increase in LOD score. The mean offset for cis-QTLs with LOD scores 3–4 (genome-wide adjusted p-value of 0.1–0.01) is 900 kb, and the offset decreases to 650 kb at 4–5 LOD scores (p-value of 0.01– 0.001). Cis-QTLs with LOD scores greater than 11 (p-value,1026) have mean offset of only 450 kb. doi:10.1371/journal.pgen.1000260.g003 p = 0.001), and structural constituents of ribosomes (p = 0.003). Transcripts modulated by Qrr1d are highly enriched in genes involved in RNA metabolism (p = 461027), tRNA aminoacylation (p = 161025) and translation (p = 261025), RNA transport (p = 0.003), cell cycle (p = 0.004), and ubiquitin mediated protein catabolism (p = 0.006). Other GO categories show enrichment in both Qrr1p and Qrr1d. For example, genes involved in RNA metabolism and ubiquitin-mediated protein catabolism are also overrepresented among the transcripts modulated by Qrr1p (p = 0.002 for RNA metabolism and p = 0.005 for ubiquitin- protein ligases). This may either be due to limitations in QTL resolution, or due to multiple loci in Qrr1p and Qrr1d controlling these subsets of transcripts. An Aminoacyl-tRNA Synthetase trans-QTL in Distal Qrr1 A remarkable number of transcripts of the ARS gene family map to Qrr1. A total of 16 ARS transcripts have trans-QTLs at a minimum LOD score of 3 in one or multiple BXD, B6D2F2, and B6C3H CNS datasets (table 5). In almost all cases, QTLs peak on markers on the distal part of Qrr1. Except for Hars, the B allele in Qrr1 consistently increases expression by 10% to 30%. In the case of Hars, the D allele has the positive additive effect and increases expression by about 10%. We examined all probes or probe sets that target ARS and ARS-like genes in the B66D2 CNS datasets. The Affymetrix platform measures the expression of 34 ARS and ARS-like genes; 24 of these map to Qrr1 at LOD scores ranging from a low of 2 to a high of 12. Even in the case of the suggestive trans-QTLs (i.e., QTL Hotspot on Mouse Distal Chromosome 1 LOD values between 2 and 3), the B allele in Qrr1 has the positive effect on expression. The ARS family is also highly represented among trans-QTLs in the B6C3HF2 brain dataset. Thirty-seven probes in this dataset target the tRNA synthetases, eleven of these have trans-QTLs in Qrr1d (LOD scores ranging from 2 to 20), and almost all have a B positive additive effect (exceptions are Hars and Qars). The co-localization of trans-QTLs to Qrr1d, the general consensus in parental allele effect, and their common biological function indicate that there is a single QTL in the distal part of Qrr1 modulating the expression of the ARS. It is crucial to note that this genetic modulation is only detected in CNS tissues. In the LXS hippocampus dataset, Qrr1 has only a limited trans- effect on gene expression. Despite the weak effect, expression of Dars2 (probe ID ILM580427) maps to the distal part of Qrr1 at a LOD of 3. Although this is only a weak detection of the ARS QTL in the LXS dataset, it nonetheless demonstrates the strong regulatory effect of Qrr1 on the expression of this gene family. In the case of the CXB hippocampus dataset, not a single trans-QTL for the ARS is detected in Qrr1. trans-QTLs for Transcripts Localized in Neuronal Processes In addition to the high overrepresentation of transcripts involved in translation and RNA metabolism, several transcripts known to be transported to neuronal processes or involved in RNA transport also map to Qrr1d, including Camk2a, Bdnf, Cdc42, Eif4e, Eif4g2, Hnrpab, Ppp1cc, Pabpc1, Eif5, Kpnb1, Rhoip3, Stau2, and Pum2 [60–63]. An interesting example is provided by the brain derived neurotrophic factor (Bdnf). Two alternative forms of Bdnf mRNA are known—one isoform has a long 39 UTR and is specifically transported into the dendrites; the other isoform has a short 39 UTR and remains primarily in the somatic cytosol [64]. The Affymetrix M430 arrays contain two different probe sets that target these Bdnf isoforms. Probe set 1422169_a_at targets the distal 39 UTR and is essentially specific for the dendritic isoform, and probe set 1422168_a_at targets a coding sequence common to both isoforms. Although both probe sets detect high expression signal in the hippocampus, only the dendritic isoform maps as a trans-QTL to Qrr1d. This enrichment in transcripts that are transported to neuronal processes raises the possibility that this CNS specific trans-effect may be related to local protein synthesis. tRNAs in Qrr1 Prompted by the many ARS transcripts that consistently map to Qrr1d, we searched the genomic tRNA database [65] for tRNAs in this region. Interestingly, distal Chr 1 is one of many tRNA hotspots in the mouse genome and several predicted tRNAs are clustered in the non-coding regions of Qrr1 (figure 2). The majority of these tRNA sequences are in the proximal end of Qrr1, over 2 Mb away from Qrr1d. We scanned the intergenic non-coding regions in Qrr1d for tRNAs using the tRNAscan-SE software [65] and uncovered tRNAs for arginine and serine, and three pseudo- tRNA sequences between genes Igsf4b and Aim2 (175.204– 175.257 Mb) in Qrr1d (dataset S3). Transfer RNAs are involved in regulating transcription of the ARS in response to cellular amino acid levels [66] and are functionally highly relevant candidates in Qrr1d. Polymorphism in the tRNA clusters (e.g., possible copy number variants, differences in tRNA species) may have significant impact on the expression of the ARS. Sequence Analysis of Crosses Trans-regulation of large number of transcripts by Qrr1 is a strong feature of crosses between B6 and D2—both the BXD RI PLoS Genetics | www.plosgenetics.org 7 November 2008 | Volume 4 | Issue 11 | e1000260