Dissection of a QTL Hotspot on Mouse Distal Chromosome 1 that Modulates Neurobehavioral Phenotypes and Gene Expression Khyobeni Mozhui, Daniel C. Ciobanu, Thomas Schikorski, Xusheng Wang, Lu Lu, Robert W. Williams* Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America Abstract A remarkably diverse set of traits maps to a region on mouse distal chromosome 1 (Chr 1) that corresponds to human Chr 1q21–q23. This region is highly enriched in quantitative trait loci (QTLs) that control neural and behavioral phenotypes, including motor behavior, escape latency, emotionality, seizure susceptibility (Szs1), and responses to ethanol, caffeine, pentobarbital, and haloperidol. This region also controls the expression of a remarkably large number of genes, including genes that are associated with some of the classical traits that map to distal Chr 1 (e.g., seizure susceptibility). Here, we ask whether this QTL-rich region on Chr 1 (Qrr1) consists of a single master locus or a mixture of linked, but functionally unrelated, QTLs. To answer this question and to evaluate candidate genes, we generated and analyzed several gene expression, haplotype, and sequence datasets. We exploited six complementary mouse crosses, and combed through 18 expression datasets to determine class membership of genes modulated by Qrr1. Qrr1 can be broadly divided into a proximal part (Qrr1p) and a distal part (Qrr1d), each associated with the expression of distinct subsets of genes. Qrr1d controls RNA metabolism and protein synthesis, including the expression of ,20 aminoacyl-tRNA synthetases. Qrr1d contains a tRNA cluster, and this is a functionally pertinent candidate for the tRNA synthetases. Rgs7 and Fmn2 are other strong candidates in Qrr1d. FMN2 protein has pronounced expression in neurons, including in the dendrites, and deletion of Fmn2 had a strong effect on the expression of few genes modulated by Qrr1d. Our analysis revealed a highly complex gene expression regulatory interval in Qrr1, composed of multiple loci modulating the expression of functionally cognate sets of genes. Citation: Mozhui K, Ciobanu DC, Schikorski T, Wang X, Lu L, et al. (2008) Dissection of a QTL Hotspot on Mouse Distal Chromosome 1 that Modulates Neurobehavioral Phenotypes and Gene Expression. PLoS Genet 4(11): e1000260. doi:10.1371/journal.pgen.1000260 Editor: Jonathan Flint, The Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom Received May 27, 2008; Accepted October 14, 2008; Published November 14, 2008 Copyright: 2008 Mozhui 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. Funding: This study was supported by NIAAA INIA (grants U01AA13499, U24AA13513, and U01AA014425). GeneNetwork is supported by NIDA, NIMH and NIAAA (grant P20-DA 21131), the NCRR BIRN (U01NR 105417), and the NCI MMHCC (U01CA105417). Competing Interests: The authors have declared that no competing interests exist. * E-mail: rwilliam@nb.utmem.edu Introduction The distal part of mouse Chr 1 harbors a large number of QTLs that generate differences in behavior. Open field activity [1], fear conditioning [2], rearing behavior [3], and several other measures of emotionality [4,5] have been repeatedly mapped to distal Chr 1. This region is also notable because it appears to influence responses to a wide range of drugs including ethanol [6], caffeine [7], pentobarbital [8], and haloperidol [9]. In addition to the behavioral traits, a number of metabolic, physiological and immunological phenotypes have been mapped to this region (table 1) [10–36]. This QTL rich region on mouse distal Chr 1 exhibits reasonably compelling functional and genetic concordance with the ortholo- gous region on human Chr 1q21–q23. Prime examples of genes in this region that have been associated with similar traits in mouse and human are Rgs2 (anxiety in both species), Apoa2 (atherosclerosis), and Kcnj10 (seizure susceptibility) [37–42]. Studies of gene expression in the central nervous system (CNS) of mice have revealed major strain differences in the expression level of numerous genes located on distal Chr 1, e.g., Copa, Atp1a2, and Kcnj9 [26,43–45]. These differentially expressed genes are strong candidates for the behavioral and neuropharmacological traits that map to this region. We have recently shown that sequence variants near each of these candidate genes are often responsible for the prominent differences in expression [26,46,47]. In other words, sequence differences near genes such as Kcnj9 cause expression to differ, and variation in transcript level maps back to the location of the source gene itself. Transcripts of this type are associated with cis-QTLs. These expression genetic studies have also uncovered another unusual characteristic of mouse distal Chr 1. In addition to the extensive cis-effects, a large number of transcripts of genes located on other chromosomes map into this same short interval on distal Chr 1 [47,48]. These types of QTLs are often referred to as trans- QTLs. The clustering of trans-QTLs to distal Chr 1 has been replicated in multiple crosses and CNS microarray datasets [47]. We refer to this region of Chr 1, extending from Fcgr3 (172.5 Mb) to Rgs7 (177.5 Mb) as the QTL-rich region on Chr 1, or Qrr1. It is possible that these modulatory effects on expression are the first steps in a cascade of events that are ultimately responsible for many of the prominent differences in behavior and neurophar- macology. For example, Qrr1 modulates the expression of several genes that have been implicated in seizure (e.g., Scn1b, Pnpo, Cacna1g), and this may be a basis for the strong influence Qrr1 has on seizure susceptibility [41]. In this study, we exploited 18 diverse array datasets derived from different mouse crosses to systematically dissect the expression QTLs in Qrr1. The strong trans effects are consistently PLoS Genetics | www.plosgenetics.org 1 November 2008 | Volume 4 | Issue 11 | e1000260