Heritability and Tissue Specificity of Expression Quantitative Trait Loci

Variation in gene expression is heritable and has been mapped to the genome in humans and model organisms as expression quantitative trait loci (eQTLs). We applied integrated genome-wide expression profiling and linkage analysis to the regulation of gene expression in fat, kidney, adrenal, and heart tissues using the BXH/HXB panel of rat recombinant inbred strains. Here, we report the influence of heritability and allelic effect of the quantitative trait locus on detection of cis- and trans-acting eQTLs and discuss how these factors operate in a tissue-specific context. We identified several hundred major eQTLs in each tissue and found that cis-acting eQTLs are highly heritable and easier to detect than trans-eQTLs. The proportion of heritable expression traits was similar in all tissues; however, heritability alone was not a reliable predictor of whether an eQTL will be detected. We empirically show how the use of heritability as a filter reduces the ability to discover trans-eQTLs, particularly for eQTLs with small effects. Only 3% of cis- and trans-eQTLs exhibited large allelic effects, explaining more than 40% of the phenotypic variance, suggestive of a highly polygenic control of gene expression. Power calculations indicated that, across tissues, minor differences in genetic effects are expected to have a significant impact on detection of trans-eQTLs. Trans-eQTLs generally show smaller effects than cis-eQTLs and have a higher false discovery rate, particularly in more heterogeneous tissues, suggesting that small biological variability, likely relating to tissue composition, may influence detection of trans-eQTLs in this system. We delineate the effects of genetic architecture on variation in gene expression and show the sensitivity of this experimental design to tissue sampling variability in large-scale eQTL studies

Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass

Left ventricular mass (LVM) and cardiac gene expression are complex traits regulated by factors both intrinsic and extrinsic to the heart. To dissect the major determinants of LVM, we combined expression quantitative trait locus1 and quantitative trait transcript (QTT) analyses of the cardiac transcriptome in the rat. Using these methods and in vitro functional assays, we identified osteoglycin (Ogn) as a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM. We also applied genome-wide QTT analysis to the human heart and observed that, out of 22,000 transcripts, OGN transcript abundance had the highest correlation with LVM. We further confirmed a role for Ogn in the in vivo regulation of LVM in Ogn knockout mice. Taken together, these data implicate Ogn as a key regulator of LVM in rats, mice and humans, and suggest that Ogn modifies the hypertrophic response to extrinsic factors such as hypertension and aortic stenosi

YABBY Polarity Genes Mediate the Repression of KNOX Homeobox Genes in Arabidopsis

The YABBY (YAB) genes specify abaxial cell fate in lateral organs in Arabidopsis. Loss-of-function mutants in two early-expressing YAB genes, FILAMENTOUS FLOWER (FIL) and YAB3, do not exhibit vegetative phenotypes as a result of redundancy. Mutations in these genes result in the derepression of the KNOX homeobox genes SHOOTMERISTEMLESS (STM), BREVIPEDICELLUS, and KNAT2 in the leaves and in the partial rescue of stm mutants. Here, we show that fil yab3 double mutants exhibit ectopic meristem formation on the adaxial surfaces of cotyledons and leaf blades. We propose that in addition to abaxial specification, lateral organ development requires YAB function to downregulate KNOTTED homeobox genes so that meristem initiation and growth are restricted to the apex

A point mutation at the junction of domain 2?3/2?4 of transcription factor σ⁷⁰ abrogates productive transcription and restores its expected mobility on a denaturing gel

Region 2 of eubacterial s factors is highly conserved and the subdomain 2?4 is involved in -10 promote recognition. An evolutionary conserved "RpoD box" has been identified at the junction of subdomain 2?3/2?4 in class I and class II σ factors and there are two tryptophan residues at position 433 and 434 which can be used as intrinsic fluorescent markers to study their structure-function relationship. Site-directed mutagenesis of these two tryptophan residues has been carried out to generate three variants of σ70 of Escherichia coli RNA polymerase. These are W433F, W433G and W434G. σ70-W433F is found to be indistinguishable from the native σ factor by both structural and functional analysis. σ70-W433G shows anomalous mobility on SDS-PAGE like the native σ factor, is σ -helical in conformation (50% helicity although found to be less active in total transcription when reconstituted with core RNA polymerase. Free σ70-W434G, unlike the native σ factor, shows the expected mobility of a 70 kDa protein on SDS-PAGE and has 20% helicity. Time-resolved fluorescence analysis indicates that free σ70-W434G has DNA binding ability, and displays a normal abortive initiation reaction but a decreased level of productive transcription after reconstitution with core RNA polymerase. A model is proposed in which tryptophan at position 434 interacts with the hydrophobic 1?1 domain of σ70 giving rise to the stability of the protein under denaturing conditions

Coordinated Activation of ARF1 GTPases by ARF-GEF GNOM Dimers Is Essential for Vesicle Trafficking in Arabidopsis

Membrane trafficking maintains the organization of the eukaryotic cell and delivers cargo proteins to their subcellular destinations, such as sites of action or degradation. The formation of membrane vesicles requires the activation of the ADP-ribosylation factor ARF GTPase by the SEC7 domain of ARF guanine-nucleotide exchange factors (ARF-GEFs), resulting in the recruitment of coat proteins by GTP-bound ARFs. In vitro exchange assays were done with monomeric proteins, although ARF-GEFs form dimers in vivo. This feature is conserved across eukaryotes, although its biological significance is unknown. Here, we demonstrate the proximity of ARF1•GTPs in vivo by fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy, mediated through coordinated activation by dimers of Arabidopsis (Arabidopsis thaliana) ARF-GEF GNOM, which is involved in polar recycling of the auxin transporter PIN-FORMED1. Mutational disruption of ARF1 spacing interfered with ARF1-dependent trafficking but not with coat protein recruitment. A mutation impairing the interaction of one of the two SEC7 domains of the GNOM ARF-GEF dimer with its ARF1 substrate reduced the efficiency of coordinated ARF1 activation. Our results suggest a model of coordinated activation-dependent membrane insertion of ARF1•GTP molecules required for coated membrane vesicle formation. Considering the evolutionary conservation of ARFs and ARF-GEFs, this initial regulatory step of membrane trafficking might well occur in eukaryotes in general

FDR in LV, Fat, Kidney, and Adrenal Tissues

<div><p>(A) For each major eQTL detected in LV, fat, kidney, and adrenal tissue, the expected FDR was calculated and plotted against different <i>p</i>-value thresholds in the range 10⁻⁶–0.05. Insert: FDR for various <i>p</i>-values in the range 10⁻⁶–10⁻³.</p><p>(B) Vase box-plots for the FDRs of the <i>cis-</i> and <i>trans</i>-acting eQTLs detected at <i>p</i> = 0.05 in LV, fat, kidney, and adrenal tissue. Vase box-plots are box-plots where the width of the box at each point is proportional to the density of the data there. The thick line indicates the median FDR for each distribution.</p></div

Genetic Architecture of Genetic Variation in Gene Expression

<p>For each considered transcript the major eQTL was identified by linkage analysis (genome-wide significance, <i>p</i> = 0.05) and characterised as <i>cis</i> or <i>trans</i>. Additive allelic effect and heritability (<i>h</i>²_QTL) for each <i>cis-</i>eQTL (black symbol) and <i>trans-</i>eQTL (grey symbol) were plotted for LV, fat, kidney, and adrenal tissues.</p

Power to Detect a Major eQTL in the RI Strains

<div><p>(A) Statistical power to detect an eQTL of given allelic effect is shown for various estimates of heritability of gene expression in 30 RI strains with four biological replicates. The eQTL allelic effect is an estimate of the absolute change in the transcript abundance that would be produced by substituting a single allele of one type with that of another type in the population (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020172#s4" target="_blank">Materials and Methods</a>). Absolute FCs, corresponding to the allelic effects on the primary <i>x</i>-axis, are also reported on the secondary <i>x</i>-axis.</p><p>(B) Statistical power to detect <i>cis-</i>eQTLs (solid line) and <i>trans-</i>eQTLs (dashed line) (detected with genome-wide significance, <i>p</i> = 0.05) is shown for various heritabilities of gene expression (<i>h</i>²_trait) in LV, fat, kidney, and adrenal tissues. Specific allelic effects for <i>cis-</i> and <i>trans</i>-eQTLs were defined in accordance with those observed in this study at <i>p</i> = 0.05 (reported in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020172#pgen-0020172-t001" target="_blank">Table 1</a>).</p></div

The Transcriptional Corepressor RIP140 Regulates Oxidative Metabolism in Skeletal Muscle

Nuclear receptor signaling plays an important role in energy metabolism. In this study we demonstrate that the nuclear receptor corepressor RIP140 is a key regulator of metabolism in skeletal muscle. RIP140 is expressed in a fiber type-specific manner, and manipulation of its levels in null, heterozygous, and transgenic mice demonstrate that low levels promote while increased expression suppresses the formation of oxidative fibers. Expression profiling reveals global changes in the expression of genes implicated in both myofiber phenotype and metabolic functions. Genes involved in fatty-acid oxidation, oxidative phosphorylation, and mitochondrial biogenesis are upregulated in the absence of RIP140. Analysis of cultured myofibers demonstrates that the changes in expression are intrinsic to muscle cells and that nuclear receptor-regulated genes are direct targets for repression by RIP140. Therefore RIP140 is an important signaling factor in the regulation of skeletal muscle function and physiology