No abstract

Variation in DNA sequence contributes to individual differences in quantitative traits, but in humans the specific sequence variants are known for very few traits. We characterized variation in gene expression in cells from individuals belonging to three major population groups. This quantitative phenotype differs significantly between European-derived and Asian-derived populations for 1,097 of 4,197 genes tested. For the phenotypes with the strongest evidence of cis determinants, most of the variation is due to allele frequency differences at cis-linked regulators. The results show that specific genetic variation among populations contributes appreciably to differences in gene expression phenotypes. Populations differ in prevalence of many complex genetic diseases, such as diabetes and cardiovascular disease. As some of these are probably influenced by the level of gene expression, our results suggest that allele frequency differences at regulatory polymorphisms also account for some population differences in prevalence of complex diseases.The expression levels of genes determine the distinctive characteristics of cells. Recent studies have shown that gene expression levels in humans differ not only among cell types within an individual but also among individuals 1,2 . This observation led to analysis of gene expression as a phenotype and to the identification of polymorphic genetic variants that influence individual differences in expression level [3][4][5][6][7][8] . However, these studies of the genetics of human gene expression have been restricted to individuals from one Europeanderived sample, the families collected by the Centre d'Etude du Polymorphisme Humain Correspondence should be addressed to V.G.C. (vcheung@mail.med.upenn.edu) or R.S.S. (spielman@pobox.upenn.edu). Accession codes. Gene Expression Omnibus (GEO): GSE5859.URLs. Human Variation Panel: http://ccr.coriell.org/nigms/cells/humdiv.html. MultiExperiment Viewer: http://www.tm4.org. Information on HapMap SNP markers can be found at http://www.hapmap.org.Note: Supplementary information is available on the Nature Genetics website. COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. Much of the recognized genetic variation among populations is in DNA polymorphisms with no known functional significance. On the other hand, some allele frequency differences between populations have highly significant phenotypic consequences. Among the bestestablished are the differences in allele frequencies for mendelian genetic diseases. The marked population differences in prevalence of these qualitative phenotypes (such as cystic fibrosis 9 and Tay-Sachs disease 10 ) are entirely due to differences in frequencies of the mutant alleles. However, genetic differences among populations in quantitative phenotypes are potentially just as important functionally.Here we extend the comparative genetic analysis of population differences from qualitative phenotypes to a particular quantitative phenotype, the expression ...

R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins.

RNA/DNA hybrids form when RNA hybridizes with its template DNA generating a three-stranded structure known as the R-loop. Knowledge of how they form and resolve, as well as their functional roles, is limited. Here, by pull-down assays followed by mass spectrometry, we identified 803 proteins that bind to RNA/DNA hybrids. Because these proteins were identified using in vitro assays, we confirmed that they bind to R-loops in vivo. They include proteins that are involved in a variety of functions, including most steps of RNA processing. The proteins are enriched for K homology (KH) and helicase domains. Among them, more than 300 proteins preferred binding to hybrids than double-stranded DNA. These proteins serve as starting points for mechanistic studies to elucidate what RNA/DNA hybrids regulate and how they are regulated.