The genetics of gene expression in a C. elegans multi parental recombinant inbred line population

Studying genetic variation of gene expression provides a powerful way to unravel the molecular components underlying complex traits. Expression QTL studies have been performed in several different model species, yet most of these linkage studies have been based on genetic segregation of two parental alleles. Recently we developed a multi-parental segregating population of 200 recombinant inbred lines (mpRILs) derived from four wild isolates (JU1511, JU1926, JU1931 and JU1941) in the nematode Caenorhabditis elegans. We used RNA-seq to investigate how multiple alleles affect gene expression in these mpRILs. We found 1,789 genes differentially expressed between the parental lines. Transgression, expression beyond any of the parental lines in the mpRILs, was found for 7,896 genes. For expression QTL mapping almost 9,000 SNPs were available. By combining these SNPs and the RNA-seq profiles of the mpRILs, we detected almost 6,800 eQTLs. Most trans-eQTLs (63%) co-locate in six newly identified trans-bands. The trans-eQTLs found in previous 2-parental allele eQTL experiments and this study showed some overlap (17.5%-46.8%), highlighting on the one hand that a large group of genes is affected by polymorphic regulators across populations and conditions, on the other hand it shows that the mpRIL population allows identification of novel gene expression regulatory loci. Taken together, the analysis of our mpRIL population provides a more refined insight into C. elegans complex trait genetics and eQTLs in general, as well as a starting point to further test and develop advanced statistical models for detection of multi-allelic eQTLs and systems genetics studying the genotype-phenotype relationship.

Variant Intronic Enhancer Controls SCN10A-Short Expression and Heart Conduction

Background: Genetic variants in SCN10A , encoding the neural voltage-gated sodium channel NaV1.8, are strongly associated with atrial fibrillation, Brugada syndrome, cardiac conduction velocities and heart rate. The cardiac function of SCN10A has not been resolved, however, and diverging mechanisms have been proposed. Here, we investigated the cardiac expression of SCN10A and the function of a variant-sensitive intronic enhancer previously linked to the regulation of SCN5A , encoding the major essential cardiac sodium channel NaV1.5. Methods: The expression of SCN10A was investigated in mouse and human hearts. Using CRISPR/Cas9 genome editing, the mouse intronic enhancer was disrupted, and mutant mice were characterized by transcriptomic and electrophysiological analyses. The association of genetic variants at SCN5A-SCN10A enhancer regions and gene expression were evaluated by GWAS SNP mapping and expression QTL analysis. Results: We found that cardiomyocytes of the atria, sinoatrial node and ventricular conduction system express a short transcript comprising the last 7 exons of the gene ( Scn10a-short ). Transcription occurs from an intronic enhancer-promoter complex, while full length Scn10a transcript was undetectable in the human and mouse heart. Expression QTL analysis revealed that the genetic variants in linkage disequilibrium with genetic variant rs6801957 in the intronic enhancer associate with SCN10A transcript levels in the heart. Genetic modification of the enhancer in the mouse genome led to reduced cardiac Scn10a-short expression in atria and ventricles, reduced cardiac sodium current in atrial cardiomyocytes, atrial conduction slowing and arrhythmia, while expression of Scn5a , the presumed enhancer target gene, remained unaffected. In patch-clamp transfection experiments, expression of Scn10a-short -encoded NaV1.8-short increased NaV1.5-mediated sodium current. We propose that non-coding genetic variation modulates transcriptional regulation of Scn10a-short in cardiomyocytes that impacts on NaV1.5-mediated sodium current and heart rhythm. Conclusions: Genetic variants in and around SCN10A modulate enhancer function and expression of a cardiac-specific SCN10A-short transcript. We propose that non-coding genetic variation modulates transcriptional regulation of a functional C-terminal portion of NaV1.8 in cardiomyocytes that impacts on NaV1.5 function, cardiac conduction velocities and arrhythmia susceptibility.

The genetics of gene expression in a C. elegans multi parental recombinant inbred line population

Studying genetic variation of gene expression provides a powerful way to unravel the molecular components underlying complex traits. Expression QTL studies have been performed in several different model species, yet most of these linkage studies have been based on genetic segregation of two parental alleles. Recently we developed a multi-parental segregating population of 200 recombinant inbred lines (mpRILs) derived from four wild isolates (JU1511, JU1926, JU1931 and JU1941) in the nematode Caenorhabditis elegans. We used RNA-seq to investigate how multiple alleles affect gene expression in these mpRILs. We found 1,789 genes differentially expressed between the parental lines. Transgression, expression beyond any of the parental lines in the mpRILs, was found for 7,896 genes. For expression QTL mapping almost 9,000 SNPs were available. By combining these SNPs and the RNA-seq profiles of the mpRILs, we detected almost 6,800 eQTLs. Most trans-eQTLs (63%) co-locate in six newly identified trans-bands. The trans-eQTLs found in previous 2-parental allele eQTL experiments and this study showed some overlap (17.5%- 46.8%), highlighting on the one hand that a large group of genes is affected by polymorphic regulators across populations and conditions, on the other hand it shows that the mpRIL population allows identification of novel gene expression regulatory loci. Taken together, the analysis of our mpRIL population provides a more refined insight into C. elegans complex trait genetics and eQTLs in general, as well as a starting point to further test and develop advanced statistical models for detection of multi-allelic eQTLs and systems genetics studying the genotype-phenotype relationship.

PSV-27 Program Chair Poster Pick: Expression QTL mapping for meat quality in beef cattle

Expression QTL mapping provides information about genetic variant with modulatory effects on gene expression which are useful for understanding the genetic architecture of complex phenotypes. This mapping allows for uncovering of genomic regions associated with transcription regulation of genes which can be related to phenotypic variation when they colocalize with QTLs (cis and trans effects), providing a molecular basis for the phenotype-genotype association. The objectives of the present research were to perform eQTL mapping for meat quality traits in longissimus dorsi muscle and to uncover genes whose expression is influenced by local or distant genetic variation. A total of 120 steers from the University of Florida Beef Unit multibreed Angus-Brahman herd born between 2013 and 2014 were used in this study. The first three principal components from a principal component analysis for all meat quality phenotypes were used to construct a meat quality index. Eighty animals were selected based on extreme meat quality index for mRNA sequencing and 100 bp paired-end reads were mapped against to the Btau_4.6.1 reference genome. eQTL mapping was performed using 112,042 SNPs and 8,588 genes. A cis QTL was defined as an SNP located no more than 1 Mb upstream of the transcription start site or downstream of the transcription end site of an annotated gene. Polymorphisms associated with expression of at least 20 genes in the case of eQTL were considered hot spots. The harboring or adjacent gene was defined as master regulators. Multiple cis eQTLs and sQTLs effects were identified and genes such as LSM2, SOAT1, TTN and TEK are a few examples of potential expression and splicing regulatory genes. A total of 27 expression and 13 splicing master regulator genes were uncovered, mainly cytoskeletal or membrane-associated proteins, transcription factors and DNA methylases.