Intergenic Locus Research Articles

Genome-wide association study identifies MAPT locus influencing human plasma tau levels.

To identify genetic loci associated with plasma tau concentrations in healthy elders and individuals with Alzheimer disease. Four hundred sixty-three non-Hispanic white individuals exceeding quality control criteria were included from the Alzheimer's Disease Neuroimaging Initiative (ADNI-1) cohort. Association of plasma tau with genetic polymorphisms was performed with a linear regression model. Significant associations were validated in an independent replication cohort consisting of 431 healthy elders or individuals with mild cognitive impairment recruited from the University of California, San Francisco Memory and Aging Center. The minor allele (A) of rs242557 in the microtubule-associated protein tau gene (MAPT) was associated with higher plasma tau levels at genome-wide significance (p = 4.85 × 10-9, empiric family-wise error corrected p = 0.0024) in a dose-dependent fashion. This association was also observed in the replication cohort (p = 1.0 × 10-5; joint analysis p = 1.2 × 10-12). Single nucleotide polymorphisms near PARK2 (rs2187213) (p = 6.15 × 10-6), IL2RA (rs7072793, rs7073236) (p = 7.89 × 10-6), and an intergenic locus on 9p21.3 (rs7047280) (p = 8.13 × 10-6) were identified as suggestive loci associated with plasma tau levels. MAPT H1c haplotype (rs242557) has previously been identified as a genetic risk factor for progressive supranuclear palsy and corticobasal degeneration. The current findings suggest that plasma tau concentration could be an endophenotype for identifying risk for 4-repeat tauopathies in older individuals.

Pharmacogenomics of Mood Disorders

Overall Abstract Single gene and GWAS analyses of pharmacological treatment response in depression and bipolar disorder have had varying success in identifying functionally relevant genes associated with pharmacological treatment response such as response to SSRI in depression and lithium in bipolar disorder. Hence, the need to better understand the complex genetic underpinnings of pharmacoresponse may include methodologies such as RNA-seq and microarray analyses. Such approaches contribute to a more in in-depth functional characterization of risk loci related to treatment response and to characterize the genetic underpinnings of both adverse events (e.g. induction of mania by antidepressants) and of medical comorbidity contributing to poor treatment response. In addition, gene expression profile and eQTLs can assist an improved understanding of the functional genomics of mood disorders. Specifically, recent large-scale GWAS meta-analyses (ConLiGen) have implicated multiple novel loci, two of which met the threshold for genome-wide significance: GADL1 (Chen et al., 2014) and an intergenic locus on chromosome 21 (Hou et al., 2016). The functional implications of the related genes remain to be described. In a first presentation, results will be presented from whole blood RNA-seq-data in a subsample of ConLiGen to validate and characterize these associations with clinical lithium treatment response and how these loci impact gene function and lithium response (David Stacey). Addressing the need to investigate the genetic underpinning of a broader range of treatment outcomes and adverse events, the genetic contribution of a potential induction of mania by antidepressants will be discussed in a second presentation, that shows results from a GWAS of antidepressant-induced mania (Joanna Biernacka). Among other factors, the co-morbidity of depression with other psychiatric and cardiometabolic disorders may negatively influence antidepressants treatment outcome. Moreover, response to antidepressants is a complex trait with substantial contribution from a large number of common genetic variants of small effect. Hence, use of polygenic scores (PGS) could be a better alternative to estimate the overall effect of genetic factors on treatment response and assess the importance of co-morbidities and related phenotypes. To investigate this further, we evaluated whether PGS derived from 25 recognized comorbid cardiometabolic and psychiatric disorders, personality traits and educational attainment predict treatment outcome to SSRIs in major depressive disorder using the ISPC data (Bernhard Baune). Previous studies aiming to identify the transcriptome signature of depression are inconsistent with low replicability at the single gene level in both brain and peripheral tissues. In a fourth presentation, results from analyses of whole blood transcriptomes of 521 elderly people from the general population (The Sydney Memory and Age Study, MAS, Sydney) are shown to describe molecular networks involved in geriatric depression. Functional characterisation of two out of 29 modules of the co-expression network indicated that abnormalities in structural constituents of ribosome may be involved in the pathophysiology of geriatric depression. In addition, results of pathway analyses using Ingenuity Pathway Analysis software will be shown (Liliana Ciobanu).

Copy number variation analysis reveals additional variants contributing to endometriosis development.

Endometriosis is a gynecological disease influenced by multiple genetic and environmental factors. The aim of the current study was to use SNP-array technology to identify genomic aberrations that may possibly contribute to the development of endometriosis. We performed an SNP-array genotyping of pooled DNA samples from both patients (n = 100) and controls (n = 50). Copy number variation (CNV) calling and association analyses were performed using PennCNV software. MLPA and TaqMan Copy-Number assays were used for validation of CNVs discovered. We detected 49 CNV loci that were present in patients with endometriosis and absent in the control group. After validation procedures, we confirmed six CNV loci in the subtelomeric regions, including 1p36.33, 16p13.3, 19p13.3, and 20p13, representing gains, while 17q25.3 and 20q13.33 showed losses. Among the intrachromosomal regions, our results revealed duplication at 19q13.1 within the FCGBP gene (p = 0.007). We identified CNVs previously associated with endometriosis, together with six suggestive novel loci possibly involved in this disease. The intergenic locus on chromosome 19q13.1 shows strong association with endometriosis and is under further functional investigation.

Variant rs10911021 that associates with coronary heart disease in type 2 diabetes, is associated with lower concentrations of circulating HDL cholesterol and large HDL particles but not with amino acids.

AimsAn intergenic locus on chromosome 1 (lead SNP rs10911021) was previously associated with coronary heart disease (CHD) in type 2 diabetes (T2D). Using data from the UCLEB consortium we investigated the relationship between rs10911021 and CHD in T2D, whether rs10911021 was associated with levels of amino acids involved in the γ-glutamyl cycle or any conventional risk factors (CRFs) for CHD in the T2D participants.MethodsFour UCLEB studies (n = 6531) had rs10911021 imputation, CHD in T2D, CRF and metabolomics data determined using a nuclear magnetic resonance based platform.ResultsThe expected direction of effect between rs10911021 and CHD in T2D was observed (1377 no CHD/160 CHD; minor allele OR 0.80, 95 % CI 0.60–1.06) although this was not statistically significant (p = 0.13). No association between rs10911021 and CHD was seen in non-T2D participants (11218 no CHD/1274 CHD; minor allele OR 1.00 95 % CIs 0.92–1.10). In T2D participants, while no associations were observed between rs10911021 and the nine amino acids measured, rs10911021 was associated with HDL-cholesterol (p = 0.0005) but the minor “protective” allele was associated with lower levels (−0.034 mmol/l per allele). Focusing more closely on the HDL-cholesterol subclasses measured, we observed that rs10911021 was associated with six large HDL particle measures in T2D (all p < 0.001). No significant associations were seen in non-T2D subjects.ConclusionsOur findings are consistent with a true association between rs10911021 and CHD in T2D. The protective minor allele was associated with lower HDL-cholesterol and reductions in HDL particle traits. Our results indicate a complex relationship between rs10911021 and CHD in T2D.Electronic supplementary materialThe online version of this article (doi:10.1186/s12933-016-0435-0) contains supplementary material, which is available to authorized users.

An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression.

Breast cancer is the most diagnosed malignancy and the second leading cause of cancer mortality in females. Previous association studies have identified variants on 2q35 associated with the risk of breast cancer. To identify functional susceptibility loci for breast cancer, we interrogated the 2q35 gene desert for chromatin architecture and functional variation correlated with gene expression. We report a novel intergenic breast cancer risk locus containing an enhancer copy number variation (enCNV; deletion) located approximately 400Kb upstream to IGFBP5, which overlaps an intergenic ERα-bound enhancer that loops to the IGFBP5 promoter. The enCNV is correlated with modified ERα binding and monoallelic-repression of IGFBP5 following oestrogen treatment. We investigated the association of enCNV genotype with breast cancer in 1,182 cases and 1,362 controls, and replicate our findings in an independent set of 62,533 cases and 60,966 controls from 41 case control studies and 11 GWAS. We report a dose-dependent inverse association of 2q35 enCNV genotype (percopy OR = 0.68 95%CI 0.55-0.83, P = 0.0002; replication OR = 0.77 95% CI 0.73-0.82, P = 2.1 × 10-19) and identify 13 additional linked variants (r2 > 0.8) in the 20Kb linkage block containing the enCNV (P = 3.2 × 10-15 - 5.6 × 10-17). These associations were independent of previously reported 2q35 variants, rs13387042/rs4442975 and rs16857609, and were stronger for ER-positive than ER-negative disease. Together, these results suggest that 2q35 breast cancer risk loci may be mediating their effect through IGFBP5.

Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize

A detailed understanding of genetic architecture of mRNA expression by millions of genetic variants is important for studying quantitative trait variation. In this study, we identified 1.25M SNPs with a minor allele frequency greater than 0.05 by combining reduced genome sequencing (GBS), high-density array technologies (600K), and previous deep RNA-sequencing data from 368 diverse inbred lines of maize. The balanced allelic frequencies and distributions in a relatively large and diverse natural panel helped to identify expression quantitative trait loci (eQTLs) associated with more than 18 000 genes (63.4% of tested genes). We found that distant eQTLs were more frequent (∼75% of all eQTLs) across the whole genome. Thirteen novel associated loci affecting maize kernel oil concentration were identified using the new dataset, among which one intergenic locus affected the kernel oil variation by controlling expression of three other known oil-related genes. Altogether, this study provides resources for expanding our understanding of cellular regulatory mechanisms of transcriptome variation and the landscape of functional variants within the maize genome, thereby enhancing the understanding of quantitative variations.

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA.

BackgroundIt has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive modeling of disease phenotype for the prioritization of candidate biomarkers. The continuous nature of SNV allele fraction features allows the concurrent investigation of several genomic phenomena, including allele specific expression, clonal expansion and/or deletion, and copy number variation.ResultsThe proposed software pipeline and package, SNV Discriminant Analysis (SNV-DA), was applied on two RNA-Seq datasets with varying sample sizes sequenced at different depths: a dataset containing primary tumors from twenty patients with different disease outcomes in lung adenocarcinoma and a larger dataset of primary tumors representing two major breast cancer subtypes, estrogen receptor positive and triple negative. Predictive models were generated using the machine learning algorithm, sparse projections to latent structures discriminant analysis. Training sets composed of RNA-Seq SNV features limited to genomic regions of origin (e.g. exonic or intronic) and/or RNA-editing sites were shown to produce models with accurate predictive performances, were discriminant towards true label groupings, and were able to produce SNV rankings significantly different from than univariate tests. Furthermore, the utility of the proposed methodology is supported by its comparable performance to traditional models as well as the enrichment of selected SNVs located in genes previously associated with cancer and genes showing allele-specific expression. As proof of concept, we highlight the discovery of a previously unannotated intergenic locus that is associated with epigenetic regulatory marks in cancer and whose significant allele-specific expression is correlated with ER+ status; hereafter named ER+ associated hotspot (ERPAHS).ConclusionThe use of models from RNA-Seq SNVs to identify and prioritize candidate molecular targets for biomarker discovery is supported by the ability of the proposed method to produce significantly accurate predictive models that are discriminant towards true label groupings. Importantly, the proposed methodology allows investigation of mutations outside of exonic regions and identification of interesting expressed loci not included in traditional gene annotations. An implementation of the proposed methodology is provided that allows the user to specify SNV filtering criteria and cross-validation design during model creation and evaluation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2542-4) contains supplementary material, which is available to authorized users.

Abstract P264: Association of D-dimer with Incident Cardiovascular Disease Events and F3 Gene Variants in African Americans: Results From the Jackson Heart Study

Plasma D-dimer, a fibrin degradation product, is a biomarker of both coagulation and fibrinolysis and a risk factor for both arterial and venous thrombosis. African Americans (AAs) have increased risk of thrombosis and higher levels of D-dimer as compared to European populations, but little is known about the genetic architecture of D-dimer in AAs. D-dimer was assessed in 4163 AAs from the Jackson Heart Study (mean age 55 years, 62.1% female). We hypothesized that D-dimer levels would associate with incident cardiovascular disease events and with both coding and noncoding genetic variants. Median (interquartile range) D-dimer in the cohort was 0.40 (0.26-0.64) μg/ml. D-dimer was associated with increased risk of coronary heart disease (hazard ratio (HR) per standard deviation (SD)=1.26, p=0.012), stroke (HR=1.27, p=0.018), heart failure (HR=1.33, p=0.001), and mortality (HR=1.25, p&lt;0.0001) in models adjusted for age, sex, BMI, current smoking, diabetes, hypertension, systolic blood pressure, and low-density lipoprotein cholesterol. Using data from the Affymetrix Genome-Wide Human SNP Array 6.0, imputation based on the 1000 Genomes project reference panel (Phase I, Version 3, March 2012 release) was completed using MACH 1.0 and minimac in 2709 participants with D-dimer. Associations were assessed using MACH2QTL v.1.13, with models adjusted for age, sex, and the first ten principal components for global ancestry calculated using EIGENSOFT. The most significant signal was for an intergenic locus near F3 (top variant rs2022030, p=5.71x10 -12 , minor allele frequency=10.6%, imputation r 2 =1). F3 codes for tissue factor, a necessary co-factor for factor VIIa in the initiation of the extrinsic blood coagulation pathway. The F3 locus had been previously associated with D-dimer levels in European populations but has not been reported for AAs. Data were also available from the Illumina HumanExome Beadchip, version 1.1, in 2502 individuals; single variant analyses and gene-based tests for nonsynonymous, splicing, and nonsense variants with a minor allele frequency &lt;5% were performed using RAREMETAL, adjusted for age, sex, and the first ten principal components. For single variant analyses, a nonsynonymous variant in GPRASP1 (G protein-coupled receptor associated sorting protein 1, rs145805077, p= 1.84x10 -7 , minor allele frequency=0.3%) was significantly associated with decreased D-dimer. No gene-based test result met the strict multiple comparison significance threshold; the top gene-based result with the sequence kernel association test (SKAT) was for six variants in PPM1M (protein phosphatase, Mg2+/Mn2+ dependent, 1M, p=6.09x10 -6 ). These results highlight D-dimer as an important predictor of cardiovascular disease risk in AAs and that levels of this biomarker are associated with the F3 locus.

Xenobiotic Compounds Degradation by Heterologous Expression of a Trametes sanguineus Laccase in Trichoderma atroviride

Fungal laccases are enzymes that have been studied because of their ability to decolorize and detoxify effluents; they are also used in paper bleaching, synthesis of polymers, bioremediation, etc. In this work we were able to express a laccase from Trametes (Pycnoporus) sanguineus in the filamentous fungus Trichoderma atroviride. For this purpose, a transformation vector was designed to integrate the gene of interest in an intergenic locus near the blu17 terminator region. Although monosporic selection was still necessary, stable integration at the desired locus was achieved. The native signal peptide from T. sanguineus laccase was successful to secrete the recombinant protein into the culture medium. The purified, heterologously expressed laccase maintained similar properties to those observed in the native enzyme (Km and kcat and kcat/km values for ABTS, thermostability, substrate range, pH optimum, etc). To determine the bioremediation potential of this modified strain, the laccase-overexpressing Trichoderma strain was used to remove xenobiotic compounds. Phenolic compounds present in industrial wastewater and bisphenol A (an endocrine disruptor) from the culture medium were more efficiently removed by this modified strain than with the wild type. In addition, the heterologously expressed laccase was able to decolorize different dyes as well as remove benzo[α]pyrene and phenanthrene in vitro, showing its potential for xenobiotic compound degradation.

Biochip-Based Genotyping Assay for Detection of Polymorphisms in Pigmentation Genes Associated with Cutaneous Melanoma.

The purpose of the study was to develop a new assay for genotyping nine single nucleotide polymorphisms (SNPs) that are known to be associated with melanoma. Two-stage single tube polymerase chain reaction (PCR) followed by hybridization on a biochip was developed and applied in the study. A total of nine SNPs were selected from five genes: MC1R (rs1805006, rs1805007, rs1805009, rs11547464), HERC2 (rs12913832), OCA2 (rs1800407), SLC45A2 (rs16891982), TYR (rs1393350), and a SNP from the intergenic locus rs12896399 were used for the synthesis of ssDNAs via a single-stage PCR process. The assays were performed on a biochip-based platform that is capable of SNP genotyping via a single reaction-tube PCR, followed by on chip hybridization. We tested 69 DNAs obtained from healthy persons and demonstrated the assays' ability to discriminate all three genotypes for almost all of the SNPs. The developed approach proved robust, suggesting that it might be useful for the personalized genotyping of large cohorts of patients.

The CASC15 Long Intergenic Noncoding RNA Locus Is Involved in Melanoma Progression and Phenotype Switching

In recent years, considerable advances have been made in the characterization of protein-coding alterations involved in the pathogenesis of melanoma. However, despite their growing implication in cancer, little is known about the role of long non-coding RNAs in melanoma progression. We hypothesized that copy number alterations of intergenic non-protein coding domains could help identify long intergenic non-coding RNAs (lincRNAs) associated with metastatic cutaneous melanoma. Among several candidates, our approach uncovered the chromosome 6p22.3 CASC15 lincRNA locus as a frequently gained genomic segment in metastatic melanoma tumors and cell lines. The locus was actively transcribed in metastatic melanoma cells, and up-regulation of CASC15 expression was associated with metastatic progression to brain metastasis in a mouse xenograft model. In clinical specimens, CASC15 levels increased during melanoma progression and were independent predictors of disease recurrence in a cohort of 141 patients with AJCC stage III lymph node metastasis. Moreover, siRNA knockdown experiments revealed that CASC15 regulates melanoma cell phenotype switching between proliferative and invasive states. Accordingly, CASC15 levels correlated with known gene signatures corresponding to melanoma proliferative and invasive phenotypes. These findings support a key role for CASC15 in metastatic melanoma.

Genetic differentiation of local populations of the dark European bee Apis mellifera mellifera L. in the Urals

For the last two centuries, beekeepers in Russia and Europe have been introducing bees from the southern regions to the northern ones, subjecting the genetic pool of the dark European bee Apis mellifera mellifera L. subspecies to extensive hybridization. In order to reconfirm on the genetic level the previously published morphological data on the native bee population in the Urals, the Bashkortostan Republic, and the Perm Krai, we analyzed the polymorphism of the mitochondrial (mtDNA COI-COII intergenic locus) and nuclear (two microsatellite loci, ap243 and 4a110) DNA markers. Four local populations of the dark European bee A. m. mellifera surviving in the Urals have been identified, and their principal genetic characteristics have been determined. Data on the genetic structure and geographical localization of the areals of the dark European bee local populations in the Urals may be of use in restoring the damaged genetic pool of A. m. mellifera in Russia and other northern countries.

Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia.

Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern-southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity.

Glucose-Based Regulation of miR-451/AMPK Signaling Depends on the OCT1 Transcription Factor

In aggressive, rapidly growing solid tumors such as glioblastoma multiforme (GBM), cancer cells face frequent dynamic changes in their microenvironment, including the availability of glucose and other nutrients. These challenges require that tumor cells have the ability to adapt in order to survive periods of nutrient/energy starvation. We have identified a reciprocal negative feedback loop mechanism in which the levels of microRNA-451 (miR-451) are negatively regulated through the phosphorylation and inactivation of its direct transcriptional activator OCT1 by 5' AMP-activated protein kinase (AMPK), which is activated by glucose depletion-induced metabolic stress. Conversely, in a glucose-rich environment, unrestrained expression of miR-451 suppresses AMPK pathway activity. These findings uncover miR-451 as a major effector of glucose-regulated AMPK signaling, allowing tumor cell adaptation to variations in nutrient availability in the tumor microenvironment.

Identification of Susceptibility Loci in IL6, RPS9/LILRB3, and an Intergenic Locus on Chromosome 21q22 in Takayasu Arteritis in a Genome-Wide Association Study.

Takayasu arteritis is a rare large vessel vasculitis with incompletely understood etiology. This study was undertaken to perform the first unbiased genome-wide association analysis of Takayasu arteritis. Two independent cohorts of patients with Takayasu arteritis from Turkey and North America were included in our study. The Turkish cohort consisted of 559 patients and 489 controls, and the North American cohort consisted of 134 patients and 1,047 controls of European ancestry. Genotyping was performed using the Omni1-Quad and Omni2.5 genotyping arrays. Genotyping data were subjected to rigorous quality control measures and subsequently analyzed to discover genetic susceptibility loci for Takayasu arteritis. We identified genetic susceptibility loci for Takayasu arteritis with a genome-wide level of significance in IL6 (rs2069837) (odds ratio [OR] 2.07, P = 6.70 × 10(-9)), RPS9/LILRB3 (rs11666543) (OR 1.65, P = 2.34 × 10(-8)), and an intergenic locus on chromosome 21q22 (rs2836878) (OR 1.79, P = 3.62 × 10(-10)). The genetic susceptibility locus in RPS9/LILRB3 lies within the leukocyte receptor complex gene cluster on chromosome 19q13.4, and the disease risk variant in this locus correlates with reduced expression of multiple genes including the inhibitory leukocyte immunoglobulin-like receptor gene LILRB3 (P = 2.29 × 10(-8)). In addition, we identified candidate susceptibility genes with suggestive levels of association (P < 1 × 10(-5)) with Takayasu arteritis, including PCSK5, LILRA3, PPM1G/NRBP1, and PTK2B. Our findings indicate novel genetic susceptibility loci for Takayasu arteritis and uncover potentially important aspects of the pathophysiology of this form of vasculitis.

Common genetic variants influence human subcortical brain structures.

The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10(-33); 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.

Genome-wide enrichment analysis between endometriosis and obesity-related traits reveals novel susceptibility loci.

Endometriosis is a chronic inflammatory condition in women that results in pelvic pain and subfertility, and has been associated with decreased body mass index (BMI). Genetic variants contributing to the heritable component have started to emerge from genome-wide association studies (GWAS), although the majority remain unknown. Unexpectedly, we observed an intergenic locus on 7p15.2 that was genome-wide significantly associated with both endometriosis and fat distribution (waist-to-hip ratio adjusted for BMI; WHRadjBMI) in an independent meta-GWAS of European ancestry individuals. This led us to investigate the potential overlap in genetic variants underlying the aetiology of endometriosis, WHRadjBMI and BMI using GWAS data. Our analyses demonstrated significant enrichment of common variants between fat distribution and endometriosis (P = 3.7 × 10−3), which was stronger when we restricted the investigation to more severe (Stage B) cases (P = 4.5 × 10−4). However, no genetic enrichment was observed between endometriosis and BMI (P = 0.79). In addition to 7p15.2, we identify four more variants with statistically significant evidence of involvement in both endometriosis and WHRadjBMI (in/near KIFAP3, CAB39L, WNT4, GRB14); two of these, KIFAP3 and CAB39L, are novel associations for both traits. KIFAP3, WNT4 and 7p15.2 are associated with the WNT signalling pathway; formal pathway analysis confirmed a statistically significant (P = 6.41 × 10−4) overrepresentation of shared associations in developmental processes/WNT signalling between the two traits. Our results demonstrate an example of potential biological pleiotropy that was hitherto unknown, and represent an opportunity for functional follow-up of loci and further cross-phenotype comparisons to assess how fat distribution and endometriosis pathogenesis research fields can inform each other.

Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1) combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2) independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were “shut down” by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference between enhancer activities was a possible factor necessitating enhancer independence in our model.

GENETIC DIFFERENTIATION OF POPULATIONS OF HONEY BEE (Apis mellifera L.) AND DISTRIBUTION OF RNA-CONTAINING VIRUSES AT THE BACKGROUND OF EPIZOOTIA OF Varroa destructor ON THE TERRITORY OF UDMURTIA

GENETIC DIFFERENTIATION OF POPULATIONS OF HONEY BEE (Apis mellifera L.) AND DISTRIBUTION OF RNA-CONTAINING VIRUSES AT THE BACKGROUND OF EPIZOOTIA OF Varroa destructor ON THE TERRITORY OF UDMURTIA Alexander E. Kalashnikov*, Ivan V. Maslennikov**, Ludmila M. Kolbina**, Irina G. Udina* *N.I. Vavilov Institute of General Genetics RAS **Udmurt Research Institute of Agriculture Abstract The bees of dark forest species (Apis mellifera mellifera L.) are winter-hardy. These bees are able to effectively use a short honey harvest. Introgression of southern bee species in the Russia affects ro the economic quality of local northern species of bees. Introgression of species reduces their immunity, thereby It was enhancing susceptibility bees to infection with ectoparasites, as well as distribution of various viral diseases. Varroa destructor mite infestations on bees may predispose to infection by viruses. We have presented data about population differentiation of bees of dark forest species in Udmurtia, which were obtained based on the study using PCR method, morphometric parameters (cubital index of wing) and estimation of variability in intergenic locus of the CO-I-CO-II of mtDNA. Based on the analysis of the mtDNA the hybridization degree in samples of bees from Udmurtia 1UD_S and 5UD_S (maternal line) was 15.4 and 60.0%, respectively. Sample 2D_S-4UD_S meet the standards of dark forest bee species. For all analyzed samples (1UD_S-5UD_S) obtained average rating of cubital index> 0.55. These data confirmed the high probability of belonging of bees of sample data to the dark forest bee species. However, the variability analysis (according to the length of the intergenic locus CO-I-CO-II) with Southern species hybridization was observed only in samples 2UD_S-4UD_S, whereas in the other samples 1UD_S 5UD_S hybridization has occurred. This indicates a greater degree of reliability of molecular techniques in the evaluation of the degree of hybridization when samples of bees were studied. It's interesting that in one of the samples 2UD_S we founded a heteroplasmy PQ/P3*Q. In bees exposed to Varroa destructor defeat was detected deformed wing virus (DWV) (23,3% of families), chronic bee paralysis virus (CBPV) and sacbrood bee virus (SBV) (13, 3%). Keywords honey bee, Apis mellifera L., mitochondrial DNA, cubital index, deformed wing virus, sacbrood virus, chronic paralysis virus, Varroa destructor Introduction The dark forest bee Apis mellifera mellifera L. and related subspecies of Central Russian bee breed was widespread in Russia (1), including Udmurtia (2) and Bashkortostan (3). These bees have winter hardiness, resistance to several diseases, the ability efficiently uses a short honey harvest. The proboscis of these bees is short (6.0-6.4 mm). They have a dark color of the body. For these bees is a characteristic light dry seal of honey. However, these bees are aggressive and have a tendency to increase swarming. The cubital index value of the breed standard of these bees is in the range 0.60-0.65 (4). Under the influence of anthropogenic factor in Russia, like in Western Europe and North America, there was observes a hybridization of A. m. mellifera subspecies with subspecies, which are spread in the more southern latitudes. Integration of the southern subspecies effect on economic quality of the local northern species, as well as have a negative impact on their adaptability to environmental conditions. It also reduces immunity, thereby enhancing susceptibility of bees to infection of ectoparasites and distribution of various diseases, including viral (5). Infection bee mite Varroa destructor bees predispose to infection by viruses (5-7). Mite serves as a reservoir for virus bee mite infestation therefore weaken their immunity and promotes viral infection (8). Six of the studied viruses of the honey bee cause serious consequences if infected, up

ГЕНЕТИЧЕСКАЯ ДИФФЕРЕНЦИАЦИЯ ПОПУЛЯЦИЙ МЕДОНОСНОЙ ПЧЕЛЫ (Apis mellifera L.) И РАСПРОСТРАНЕНИЕ РНК-СОДЕРЖАЩИХ ВИРУСОВ ПЧЕЛ НА ФОНЕ ЭПИЗООТИИ КЛЕЩА Varroa destructor НА ТЕРРИТОРИИ УДМУРТИИ

Bees Apis mellifera mellifera L. of the Middle Russian breed are resistant to cold winter and a number of diseases, and can effective use short summer for nectar collection. Introgression of Southern bees affects the trait of local Northern breed and changes negatively their adaptation to environment, decreases the immunity and, as a result, increases a susceptibility to ectoparasites and viruses. Mite infestation with Varroa destructor predisposes the bee to viral infection. Assessment of the purity degree of breed affiliation to Middle Russian breed or to dark forest honey bee Apis m. mellifera L. of Udmurt populations of honey bee by the analysis of cubital index (detected by wing parameters) and the study of variation of the intergenic locus COI-COII of mtDNA in PCR was fulfilled. On mtDNA variation, the hybridization in 1UD_S and 5UD_S specimen makes 15.38 и 60.00 %, respectively, and 2UD_S-4UD_S specimen meet the standards of the Middle Russian breed. In 1UD_S-5UD_S, an average cubital index was more than 0.55, so the bees can be referred to Middle Russian breed with high probability. Nevertheless, with regard to variability on the intergenic locus COI-COII of mtDNA, the hybridization with Southern bees occurred in 2UD_S-4UD_S specimen, but not in 1UD_S and 5UD_S. In 2UD_S a heteroplasmy PQ/p3½Q was found. RNA viruses were indicated by RT-PCR in bees under mite infestation with V. destructor. DWV, ABPV and SBV were found in 23.3 %, 13.3 % and 13.3 % of bee colonies, respectively. A combination of two or more types of viruses was identified in 13.3 % of bee colonies, and at least three types were detected in 3.0 %. A simultaneous infection was observed for DWV and SBV, and for DWV и ABPV.