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Background: Patellar luxation is an orthopedic disorder in which the patella moves out of its normal location within the femoral trochlea of the knee and it can lead to osteoarthritis, lameness, and pain. In dogs it is a heritable trait, with both environmental and genetic factors contributing to the phenotype. The prevalence of patellar luxation in the Dutch Flat-Coated Retriever population is 24%. In this study, we investigated the molecular genetics of the disorder in this population. Results: Genome-wide association analysis of 15,823 single nucleotide polymorphisms (SNPs) in 45 cases and 40 controls revealed that patellar luxation was significantly associated with a region on chromosome CFA07, and possibly with regions on CFA03, CFA31, and CFA36. The exons of the genes in these regions, 0.5 Mb combined, were analyzed further. These exons from 15 cases and a pooled sample from 15 controls were enriched using custom genomic hybridization arrays and analyzed by massive parallel DNA sequencing. In total 7257 variations were detected. Subsequently, a selection of 144 of these SNPs were genotyped in 95 Flat-Coated Retrievers. Nine SNPs, in eight genes on CFA07 and CFA31, were associated with patellar luxation (P

Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and post-transcriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We obtained peptide evidence for 26,463 rat liver proteins. We validated 1,195 gene predictions, 83 splice events, 126 proteins with nonsynonymous variants, and 20 isoforms with nonsynonymous RNA editing. Quantitative RNA sequencing and proteomics data correlate highly between strains but poorly among each other, indicating extensive nongenetic regulation. Our multilevel analysis identified a genomic variant in the promoter of the most differentially expressed gene Cyp17a1, a previously reported top hit in genome-wide association studies for human hypertension, as a potential contributor to the hypertension phenotype in SHR rats. These results demonstrate the power of and need for integrative analysis for understanding genetic control of molecular dynamics and phenotypic diversity in a system-wide manner.

Background Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. Here, we provide the structural and thermodynamic basis for the recognition of H3K36-methylated (H3K36me) nucleosomes by the PSIP1-PWWP domain, based on extensive mutational analysis, advanced nuclear magnetic resonance (NMR), and computational approaches. Results The PSIP1-PWWP domain binds H3K36me3 peptide and DNA with low affinity, through distinct, adjacent binding surfaces. PWWP binding to H3K36me nucleosomes is enhanced approximately 10,000-fold compared to a methylated peptide. Based on mutational analyses and NMR data, we derive a structure of the complex showing that the PWWP domain is bound to H3K36me nucleosomes through simultaneous interactions with both methylated histone tail and nucleosomal DNA. Conclusion Concerted binding to the methylated histone tail and nucleosomal DNA underlies the high- affinity, specific recognition of H3K36me nucleosomes by the PSIP1-PWWP domain. We propose that this bipartite binding mechanism is a distinctive and general property in the recognition of histone modifications close to the nucleosome core.

E2F transcription factors are known to be important for timely activation of G 1 /S and G 2 /M genes required for cell cycle progression, but transcriptional mechanisms for deactivation of cell cycle-regulated genes are unknown. Here, we show that E2F7 is highly expressed during mid to late S-phase, occupies promoters of G 1 /S-regulated genes and represses their transcription. ChIP-seq analysis revealed that E2F7 binds preferentially to genomic sites containing the TTCCCGCC motif, which closely resembles the E2F consensus site. We identified 89 target genes that carry E2F7 binding sites close to the transcriptional start site and that are directly repressed by short-term induction of E2F7. Most of these target genes are known to be activated by E2Fs and are involved in DNA replication, metabolism and DNA repair. Importantly, induction of E2F7 during G 0 -G 1 /S resulted in S-phase arrest and DNA damage, whereas expression of E2F7 during G 2 /M failed to disturb cell cycle progression. These findings provide strong evidence that E2F7 directly controls the downswing of oscillating G 1 /S genes during S-phase progression.

Technological advances in DNA sequencing techniques provide new resources and opportunities to study genetic contributions to disease. Still, it remains a challenge to determine which of the many detected genetic changes have an effect and through which mechanism they contribute to phenotypes and disease. This is especially challenging for structural variants, which are larger genomic changes that can affect both coding and non-coding regions on the genome. Cancer is a genetic disease with generally unstable genomes thereby continuing to accumulate somatic DNA changes including structural variants. In this thesis, we studied recurrent structural alterations in the aryl hydrocarbon receptor (AHR) gene that we identified in the whole-genome sequencing data of urinary tract cancer tumors. We propose activating alterations in the AHR gene as a driver event in urinary tract cancer. Furthermore, we studied the causative relationship between certain cancer driver genes and the accumulation of patterns of structural variants in various tumor types to gain insights into the molecular mechanisms of the development of SVs and their contribution to tumorigenesis. Structural variants are also present in the germline and although de novo SVs in the germline are a rare event, such structural variations are causative for congenital disorders such as intellectual disability and autism spectrum disorders. Integration of different layers of genomic and phenotypic information was found to provide additional benefit in determining the molecular consequences and interpreting pathogenicity of structural variations in patients with congenital disorders. Finally, we describe the discovery of inherited splice site mutations in the POLR3GL gene that cause teeth and bone abnormalities that fit in the spectrum of POLR3 pathologies and suggest that POLR3GL mutations should be considered in patients with POLR3 pathology.