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Members of diverse protein families often perform overlapping or redundant functions meaning that different variations within them could reflect differences between individual organisms. We investigated likely functional positions within aligned protein families that contained a significant enrichment of nonsynonymous variants in genomes of healthy individuals. We identified more than a thousand enriched positions across hundreds of family alignments with roles indicative of mammalian individuality, including sensory perception and the immune system. The most significant position is the Arginine from the Olfactory receptor “DRY” motif, which has more variants in healthy individuals than all other positions in the proteome. Odorant binding data suggests that these variants lead to receptor inactivity, and they are mostly mutually exclusive with other loss-of-function (stop/frameshift) variants. Some DRY Arginine variants correlate with smell preferences in sub-populations and all 2,504 humans studied contain a unique spectrum of active and inactive receptors. The many other variant enriched positions, across hundreds of other families might also provide insights into individual differences.

The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/. This work was supported by the European Community’s Seventh Framework Programme [241955, 278568 to MU and KB, 602273 to RS]; the Virgo consortium, funded by the Dutch government [FES0908 to TvD, RvdL and MAH]; the Netherlands Genomics Initiative [050-060-452 to TvD, RvdL and MAH]; the Canadian Institutes of Health Research [MOP-142243, MOP-82870 and PJT-156042 to MRL]; Michael Smith Foundation for Health Research to MRL and VLJ; Kidney Research Scientist Core Education and National Training fellowship to VLJ; The Foundation Fighting Blindness [PPA-0717-0719-RAD to UW, RR, and MU]; the Dutch Kidney Foundation “KOUNCIL” consortium [CP11.18 to RHG, PLB and RR]; The Deutsche Forschungsgemeinschaft [Excellence grant CellNetworks to RBR and QL, CRC1140 “Kidney Disease – From Genes to Mechanisms” to MS, collaborative research center grant SFB-1411 KIDGEM to MS]; Metakids Foundation to RS; the National Institute for Health Research to PLB and VH-H. PLB is an NIHR Senior Investigator; Radboudumc Hypatia Tenure Track Fellowship, Radboud Universiteit excellence fellowship, ERC starting grant TREATCilia, grant agreement no. 716344 to MS; and the Netherlands Organization for Scientific Research [NWO Vici-865.12.005 to RR].

Although Burkitt lymphomas and follicular lymphomas both have features of germinal center B cells, they are biologically and clinically quite distinct. Here we performed whole-genome bisulfite, genome and transcriptome sequencing in 13 IG-MYC translocation-positive Burkitt lymphoma, nine BCL2 translocation-positive follicular lymphoma and four normal germinal center B cell samples. Comparison of Burkitt and follicular lymphoma samples showed differential methylation of intragenic regions that strongly correlated with expression of associated genes, for example, genes active in germinal center dark-zone and light-zone B cells. Integrative pathway analyses of regions differentially methylated in Burkitt and follicular lymphomas implicated DNA methylation as cooperating with somatic mutation of sphingosine phosphate signaling, as well as the TCF3-ID3 and SWI/SNF complexes, in a large fraction of Burkitt lymphomas. Taken together, our results demonstrate a tight connection between somatic mutation, DNA methylation and transcriptional control in key B cell pathways deregulated differentially in Burkitt lymphoma and other germinal center B cell lymphomas.

Martin Hasselblatt · Inga Nagel · Florian Oyen · Kerstin Bartelheim · Robert B. Russell · Ulrich Schuller · Reimar Junckerstorff · Marc Rosenblum · Ali H. Alassiri · Sabrina Rossi · Irene Schmid · Nicholas G. Gottardo · Helen Toledano · Elisabetta Viscardi · Milagros Balbin · Leora Witkowski · Qianhao Lu · Matthew J. Betts · William D. Foulkes · Reiner Siebert · Michael C. Fruhwald · Reinhard Schneppenheim

The best understanding of complex biological systems ultimately comes from details of the underlying atomic structures within it. In the absence of known structures of all protein complexes and interactions in a system, structural bioinformatics or modeling fill an important niche in providing predicted mechanistic information which can guide experiments, aid the interpretation of high-throughput datasets and help provide key details to model biological systems. This introductory review discusses the current state of this field and suggests how current datasets in systems studies can profit from a better integration of predicted or known structural information.

The Gene Ontology (GO) initiative is a collaborative effort that uses controlled vocabularies for annotating genetic information. We here present AGENDA (Application for mining Gene Ontology Data), a novel web-based tool for accessing the GO database. AGENDA allows the user to simultaneously retrieve and compare gene lists linked to different GO terms in diverse species using batch queries, facilitating comparative approaches to genetic information. The web-based application offers diverse search options and allows the user to bookmark, visualize, and download the results. AGENDA is an open source web-based application that is freely available for non-commercial use at the project homepage. URL: http://sourceforge.net/projects/bioagenda .

Objective Understanding the molecular and cellular mechanisms of ciliopathies is vital for dissecting their pathogenesis, identifying appropriate therapeutic targets and designing effective treatments. Recent advances in DNA sequencing technology have provided a torrent of genetic data that can now be used to elucidate the genetic basis of human diseases. A consensus has emerged among biologists that to fully exploit the available data, they have to be correlated with additional research. This is especially important for rare-disease genetics, because of the small number of available patients.

Objective Mutations in different ciliopathy-associated genes often result in overlapping clinical phenotypes, which can in part be explained by disruption of overlapping functional protein modules. In this study we conducted large-scale affinity proteomics in a systems biologybased approach to boost insights into the assembly of these ciliary modules, and their connectivity in larger functional protein networks: the ciliary protein interaction landscape. This provides an important framework to deconvolute the pathways and processes that drive ciliopathies, and to understand the general importance of ciliary function for cellular homeostasis.

Objective: The assembly of protein interaction networks (PIN) is an important step to understand the biological function of proteins. Affinity purification coupled to mass spectrometry (AP-MS) has become the technique of choice for the assembly and analysis of PINs. However, most current studies, especially in human cells, are focused on specific biological systems (e.g. the cilium) resulting in datasets of a small to intermediate scale. In such cases, methods that developed for genome-scale datasets are of limited utility. We propose here a framework that is specifically designed for the analysis of incomplete proteomic data focused on ciliary function and ciliopathies.

Systematic interrogation of mutation or protein modification data is important to identify sites with functional consequences and to deduce global consequences from large data sets. Mechismo (mechismo.russellab.org) enables simultaneous consideration of thousands of 3D structures and biomolecular interactions to predict rapidly mechanistic consequences for mutations and modifications. As useful functional information often only comes from homologous proteins, we benchmarked the accuracy of predictions as a function of protein/structure sequence similarity, which permits the use of relatively weak sequence similarities with an appropriate confidence measure. For protein–protein, protein–nucleic acid and a subset of protein–chemical interactions, we also developed and benchmarked a measure of whether modifications are likely to enhance or diminish the interactions, which can assist the detection of modifications with specific effects. Analysis of high-throughput sequencing data shows that the approach can identify interesting differences between cancers, and application to proteomics data finds potential mechanistic insights for how post-translational modifications can alter biomolecular interactions.

The phylogenetic distribution and sequence conservation of KIAA0556 orthologs in eukaryotes. Presence and sequence conservation of KIAA0556 are projected on the eukaryotic species tree to visualise the phylogenetic distribution of KIAA0556 orthologues as well as the distribution of the triple-repeat and quadruple-repeat configurations of the DUF4457 domains of unknown function. The black circles and white circles indicate which eukaryotic species contain or lack cilia/flagella. Recent KIAA0556 duplicates in Branchiostoma floridae and Paramecium tetraurelia are denoted by x2. *Dictyostelium discoideum protein sequence contains many â Nâ s (uncalled bases) in the N-terminal part of the sequence, indicative of sequencing errors. As a result we are unable to identify whether this region is indeed homologous to the human KIAA0556 N-terminus. Boxed schematic at bottom shows examples of C. elegans and human KIAA0556 with three and four repeat domains, respectively. (PDF 283 kb)

The phylogenetic distribution and sequence conservation of KIAA0556 orthologs in eukaryotes. Presence and sequence conservation of KIAA0556 are projected on the eukaryotic species tree to visualise the phylogenetic distribution of KIAA0556 orthologues as well as the distribution of the triple-repeat and quadruple-repeat configurations of the DUF4457 domains of unknown function. The black circles and white circles indicate which eukaryotic species contain or lack cilia/flagella. Recent KIAA0556 duplicates in Branchiostoma floridae and Paramecium tetraurelia are denoted by x2. *Dictyostelium discoideum protein sequence contains many â Nâ s (uncalled bases) in the N-terminal part of the sequence, indicative of sequencing errors. As a result we are unable to identify whether this region is indeed homologous to the human KIAA0556 N-terminus. Boxed schematic at bottom shows examples of C. elegans and human KIAA0556 with three and four repeat domains, respectively. (PDF 283 kb)