Figure 1. Structured domains and intrinsically disordered regions (IDRs) are two fundamental classes of functional building blocks of proteins. The synergy between disordered regions and structured domains increases the functional versatility of proteins. Adapted with permission from ref 50.

SummaryMutations in whole organisms are powerful ways of interrogating gene function in a realistic context. We describe a program, the Sanger Institute Mouse Genetics Project, that provides a step toward the aim of knocking out all genes and screening each line for a broad range of traits. We found that hitherto unpublished genes were as likely to reveal phenotypes as known genes, suggesting that novel genes represent a rich resource for investigating the molecular basis of disease. We found many unexpected phenotypes detected only because we screened for them, emphasizing the value of screening all mutants for a wide range of traits. Haploinsufficiency and pleiotropy were both surprisingly common. Forty-two percent of genes were essential for viability, and these were less likely to have a paralog and more likely to contribute to a protein complex than other genes. Phenotypic data and more than 900 mutants are openly available for further analysis.PaperClip

SummaryAlternative inclusion of exons increases the functional diversity of proteins. Among alternatively spliced exons, tissue-specific exons play a critical role in maintaining tissue identity. This raises the question of how tissue-specific protein-coding exons influence protein function. Here we investigate the structural, functional, interaction, and evolutionary properties of constitutive, tissue-specific, and other alternative exons in human. We find that tissue-specific protein segments often contain disordered regions, are enriched in posttranslational modification sites, and frequently embed conserved binding motifs. Furthermore, genes containing tissue-specific exons tend to occupy central positions in interaction networks and display distinct interaction partners in the respective tissues, and are enriched in signaling, development, and disease genes. Based on these findings, we propose that tissue-specific inclusion of disordered segments that contain binding motifs rewires interaction networks and signaling pathways. In this way, tissue-specific splicing may contribute to functional versatility of proteins and increases the diversity of interaction networks across tissues.

Nucleophosmin (NPM1) is a multifunctional phospho-protein with critical roles in ribosome biogenesis, tumor suppression, and nucleolar stress response. Here we show that the N-terminal oligomerization domain of NPM1 (Npm-N) exhibits structural polymorphism by populating conformational states ranging from a highly ordered, folded pentamer to a highly disordered monomer. The monomerpentamer equilibrium is modulated by posttranslational modification and protein binding. Phosphorylation drives the equilibrium in favor of monomeric forms, and this effect can be reversed by Npm-N binding to its interaction partners. We have identified a short, arginine-rich linear motif in NPM1 binding partners that mediates Npm-N oligomerization. We propose that the diverse functional repertoire associated with NPM1 is controlled through a regulated unfolding mechanism signaled through posttranslational modifications and intermolecular interactions.NMR | X-ray crystallography N ucleophosmin (NPM1) is a highly abundant nucleolar phosphoprotein with functions associated with ribosome biogenesis (1, 2), maintenance of genome stability (1), nucleolar stress response (3), modulation of the p53 tumor suppressor pathway (4), and regulation of apoptosis (5). Importantly, genetic alterations that affect the NPM1 protein sequence or expression level are associated with oncogenesis. For example, NPM1 overexpression was observed in a variety of solid tumors, and mutations within the protein and genetic translocations involving NPM1 are associated with hematological malignancies (reviewed in ref. 6).NPM1 primarily resides in the nucleolus which is a membraneless compartment and the site of rRNA synthesis, processing, and assembly with ribosomal proteins (7). In the nucleolus, NPM1 is involved in processing preribosomal RNA (4), chaperoning the nucleolar entry of ribosomal (1, 8) and viral (9) proteins, and stabilizing the alternate reading frame (ARF) tumor suppressor protein (4, 5, 10, 11), while also playing a role in the shuttling of preribosomal particles assembled in the nucleolus to the cytoplasm (12-14).NPM1 is a member of the nucleoplasmin protein family, which includes the histone chaperones NPM2 and NPM3. These proteins share a conserved N-terminal oligomerization domain that mediates homopentamerization (15). Disruption of NPM1 oligomerization by a small molecule (16) or an RNA aptamer (17) causes exclusive nucleoplasmic localization, loss of colocalization with ARF, and induction of p53-dependent apoptosis (16, 17). These observations suggest that changes in the oligomeric state of NPM1 may influence its biological functions. However, although it is hypothesized (1) that NPM1 function is modulated through control of its oligomeric state, experimental data are currently lacking. Intriguingly, NPM1 exhibits 40 putative phosphorylation sites, the majority of which are evolutionarily conserved (18,19). Modification of these sites that is influenced by subcellular localization and cell cycle phase (20, 21) modulates the biological function...