72 research outputs found
A Dynamic Splicing Program Ensures Proper Synaptic Connections in the Developing Cerebellum
Tight coordination of gene expression in the developing cerebellum is crucial for establishment of neuronal circuits governing motor and cognitive function. However, transcriptional changes alone do not explain all of the switches underlying neuronal differentiation. Here we unveiled a widespread and highly dynamic splicing program that affects synaptic genes in cerebellar neurons. The motifs enriched in modulated exons implicated the splicing factor Sam68 as a regulator of this program. Sam68 controls splicing of exons with weak branchpoints by directly binding near the 3′ splice site and competing with U2AF recruitment. Ablation of Sam68 disrupts splicing regulation of synaptic genes associated with neurodevelopmental diseases and impairs synaptic connections and firing of Purkinje cells, resulting in motor coordination defects, ataxia, and abnormal social behavior. These findings uncover an unexpectedly dynamic splicing regulatory network that shapes the synapse in early life and establishes motor and cognitive circuitry in the developing cerebellum
A Dynamic Splicing Program Ensures Proper Synaptic Connections in the Developing Cerebellum
Tight coordination of gene expression in the developing cerebellum is crucial for establishment of neuronal circuits governing motor and cognitive function. However, transcriptional changes alone do not explain all of the switches underlying neuronal differentiation. Here we unveiled a widespread and highly dynamic splicing program that affects synaptic genes in cerebellar neurons. The motifs enriched in modulated exons implicated the splicing factor Sam68 as a regulator of this program. Sam68 controls splicing of exons with weak branchpoints by directly binding near the 3′ splice site and competing with U2AF recruitment. Ablation of Sam68 disrupts splicing regulation of synaptic genes associated with neurodevelopmental diseases and impairs synaptic connections and firing of Purkinje cells, resulting in motor coordination defects, ataxia, and abnormal social behavior. These findings uncover an unexpectedly dynamic splicing regulatory network that shapes the synapse in early life and establishes motor and cognitive circuitry in the developing cerebellum
Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways
Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also
between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles,
while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi
apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics
of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main
routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder
content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups
contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some
of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more
disordered (,23%) than the other two, COPI (,9%) and COPII (,8%). We show that this structural phenomenon enhances
the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other
two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its
prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest
capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific
functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for
protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of
structural disorder in vesicle trafficking and suggest major roles for this structural property in shaping the differences of
evolutionary adaptability in the three routes
The identification of short linear motif-mediated interfaces within the human interactome
Motivation: Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein–protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by short linear motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding motifs. However, these motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of motif instances
Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences
Extent of pre-translational regulation for the control of nucleocytoplasmic protein localization
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad
It has become clear in outline though not yet in detail how cellular regulatory and signalling systems are constructed. The essential machines are protein complexes that effect regulatory decisions by undergoing internal changes of state. Subcomponents of these cellular complexes are assembled into molecular switches. Many of these switches employ one or more short peptide motifs as toggles that can move between one or more sites within the switch system, the simplest being on-off switches. Paradoxically, these motif modules (termed short linear motifs or SLiMs) are both hugely abundant but difficult to research. So despite the many successes in identifying short regulatory protein motifs, it is thought that only the “tip of the iceberg” has been exposed. Experimental and bioinformatic motif discovery remain challenging and error prone. The advice presented in this article is aimed at helping researchers to uncover genuine protein motifs, whilst avoiding the pitfalls that lead to reports of false discovery. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12964-015-0121-y) contains supplementary material, which is available to authorized users
Machine Learning for Turbulence Model Development Using a High-Fidelity HPT Cascade Simulation
The validity of the Boussinesq approximation in the wake behind a high-pressure turbine blade is explored. We probe the mathematical assumptions of such a relationship by employing a least-squares technique. Next, we use an evolutionary algorithm to modify the anisotropy tensor a priori using highly resolved LES data. In the latter case we build a non-linear stress-strain relationship. Results show that the standard eddy-viscosity assumption underpredicts turbulent diffusion and is theoretically invalid. By increasing the coefficient of the linear term, the farwake prediction shows minor improvement. By using additional non-linear terms in the stress-strain coupling relationship, created by the evolutionary algorithm, the near-wake can also be improved upon. Terms created by the algorithm are scrutinized and the discussion is closed by suggesting a tentative non-linear expression for the Reynolds stress, suitable for the wake behind a high-pressure turbine blade
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