Les Houches 2015: Physics at TeV Colliders Standard Model Working Group Report

This Report summarizes the proceedings of the 2015 Les Houches workshop on Physics at TeV Colliders. Session 1 dealt with (I) new developments relevant for high precision Standard Model calculations, (II) the new PDF4LHC parton distributions, (III) issues in the theoretical description of the production of Standard Model Higgs bosons and how to relate experimental measurements, (IV) a host of phenomenological studies essential for comparing LHC data from Run I with theoretical predictions and projections for future measurements in Run II, and (V) new developments in Monte Carlo event generators.Comment: Proceedings of the Standard Model Working Group of the 2015 Les Houches Workshop, Physics at TeV Colliders, Les Houches 1-19 June 2015. 227 page

PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5\ub4-splice-site selection causing tissue-specific defects

\ua9 The Author(s) 2024.The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926 A > C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5’-splice site (5’SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5’SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches

The role of cis-acting sequences in the regulation of α-tropomyosin alternative splicing

The main investigation was a study of the possible role of a zero length exon (ZLE) observed 234 nucleotides downstream of exon 3, in α-TM splicing. The ZLE overlaps with the DRE, and consists of potential branchpoints, a polypyrimidine tract and a 3’ splice site (3’ss) GAG, followed immediately by a 5’ splice site (5’ss). In addition, a pseudo 5’ss is located 107 nucleotides downstream of the 3’ss. All of these sequences are conserved between rat mouse and human α-TM genes. While the initial aim was to study the role of the ZLE, results from this study suggest that the ZLE is part of a 107 nucleotide pseudoexon, formed by the ZLE 3’ss and the downstream pseudo 5’ss. RT-PCR analysis of RNA from various rat tissues allowed identification of splicing intermediates involving the 3’ss of the pseudoexon and exons 2 or 3. Transfection studies showed that activation of the ZLE 3’ss or repression of the ZLE 5’ss resulted in inclusion of the pseudoexon, together with exon 3. Blocking the ZLE in the endogenous gene using an anti-sense approach resulted in an increase in levels of exon 2 products. Exon 3 transcripts including the pseudoexon contain a premature termination codon, and therefore, are expected to be degraded by nonsense mediated decay. This may represent a mechanism of negative regulation of α-TM exon 3. In a study of the optimum distance required between the branch point and the 3’ splice site in the α-TM system, inhibition of splicing of an alternative exon may require sub-optimal recognition of some key sequences, creating a capacity for regulation. The typical distance between the branchpoint and 3’ss AG is 18-40 nucleotides. In α-TM exons 2 and 3, this distance is unusually long. The resulting sub-optimal recognition of the polypyrimidine tract by U2AF, may be essential to allow competing regulatory factors to bind.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

A bending rigidity parameter for stress granule condensates

Interfacial tension plays an important role in governing the dynamics of droplet coalescence and determining how condensates interact with and deform lipid membranes and biological filaments. We demonstrate that an interfacial tension-only model is inadequate for describing stress granules in live cells. Harnessing a high-throughput flicker spectroscopy pipeline to analyze the shape fluctuations of tens of thousands of stress granules, we find that the measured fluctuation spectra require an additional contribution, which we attribute to elastic bending deformation. We also show that stress granules have an irregular, nonspherical base shape. These results suggest that stress granules are viscoelastic droplets with a structured interface, rather than simple Newtonian liquids. Furthermore, we observe that the measured interfacial tensions and bending rigidities span a range of several orders of magnitude. Hence, different types of stress granules (and more generally, other biomolecular condensates) can only be differentiated via large-scale surveys

MERISTEM-DEFECTIVE regulates the balance between stemness and differentiation in the root meristem through RNA splicing control

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of gene regulation is RNA alternative splicing. However, the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF) Arabidopsis gene encodes an SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast Snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and to repress stress response, cell differentiation and cell death pathways