Pumilio1 haploinsufficiency leads to SCA1-like neurodegeneration by increasing wild-type Ataxin1 levels.

Spinocerebellar ataxia type 1 (SCA1) is a paradigmatic neurodegenerative proteinopathy, in which a mutant protein (in this case, ATAXIN1) accumulates in neurons and exerts toxicity; in SCA1, this process causes progressive deterioration of motor coordination. Seeking to understand how post-translational modification of ATAXIN1 levels influences disease, we discovered that the RNA-binding protein PUMILIO1 (PUM1) not only directly regulates ATAXIN1 but also plays an unexpectedly important role in neuronal function. Loss of Pum1 caused progressive motor dysfunction and SCA1-like neurodegeneration with motor impairment, primarily by increasing Ataxin1 levels. Breeding Pum1(+/-) mice to SCA1 mice (Atxn1(154Q/+)) exacerbated disease progression, whereas breeding them to Atxn1(+/-) mice normalized Ataxin1 levels and largely rescued the Pum1(+/-) phenotype. Thus, both increased wild-type ATAXIN1 levels and PUM1 haploinsufficiency could contribute to human neurodegeneration. These results demonstrate the importance of studying post-transcriptional regulation of disease-driving proteins to reveal factors underlying neurodegenerative disease.

The roles of RNA processing in translating genotype to phenotype.

A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.

A Therapeutic Double Whammy: Transcriptional or Post-transcriptional Suppression of Microsatellite Repeat Toxicity by Cas9.

Microsatellite expansion diseases are caused by unstable tandem repeats of 3-10 nucleotides that become pathogenic beyond a threshold number of copies. Two groups present different approaches to reduce pathogenesis by targeting deactivated Cas9 to either the DNA (Pinto et al., 2017) or the RNA (Batra et al., 2017) repeats with therapeutic potential for several diseases.

Alternative splicing mediates the compensatory upregulation of MBNL2 upon MBNL1 loss-of-function.

Loss of gene function can be compensated by paralogs with redundant functions. An example of such compensation are the paralogs of the Muscleblind-Like (MBNL) family of RNA-binding proteins that are sequestered and lose their function in Myotonic Dystrophy Type 1 (DM1). Loss of MBNL1 increases the levels of its paralog MBNL2 in tissues where Mbnl2 expression is low, allowing MBNL2 to functionally compensate for MBNL1 loss. Here, we show that loss of MBNL1 increases the inclusion of Mbnl2 exon 6 and exon 9. We find that inclusion of Mbnl2 exon 6 increases the translocation of MBNL2 to the nucleus, while the inclusion of Mbnl2 exon 9 shifts the reading frame to an alternative C-terminus. We show that the C-terminus lacking exon 9 contains a PEST domain which causes proteasomal degradation. Loss of MBNL1 increases the inclusion of exon 9, resulting in an alternative C-terminus lacking the PEST domain and the increase of MBNL2. We further find that the compensatory mechanism is active in a mouse DM1 model. Together, this study uncovers the compensatory mechanism by which loss of MBNL1 upregulates its paralog MBNL2 and highlights a potential role of the compensatory mechanism in DM1.

RNA and disease.

Cellular functions depend on numerous protein-coding and noncoding RNAs and the RNA-binding proteins associated with them, which form ribonucleoprotein complexes (RNPs). Mutations that disrupt either the RNA or protein components of RNPs or the factors required for their assembly can be deleterious. Alternative splicing provides cells with an exquisite capacity to fine-tune their transcriptome and proteome in response to cues. Splicing depends on a complex code, numerous RNA-binding proteins, and an enormously intricate network of interactions among them, increasing the opportunity for exposure to mutations and misregulation that cause disease. The discovery of disease-causing mutations in RNAs is yielding a wealth of new therapeutic targets, and the growing understanding of RNA biology and chemistry is providing new RNA-based tools for developing therapeutics.

Non-canonical RAN Translation of CGG Repeats Has Canonical Requirements.

Repeat expansions cause dominantly inherited neurological disorders. In this issue of Molecular Cell, Kearse et al. (2016) examine the requirements for RAN translation of the CGG repeats that cause fragile X-associated tremor/ataxia syndrome, revealing similarities and differences with canonical translation.

Are Magnetic Resonance Imaging-Generated 3Dimensional Models Comparable to Computed Tomography-Generated 3Dimensional Models for Orbital Fracture Reconstruction? An In-Vitro Volumetric Analysis.

BACKGROUND: Magnetic resonance imaging (MRI) is being increasingly considered as an alternative for the evaluation and reconstruction of orbital fractures. No previous research has compared the orbital volume of an MRI-imaged, three-dimensional (3D), reconstructed, and virtually restored bony orbit to the gold standard of computed tomography (CT). PURPOSE: To measure the orbital volumes generated from MRI-based 3D models of fractured bony orbits with virtually positioned prebent fan plates in situ and compare them to the volumes of CT-based virtually reconstructed orbital models. STUDY DESIGN: This retrospective in-vitro study used CT and MRI data from adult patients with orbital trauma assessed at the Royal Brisbane and Women's Hospital Outpatient Maxillofacial Clinic from 2011 to 2012. Only those with orbital blowout fractures were included in the study. PREDICTOR VARIABLE: The primary predictor variable was imaging modality, with CT- and MRI-based 3D models used for plate bending and placement. MAIN OUTCOME VARIABLE: The primary outcome variable was the orbital volume of the enclosed 3D models. COVARIATES: Additional data collected was age, sex, and side of fractured orbit. The effect of operator variability on plate contouring and orbital volume was quantified. ANALYSES: The Wilcoxon signed rank test was used to assess differences between orbital volumes with a significance level P < .05. RESULTS: Of 11 eligible participants, six patients (four male and two female; mean age 31 ± 8.6 years) were enrolled. Two sets of six CT-based virtually restored orbits were smaller than the intact contralateral CT models by an average of 1.02 cm3 (95% CI -0.07 to 2.11 cm3; P = .028) and 0.99 cm3 (95% CI 0.07 to 1.91 cm3; P = .028), respectively. The average volume difference between the MRI-based virtually restored orbit and the intact contralateral MRI model was 0.97 cm3 (95% CI -1.08 to 1.94 cm3; P = .75). Imaging modality did affect orbital volume difference for 1 set of CT and MRI models (0.63 cm3; 95% CI -0.11 to 1.29 cm3; P = .046) but not the other (0.69 cm3; 95% CI -0.11 to 1.23 cm3; P = .075). Single operator variability in plate bending did not result in significant (P = .75) volume differences. CONCLUSIONS: MRI can be used to reconstruct orbital volume with a clinically acceptable level of accuracy.

Insights into Cell-Specific Functions of Microtubules in Skeletal Muscle Development and Homeostasis.

The contractile cells of skeletal muscles, called myofibers, are elongated multinucleated syncytia formed and maintained by the fusion of proliferative myoblasts. Human myofibers can be hundreds of microns in diameter and millimeters in length. Myofibers are non-mitotic, obviating the need for microtubules in cell division. However, microtubules have been adapted to the unique needs of these cells and are critical for myofiber development and function. Microtubules in mature myofibers are highly dynamic, and studies in several experimental systems have demonstrated the requirements for microtubules in the unique features of muscle biology including myoblast fusion, peripheral localization of nuclei, assembly of the sarcomere, transport and signaling. Microtubule-binding proteins have also been adapted to the needs of the skeletal muscle including the expression of skeletal muscle-specific protein isoforms generated by alternative splicing. Here, we will outline the different roles microtubules play in skeletal muscle cells, describe how microtubule abnormalities can lead to muscle disease and discuss the broader implications for microtubule function.

Increased nuclear but not cytoplasmic activities of CELF1 protein leads to muscle wasting.

mRNA processing is highly regulated during development through changes in RNA-binding protein (RBP) activities. CUG-BP, Elav-like family member 1 (CELF1, also called CUGBP1) is an RBP, the expression of which decreases in skeletal muscle soon after birth. CELF1 regulates multiple nuclear and cytoplasmic RNA processing events. In the nucleus, CELF1 regulates networks of postnatal alternative splicing (AS) transitions, while in the cytoplasm, CELF1 regulates mRNA stability and translation. Stabilization and misregulation of CELF1 has been implicated in human diseases including myotonic dystrophy type 1, Alzheimer's disease and multiple cancers. To understand the contribution of nuclear and cytoplasmic CELF1 activity to normal and pathogenic skeletal muscle biology, we generated transgenic mice for doxycycline-inducible and skeletal muscle-specific expression of active CELF1 mutants engineered to be localized predominantly to either the nucleus or the cytoplasm. Adult mice expressing nuclear, but not cytoplasmic, CELF1 are characterized by strong histopathological defects, muscle loss within 10 days and changes in AS. In contrast, mice expressing cytoplasmic CELF1 display changes in protein levels of targets known to be regulated at the level of translation by CELF1, with minimal changes in AS. These changes are in the absence of overt histopathological changes or muscle loss. RNA-sequencing revealed extensive gene expression and AS changes in mice overexpressing nuclear and naturally localized CELF1 protein, with affected genes involved in cytoskeleton dynamics, membrane dynamics, RNA processing and zinc ion binding. These results support a stronger role for nuclear CELF1 functions as compared to cytoplasmic CELF1 functions in skeletal muscle wasting.

Toward a best-form CPC-like nonimaging optical concentrator.

We present near-ideal axisymmetric numerically optimized spline concentrators (OSCs) which outperform the compound parabolic concentrator (CPC). By perturbing the profile of the revolved CPC by a variable-offset spline defined in tangent-normal space, we show that ray rejection can be reduced to nearly half of that of the CPC, without increasing concentrator length. The resulting OSCs achieve acceptance efficiencies as high as 99.3% for an acceptance angle of 45°, the highest reported for any finite-length CPC-like light concentrator. A set of design curves is presented which can be used to generate near "best-form" OSCs for any acceptance angle in the range 10° to 45°.

Photophysical and Electrochemical Properties of Push-Pull Oligo(ferrocenyl-phenyleneethynylene)s: Supramolecular Orders in Molecular Films.

We report on the optoelectronic properties of a series of unsymmetrical π-conjugated phenyleneethynylene macromolecules bearing ferrocene (Fc) as the electron-donor group (D), (benzyl) benzoate (Bz) or benzoic acid (Ac) as the electron attractor group (A) and connected through 2,5-di(alcoxy) phenyleneethynylene(s) (nPE) with n = 1, 2, 3 as π-conjugated bridges. In the series, by increasing the distance between the electron-attracting and electron-donor groups, the push-pull effect decreases. The intramolecular charge transfer (D → π → A) was evaluated by static and dynamic spectroscopy, electrochemistry, and density functional theory (DFT) theoretical calculations. The longest oligomer Fc3PEBz formed the best optical quality films. A study at the atomic level by scanning tunneling microscopy (STM) revealed that the molecules self-assemble on highly ordered pyrolytic graphite (HOPG) in domains with a short-range order. Films are mesoporous and the molecules arrange in a lamellar-like pattern, with an edge-on conformation with respect to HOPG, where the conjugated backbones lie parallel to the surface. Two different assemblies were identified in the monoatomic film, which depends on the ferrocene-ferrocene or benzyl-benzyl interactions.

Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.

Alternative splicing plays important regulatory roles during periods of physiological change. During development, a large number of genes coordinately express protein isoform transitions regulated by alternative splicing; however, the mechanisms that coordinate splicing and the functional integration of the resultant tissue-specific protein isoforms are typically unknown. Here we show that the conserved Rbfox2 RNA binding protein regulates 30% of the splicing transitions observed during myogenesis and is required for the specific step of myoblast fusion. Integration of Rbfox2-dependent splicing outcomes from RNA-seq with Rbfox2 iCLIP data identified Mef2d and Rock2 as Rbfox2 splicing targets. Restored activities of Mef2d and Rock2 rescued myoblast fusion in Rbfox2-depleted cultures, demonstrating functional cooperation of protein isoforms generated by coordinated alterative splicing. The results demonstrate that coordinated alternative splicing by a single RNA binding protein modulates transcription (Mef2d) and cell signaling (Rock2) programs to drive tissue-specific functions (cell fusion) to promote a developmental transition.

Clinical and Molecular Insights into Gastrointestinal Dysfunction in Myotonic Dystrophy Types 1 & 2.

Myotonic dystrophy (DM) is a highly variable, multisystemic disorder that clinically affects one in 8000 individuals. While research has predominantly focused on the symptoms and pathological mechanisms affecting striated muscle and brain, DM patient surveys have identified a high prevalence for gastrointestinal (GI) symptoms amongst affected individuals. Clinical studies have identified chronic and progressive dysfunction of the esophagus, stomach, liver and gallbladder, small and large intestine, and rectum and anal sphincters. Despite the high incidence of GI dysmotility in DM, little is known regarding the pathological mechanisms leading to GI dysfunction. In this review, we summarize results from clinical and molecular analyses of GI dysfunction in both genetic forms of DM, DM type 1 (DM1) and DM type 2 (DM2). Based on current knowledge of DM primary pathological mechanisms in other affected tissues and GI tissue studies, we suggest that misregulation of alternative splicing in smooth muscle resulting from the dysregulation of RNA binding proteins muscleblind-like and CUGBP-elav-like is likely to contribute to GI dysfunction in DM. We propose that a combinatorial approach using clinical and molecular analysis of DM GI tissues and model organisms that recapitulate DM GI manifestations will provide important insight into defects impacting DM GI motility.

Expectations and experiences of practising veterinarians throughout an 8-week mindfulness-based stress reduction programme.

AIMS: To explore practising veterinarians' expectations of an 8-week mindfulness training programme, their perceived barriers to participating in the programme, their experiences of the programme and the extent to which they continued to engage in mindfulness practices following training. METHODS: Participants were 10 companion animal veterinarians practising in Auckland, New Zealand. All took part in an 8-week mindfulness-based training programme. A longitudinal qualitative design was used: data were collected by structured interviews prior to the programme, upon completion of the programme and 3 months after completion. Data were analysed using thematic analysis to identify recurring themes, or patterns, within the data. RESULTS: Before commencing the programme, participants generally thought mindfulness training would provide some benefits for wellbeing but were otherwise not clear on what to expect. The main concerns about taking part were time constraints and apprehensions about potentially having to share personal information, and consequently how they might be perceived by other participants. On completion of the training programme, the opportunity to share experiences within the group with the support of a trained facilitator was reported as the most valuable aspect of the programme, rather than the mindfulness practices themselves. At the 3-month follow-up, participants reported they had learnt some useful techniques for managing stressful thoughts and situations, but despite the perceived benefits, few were still practicing mindfulness techniques. CONCLUSIONS AND CLINICAL RELEVANCE: Training in mindfulness practices may have some value for helping practicing veterinarians manage their wellbeing, but it is not a complete solution in itself. Participants reported that the greatest benefits came from facilitated peer support.

Transcriptome alterations in myotonic dystrophy skeletal muscle and heart.

Myotonic dystrophy (dystrophia myotonica, DM) is a multi-systemic disease caused by expanded CTG or CCTG microsatellite repeats. Characterized by symptoms in muscle, heart and central nervous system, among others, it is one of the most variable diseases known. A major pathogenic event in DM is the sequestration of muscleblind-like proteins by CUG or CCUG repeat-containing RNAs transcribed from expanded repeats, and differences in the extent of MBNL sequestration dependent on repeat length and expression level may account for some portion of the variability. However, many other cellular pathways are reported to be perturbed in DM, and the severity of specific disease symptoms varies among individuals. To help understand this variability and facilitate research into DM, we generated 120 RNASeq transcriptomes from skeletal and heart muscle derived from healthy and DM1 biopsies and autopsies. A limited number of DM2 and Duchenne muscular dystrophy samples were also sequenced. We analyzed splicing and gene expression, identified tissue-specific changes in RNA processing and uncovered transcriptome changes strongly correlating with muscle strength. We created a web resource at http://DMseq.org that hosts raw and processed transcriptome data and provides a lightweight, responsive interface that enables browsing of processed data across the genome.

Correction: Impaired Mitochondrial Energy Production Causes Light-Induced Photoreceptor Degeneration Independent of Oxidative Stress.

[This corrects the article DOI: 10.1371/journal.pbio.1002197.].

Zn Coordination and the Identity of the Halide Ancillary Ligand Dramatically Influence the Excited-State Dynamics and Bimolecular Reactions of 2,3-Di(pyridin-2-yl)benzo[g]quinoxaline.

The optical properties of coordination complexes with ligands containing nitrogen heterocycles have been extensively studied for decades. One subclass of these materials, metal complexes utilizing substituted pyrazines and quinoxalines as ligands, has been employed in a variety of photochemical applications ranging from photodynamic therapy to organic light-emitting diodes. A vast majority of this work focuses on characterization of the metal-to-ligand charge-transfer states in these metal complexes; however, literature reports rarely investigate the photophysics of the parent pyrazine or quinoxaline ligand or perform control experiments utilizing metal complexes that lack low-lying charge-transfer (CT) states in order to determine how metal-atom coordination influences the photophysical properties of the ligand. With this in mind, we examined the steady-state and time-resolved photophysics of 2,3-di(pyridin-2-yl)benzo[g]quinoxaline (dpb) and explored how the coordination of ZnX2 (X = Cl-, Br-, I-) affects the photophysical properties of dpb. In dpb, we find that the dominant mode of deactivation from the singlet excited state is intersystem crossing (ISC). Coordination of ZnX2 perturbs the relative energies of the ππ* and nπ* excited states of dpb, leading to drastically different rates of ISC as well as radiative and nonradiative decay in the [Zn(dpb)X2] complexes compared to dpb. These differences in the rates change the dominant singlet-excited-state decay pathway from ISC in dpb to a mixture of ISC and fluorescence in [Zn(dpb)Cl2] and [Zn(dpb)Br2] and to nonradiative decay in [Zn(dpb)I2]. Coordination of ZnX2 and the choice of the halide ligand also have profound effects on the rate constants for excited-state bimolecular reactions, including triplet-triplet annihilation and oxygen quenching. These results demonstrate that metal coordination, even in complexes lacking low-lying CT states, and the choice of the ancillary ligand can dramatically alter the photophysical properties of chromophores containing nitrogen heterocycles.

Impact of iodine loading and substitution position on intersystem crossing efficiency in a series of ten methylated-meso-phenyl-BODIPY dyes.

Four core and six distyryl-extended methylated-meso-phenyl-BODIPY dyes with varying iodine content were synthesized. The influence of iodine loading and substitution position on the photophysical properties of these chromophores was evaluated. Selective iodine insertion at the 2- and 6-positions of the methylated-meso-phenyl-BODIPY core, rather than maximum iodine content, resulted in the highest intersystem crossing efficiency. Iodination of the distyryl-extended BODIPY core afforded intersystem crossing quantum yields comparable to 2,6-diiodo-BODIPY. Inclusion of an iodine at the para-meso-phenyl position generally enhanced non-radiative decay in the BODIPY excited-state, leading to lower fluorescence and intersystem crossing quantum yield values. Iodine substitution at the styryl-positions resulted in negligible changes to the excited-state dynamics. This study highlights: (1) the rate of radiative decay is similar in all ten derivatives (on the order of 1 × 108 s-1), (2) iodination of the 2,6-positions results in the greatest enhancement of intersystem crossing efficiency, (3) care must be taken when modifying the para-meso-phenyl position as it could have detrimental effects on the excited-state dynamics, (4) the excited-state is negligibly affected by iodination of the styryl groups, potentially enabling orthogonal functionalization without modifying the molecular photophysics, (5) distyryl extension of the chromophore core diminishes rates of non-radiative decay and intersystem crossing, resulting in higher fluorescence quantum yields and lower intersystem crossing yields in the π-extended derivatives compared to the core BDP derivatives, and (6) DFT calculations provide insight into the electronic and structural factors regulating intersystem crossing and vibrational relaxation in these molecules.

The spliceosome is a therapeutic vulnerability in MYC-driven cancer.

MYC (also known as c-MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. MYC is a transcription factor, and many of its pro-tumorigenic functions have been attributed to its ability to regulate gene expression programs. Notably, oncogenic MYC activation has also been shown to increase total RNA and protein production in many tissue and disease contexts. While such increases in RNA and protein production may endow cancer cells with pro-tumour hallmarks, this increase in synthesis may also generate new or heightened burden on MYC-driven cancer cells to process these macromolecules properly. Here we discover that the spliceosome is a new target of oncogenic stress in MYC-driven cancers. We identify BUD31 as a MYC-synthetic lethal gene in human mammary epithelial cells, and demonstrate that BUD31 is a component of the core spliceosome required for its assembly and catalytic activity. Core spliceosomal factors (such as SF3B1 and U2AF1) associated with BUD31 are also required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces an increase in total precursor messenger RNA synthesis, suggesting an increased burden on the core spliceosome to process pre-mRNA. In contrast to normal cells, partial inhibition of the spliceosome in MYC-hyperactivated cells leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of many essential cell processes. Notably, genetic or pharmacological inhibition of the spliceosome in vivo impairs survival, tumorigenicity and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing, and that components of the spliceosome may be therapeutic entry points for aggressive MYC-driven cancers.

Alu insertion variants alter mRNA splicing.

RNA splicing is a highly regulated process dependent on sequences near splice sites. Insertions of Alu retrotransposons can disrupt splice sites or bind splicing regulators. We hypothesized that some common inherited polymorphic Alu insertions are responsible for splicing QTLs (sQTL). We focused on intronic Alu variants mapping within 100 bp of an alternatively used exon and screened for those that alter splicing. We identify five loci, 21.7% of those assayed, where the polymorphic Alu alters splicing. While in most cases the Alu promotes exon skipping, at one locus the Alu increases exon inclusion. Of particular interest is an Alu polymorphism in the CD58 gene. Reduced CD58 expression is associated with risk for developing multiple sclerosis. We show that the Alu insertion promotes skipping of CD58 exon 3 and results in a frameshifted transcript, indicating that the Alu may be the causative variant for increased MS risk at this locus. Using RT-PCR analysis at the endogenous locus, we confirm that the Alu variant is a sQTL for CD58. In summary, altered splicing efficiency is a common functional consequence of Alu polymorphisms including at least one instance where the variant is implicated in disease risk. This work broadens our understanding of splicing regulatory sequences around exons.