Mechanisms of Drosophila Dscam mutually exclusive splicing regulation

2012 ◽  
Vol 40 (4) ◽  
pp. 804-809 ◽  
Author(s):  
Yash Hemani ◽  
Matthias Soller
Keyword(s):  
Nervous System ◽  
Cell Adhesion Molecule ◽  
Molecular Diversity ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Splicing Regulation ◽  
Protein Diversity ◽  
Major Mechanism ◽  
Variable Exon ◽  
Higher Eukaryotes

Alternative splicing of pre-mRNA is a major mechanism to increase protein diversity in higher eukaryotes. Dscam, the Drosophila homologue of human DSCAM (Down's syndrome cell adhesion molecule), generates up to 38016 isoforms through mutually exclusive splicing in four variable exon clusters. This enormous molecular diversity is functionally important for wiring of the nervous system and phagocytosis of invading pathogens. Current models explaining this complex splicing regulation include a default repressed state of the variable exon clusters to prevent the splicing together of adjacent exons, the presence of RNA secondary structures important for the release of one specific variable exon from the repressed state and combinatorial interaction of RNA-binding proteins for choosing a specific exon.

Dorsal-ventral patterning and differentiation of noggin-induced neural tissue in the absence of mesoderm

Development ◽  
1995 ◽  
Vol 121 (6) ◽  
pp. 1927-1935 ◽  
Author(s):  
A.K. Knecht ◽  
P.J. Good ◽  
I.B. Dawid ◽  
R.M. Harland
Keyword(s):  
Nervous System ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Neural Tissue ◽  
Expression Domain ◽  
Xenopus Development ◽  
Dorsal Mesoderm

In Xenopus development, dorsal mesoderm is thought to play a key role in both induction and patterning of the nervous system. Previously, we identified a secreted factor, noggin, which is expressed in dorsal mesoderm and which can mimic that tissue's neural-inducing activity, without inducing mesoderm. Here the neural tissue induced in ectodermal explants by noggin is further characterized using four neural-specific genes: two putative RNA-binding proteins, nrp-1 and etr-1; the synaptobrevin sybII; and the lipocalin cpl-1. First we determine the expression domain of each gene during embryogenesis. Then we analyze expression of these genes in noggin-treated explants. All markers, including the differentiated marker sybII, are expressed in noggin-induced neural tissue. Furthermore, cpl-1, a marker of dorsal brain, and etr-1, a marker absent in much of the dorsal forebrain, are expressed in non-overlapping territories within these explants. We conclude that the despite the absence of mesoderm, noggin-induced neural tissue shows considerable differentiation and organization, which may represent dorsal-ventral patterning of the forebrain.

scholarly journals CELF2 regulates the species-specific alternative splicing of TREM2

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Motoaki Yanaizu ◽  
Chika Washizu ◽  
Nobuyuki Nukina ◽  
Jun-ichi Satoh ◽  
Yoshihiro Kino
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Full Length ◽  
Splicing Regulation ◽  
Nonsense Mediated Mrna Decay ◽  
Specific Alternative ◽  
Species Specific ◽  
Human And Mouse ◽  
Paralogous Proteins

Abstract Genetic variations of TREM2 have been implicated as a risk factor of Alzheimer’s disease (AD). Recent studies suggest that the loss of TREM2 function compromises microglial responses to the accumulation of amyloid beta. Previously, we found that exon 3 of TREM2 is an alternative exon whose skipping leads to a reduction in full-length TREM2 protein by inducing nonsense-mediated mRNA decay. Here, we aimed to identify factors regulating TREM2 splicing. Using a panel of RNA-binding proteins, we found that exon 3 skipping of TREM2 was promoted by two paralogous proteins, CELF1 and CELF2, which were both linked previously with risk loci of AD. Although the overexpression of both CELF1 and CELF2 enhanced exon 3 skipping, only CELF2 reduced the expression of full-length TREM2 protein. Notably, the TREM2 ortholog in the green monkey, but not in the mouse, showed alternative splicing of exon 3 like human TREM2. Similarly, splicing regulation of exon 3 by CELF1/2 was found to be common to humans and monkeys. Using chimeric minigenes of human and mouse TREM2, we mapped a CELF-responsive sequence within intron 3 of human TREM2. Collectively, our results revealed a novel regulatory factor of TREM2 expression and highlighted a species-dependent difference of its regulation.

scholarly journals Alternative splicing regulation of doublesex gene by RNA-binding proteins in the silkworm Bombyx mori

RNA Biology ◽  
2019 ◽  
Vol 16 (6) ◽  
pp. 809-820 ◽  
Author(s):  
Zeng-Zhang Zheng ◽  
Xia Sun ◽  
Bei Zhang ◽  
Jia Pu ◽  
Ze-Yu Jiang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Bombyx Mori ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Splicing Regulation ◽  
Silkworm Bombyx Mori

scholarly journals Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome

2020 ◽  
Author(s):  
Diego Garrido-Martín ◽  
Beatrice Borsari ◽  
Miquel Calvo ◽  
Ferran Reverter ◽  
Roderic Guigó
Keyword(s):  
Human Genome ◽  
Genetic Variants ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Splicing Regulation ◽  
Splicing Pattern ◽  
Core Set ◽  
Regulatory Loci ◽  
Splicing Patterns ◽  
Affect Gene Expression

AbstractWe have developed an efficient and reproducible pipeline for the discovery of genetic variants affecting splicing (sQTLs), based on an approach that captures the intrinsically multivariate nature of this phenomenon. We employed it to analyze the multi-tissue transcriptome GTEx dataset, generating a comprehensive catalogue of sQTLs in the human genome. A core set of these sQTLs is shared across multiple tissues. Downstream analyses of this catalogue contribute to the understanding of the mechanisms underlying splicing regulation. We found that sQTLs often target the global splicing pattern of genes, rather than individual splicing events. Many of them also affect gene expression, but not always of the same gene, potentially uncovering regulatory loci that act on different genes through different mechanisms. sQTLs tend to be preferentially located in introns that are post-transcriptionally spliced, which would act as hotspots for splicing regulation. While many variants affect splicing patterns by directly altering the sequence of splice sites, many more modify the binding of RNA-binding proteins (RBPs) to target sequences within the transcripts. Genetic variants affecting splicing can have a phenotypic impact comparable or even stronger than variants affecting expression, with those that alter RBP binding playing a prominent role in disease.

scholarly journals The Fine Art of Writing a Message: RNA Metabolism in the Shaping and Remodeling of the Nervous System

2021 ◽  
Vol 14 ◽  
Author(s):  
María Landínez-Macías ◽  
Olivier Urwyler
Keyword(s):  
Nervous System ◽  
Binding Proteins ◽  
Neuronal Development ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Axon Growth ◽  
Rna Metabolism ◽  
Nervous System Development ◽  
Protein Isoforms ◽  
Growth Guidance

Neuronal morphogenesis, integration into circuits, and remodeling of synaptic connections occur in temporally and spatially defined steps. Accordingly, the expression of proteins and specific protein isoforms that contribute to these processes must be controlled quantitatively in time and space. A wide variety of post-transcriptional regulatory mechanisms, which act on pre-mRNA and mRNA molecules contribute to this control. They are thereby critically involved in physiological and pathophysiological nervous system development, function, and maintenance. Here, we review recent findings on how mRNA metabolism contributes to neuronal development, from neural stem cell maintenance to synapse specification, with a particular focus on axon growth, guidance, branching, and synapse formation. We emphasize the role of RNA-binding proteins, and highlight their emerging roles in the poorly understood molecular processes of RNA editing, alternative polyadenylation, and temporal control of splicing, while also discussing alternative splicing, RNA localization, and local translation. We illustrate with the example of the evolutionary conserved Musashi protein family how individual RNA-binding proteins are, on the one hand, acting in different processes of RNA metabolism, and, on the other hand, impacting multiple steps in neuronal development and circuit formation. Finally, we provide links to diseases that have been associated with the malfunction of RNA-binding proteins and disrupted post-transcriptional regulation.

Multiple Roles of RNA Regulatory Factors in Neuronal Development and Function in C. elegans

2020 ◽  
Author(s):  
Matthew G. Andrusiak ◽  
Yishi Jin
Keyword(s):  
Nervous System ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Neuronal Development ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Model Organism ◽  
Nervous System Development ◽  
Forward Genetics ◽  
C Elegans

Recent evidence has highlighted the dynamic nature of mRNA regulation, particularly in the nervous system, from complex pre-mRNA processing to long-range transport and long-term storage of mature mRNAs. In accordance with the importance for mRNA-mediated regulation of nervous system development and maintenance, various mutations in RNA-binding proteins are associated with a range of human disorders. C. elegans express many RNA-binding factors that have human orthologs and perform similar biochemical functions. This chapter focuses on the research using C. elegans to dissect molecular mechanisms involving mRNA-mediated pathways. It highlights the key approaches and findings that integrate genetic and genomic studies in the nervous system. The analyses of genetic mutants, primarily using forward genetics, offer functional insights for genes important for neuronal development, synaptic transmission, and neuronal repair. In combination with single-neuron cell biology and cell-type genomics, the knowledge learned from this model organism has continued to lead to ground-breaking discoveries.

scholarly journals Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Claudia Vivori ◽  
Panagiotis Papasaikas ◽  
Ralph Stadhouders ◽  
Bruno Di Stefano ◽  
Anna Ribó Rubio ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Somatic Cell ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cell Reprogramming ◽  
Splicing Regulation ◽  
Mouse Embryonic Fibroblasts ◽  
Embryonic Fibroblasts ◽  
Somatic Cell Reprogramming

Abstract Background Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we study the dynamics of alternative splicing changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells and compare them to those occurring during reprogramming of mouse embryonic fibroblasts. Results We observe a significant overlap between alternative splicing changes detected in the two reprogramming systems, which are generally uncoupled from changes in transcriptional levels. Correlation between gene expression of potential regulators and specific clusters of alternative splicing changes enables the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of mouse embryonic fibroblasts reprogramming. We further find that these RNA-binding proteins control partially overlapping programs of splicing regulation, involving genes relevant for developmental and morphogenetic processes. Conclusions Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process and their targets.

scholarly journals The RNA-binding protein Staufen1 is increased in DM1 skeletal muscle and promotes alternative pre-mRNA splicing

2012 ◽  
Vol 196 (6) ◽  
pp. 699-712 ◽  
Author(s):  
Aymeric Ravel-Chapuis ◽  
Guy Bélanger ◽  
Ramesh S. Yadava ◽  
Mani S. Mahadevan ◽  
Luc DesGroseillers ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Alternative Splicing ◽  
Nuclear Export ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Splicing Regulation ◽  
Ribonucleic Acids ◽  
Dystrophia Myotonica Protein Kinase

In myotonic dystrophy type 1 (DM1), dystrophia myotonica protein kinase messenger ribonucleic acids (RNAs; mRNAs) with expanded CUG repeats (CUGexp) aggregate in the nucleus and become toxic to cells by sequestering and/or misregulating RNA-binding proteins, resulting in aberrant alternative splicing. In this paper, we find that the RNA-binding protein Staufen1 is markedly and specifically increased in skeletal muscle from DM1 mouse models and patients. We show that Staufen1 interacts with mutant CUGexp mRNAs and promotes their nuclear export and translation. This effect is critically dependent on the third double-stranded RNA–binding domain of Staufen1 and shuttling of Staufen1 into the nucleus via its nuclear localization signal. Moreover, we uncover a new role of Staufen1 in splicing regulation. Overexpression of Staufen1 rescues alternative splicing of two key pre-mRNAs known to be aberrantly spliced in DM1, suggesting its increased expression represents an adaptive response to the pathology. Altogether, our results unravel a novel function for Staufen1 in splicing regulation and indicate that it may positively modulate the complex DM1 phenotype, thereby revealing its potential as a therapeutic target.

scholarly journals Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1 and TIA1

2020 ◽  
Author(s):  
Claudia Vivori ◽  
Panagiotis Papasaikas ◽  
Ralph Stadhouders ◽  
Bruno Di Stefano ◽  
Clara Berenguer Balaguer ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cell Types ◽  
Cell Reprogramming ◽  
Splicing Regulation ◽  
Somatic Cell Reprogramming ◽  
Transcriptional Changes ◽  
Induced Pluripotent

AbstractIn contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for cell reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we have studied the dynamics of alternative splicing (AS) changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells. These changes, generally uncoupled from transcriptional regulation, significantly overlapped with splicing programs reported during reprogramming of mouse embryonic fibroblasts (MEFs). Correlation between gene expression of potential regulators and specific clusters of AS changes enabled the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of MEFs reprogramming. These RNA-binding proteins control partially overlapping programs of splicing regulation affecting genes involved in developmental and morphogenetic processes. Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process.

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