scholarly journals Identification of RBPMS as a smooth muscle master splicing regulator via proximity of its gene with super-enhancers

2019 ◽  
Author(s):  
Erick E. Nakagaki-Silva ◽  
Clare Gooding ◽  
Miriam Llorian ◽  
Aishwarya Griselda Jacob ◽  
Frederick Richards ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Control Cell ◽  
Phenotypic Switching ◽  
Regulatory Rna ◽  
Splicing Regulators ◽  
Its Gene ◽  
Splicing Regulator ◽  
Transcription Regulators

AbstractAlternative splicing (AS) programs are primarily controlled by regulatory RNA binding proteins (RBPs). It has been proposed that a small number of master splicing regulators might control cell-specific splicing networks and that these RBPs could be identified by proximity of their genes to transcriptional super-enhancers. Using this approach we identified RBPMS as a critical splicing regulator in differentiated vascular smooth muscle cells (SMCs). RBPMS is highly down-regulated during phenotypic switching of SMCs from a contractile to a motile and proliferative phenotype and is responsible for 20% of the AS changes during this transition. RBPMS directly regulates AS of numerous components of the actin cytoskeleton and focal adhesion machineries whose activity is critical for SMC function in both phenotypes. RBPMS also regulates splicing of other splicing, post-transcriptional and transcription regulators including the key SMC transcription factor Myocardin, thereby matching many of the criteria of a master regulator of AS in SMCs.

scholarly journals Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Erick E Nakagaki-Silva ◽  
Clare Gooding ◽  
Miriam Llorian ◽  
Aishwarya G Jacob ◽  
Frederick Richards ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Control Cell ◽  
Phenotypic Switching ◽  
Regulatory Rna ◽  
Splicing Regulators ◽  
Its Gene ◽  
Splicing Regulator ◽  
Transcription Regulators

Alternative splicing (AS) programs are primarily controlled by regulatory RNA-binding proteins (RBPs). It has been proposed that a small number of master splicing regulators might control cell-specific splicing networks and that these RBPs could be identified by proximity of their genes to transcriptional super-enhancers. Using this approach we identified RBPMS as a critical splicing regulator in differentiated vascular smooth muscle cells (SMCs). RBPMS is highly down-regulated during phenotypic switching of SMCs from a contractile to a motile and proliferative phenotype and is responsible for 20% of the AS changes during this transition. RBPMS directly regulates AS of numerous components of the actin cytoskeleton and focal adhesion machineries whose activity is critical for SMC function in both phenotypes. RBPMS also regulates splicing of other splicing, post-transcriptional and transcription regulators including the key SMC transcription factor Myocardin, thereby matching many of the criteria of a master regulator of AS in SMCs.

scholarly journals TDP-43 and NOVA-1 RNA-binding proteins as competitive splicing regulators of the schizophrenia-associated TNIK gene

2019 ◽  
Vol 1862 (9) ◽  
pp. 194413 ◽  
Author(s):  
Valentina Gumina ◽  
Claudia Colombrita ◽  
Claudia Fallini ◽  
Patrizia Bossolasco ◽  
Anna Maria Maraschi ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Splicing Regulators

scholarly journals Functional characterization of splicing regulatory elements

2021 ◽  
Author(s):  
Scott I Adamson ◽  
Lijun Zhan ◽  
Brenton R Graveley
Keyword(s):  
High Throughput ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Small Subset ◽  
General Sequence ◽  
Splicing Regulators ◽  
Splicing Regulatory Elements

Background: RNA binding protein-RNA interactions mediate a variety of processes including pre-mRNA splicing, translation, decay, polyadenylation and many others. Previous high-throughput studies have characterized general sequence features associated with increased and decreased splicing of certain exons, but these studies are limited by not knowing the mechanisms, and in particular, the mediating RNA binding proteins, underlying these associations. Results: Here we utilize ENCODE data from diverse data modalities to identify functional splicing regulatory elements and their associated RNA binding proteins. We identify features which make splicing events more sensitive to depletion of RNA binding proteins, as well as which RNA binding proteins act as splicing regulators sensitive to depletion. To analyze the sequence determinants underlying RBP-RNA interactions impacting splicing, we assay tens of thousands of sequence variants in a high-throughput splicing reporter called Vex-seq and confirm a small subset in their endogenous loci using CRISPR base editors. Finally, we leverage other large transcriptomic datasets to confirm the importance of RNA binding proteins which we designed experiments around and identify additional RBPs which may act as additional splicing regulators of the exons studied. Conclusions: This study identifies sequence and other features underlying splicing regulation mediated specific RNA binding proteins, as well as validates and identifies other potentially important regulators of splicing in other large transcriptomic datasets.

scholarly journals Known turnover and translation regulatory RNA-binding proteins interact with the 3’ UTR of SECIS-binding protein 2

RNA Biology ◽  
2009 ◽  
Vol 6 (1) ◽  
pp. 73-83 ◽  
Author(s):  
Jodi Bubenik ◽  
Andrea Ladd ◽  
Carri A. Gerber ◽  
Michael Budiman ◽  
Driscoll Donna
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Regulatory Rna

Translational regulation of ANG II type 1 receptors in proliferating vascular smooth muscle cells

2006 ◽  
Vol 290 (1) ◽  
pp. R50-R56 ◽  
Author(s):  
Sunghou Lee ◽  
Hong Ji ◽  
Zheng Wu ◽  
Wei Zheng ◽  
Ali Hassan ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Vascular Smooth Muscle ◽  
Smooth Muscle Cells ◽  
Vascular Smooth Muscle Cells ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Muscle Cells ◽  
Distribution Analysis ◽  
Exon 2

The current study examined angiotensin receptor (ATR) regulation in proliferating rat aortic vascular smooth muscle cells (VSMCs) in culture. Radioligand competition analysis coupled with RNase protection assays (RPAs) revealed that angiotensin type 1a receptor (AT1aR) densities (Bmax) increased by 30% between 5 and 7 days in culture [Bmax (fmol/mg protein): day 5, 379 ± 8.4 vs. day 7, 481 ± 12, n = 3, P < 0.05] under conditions in which no significant changes in AT1aR mRNA expression occurred [in RPA arbitrary units (AU): day 5, 0.23 ± 0.01 vs. day 7, 0.24 ± 0.04, n = 4] or in mRNA synthesis determined by nuclear run-on assays [AU: day 5, 0.35 ± 0.14 vs. day 7, 0.33 ± 0.11, n = 5]. In contrast, polysome distribution analysis indicated that AT1aR mRNA was more efficiently translated in day 7 cells compared with day 5 [% of AT1aR mRNA in fraction 2 out of total AT1R mRNA recovered from the sucrose gradient: day 5, 20.9 ± 9.9 vs. day 7, 56.8 ± 5.6, n = 3, P < 0.001]. Accompanying the polysome shift was 50% less RNA-protein complex (RPC) formation between VSMC cytosolic RNA binding proteins in day 7 cells compared with 5-day cultures and the 5′ leader sequence (5′LS) of the AT1aR [5′LS RPC (AU): day 5, 0.62 ± 0.15 vs. day 7, 0.23 ± 0.03; n = 4, P < 0.05] and also with exon 2 [Exon 2 RPC (AU): day 5, 35.0 ± 5.7 vs. day 7, 17.2 ± 3.6; n = 4, P < 0.05]. Taken together, these results suggest that AT1aR expression is regulated by translation during VSMC proliferation in part by RNA binding proteins that interact within exon 2 in the 5′LS of the AT1aR mRNA.

scholarly journals Neuron-enriched RNA-binding Proteins Regulate Pancreatic Beta Cell Function and Survival

2017 ◽  
Vol 292 (8) ◽  
pp. 3466-3480 ◽  
Author(s):  
Jonàs Juan-Mateu ◽  
Tatiana H. Rech ◽  
Olatz Villate ◽  
Esther Lizarraga-Mollinedo ◽  
Anna Wendt ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Beta Cell ◽  
Beta Cells ◽  
Insulin Release ◽  
Beta Cell Function ◽  
Rna Binding ◽  
Cell Function ◽  
Rna Binding Proteins ◽  
Pancreatic Beta Cell ◽  
Splicing Regulators

Pancreatic beta cell failure is the central event leading to diabetes. Beta cells share many phenotypic traits with neurons, and proper beta cell function relies on the activation of several neuron-like transcription programs. Regulation of gene expression by alternative splicing plays a pivotal role in brain, where it affects neuronal development, function, and disease. The role of alternative splicing in beta cells remains unclear, but recent data indicate that splicing alterations modulated by both inflammation and susceptibility genes for diabetes contribute to beta cell dysfunction and death. Here we used RNA sequencing to compare the expression of splicing-regulatory RNA-binding proteins in human islets, brain, and other human tissues, and we identified a cluster of splicing regulators that are expressed in both beta cells and brain. Four of them, namely Elavl4, Nova2, Rbox1, and Rbfox2, were selected for subsequent functional studies in insulin-producing rat INS-1E, human EndoC-βH1 cells, and in primary rat beta cells. Silencing of Elavl4 and Nova2 increased beta cell apoptosis, whereas silencing of Rbfox1 and Rbfox2 increased insulin content and secretion. Interestingly, Rbfox1 silencing modulates the splicing of the actin-remodeling protein gelsolin, increasing gelsolin expression and leading to faster glucose-induced actin depolymerization and increased insulin release. Taken together, these findings indicate that beta cells share common splicing regulators and programs with neurons. These splicing regulators play key roles in insulin release and beta cell survival, and their dysfunction may contribute to the loss of functional beta cell mass in diabetes.

scholarly journals Tyramine induces dynamic RNP granule remodeling and translation activation in the Drosophila brain

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Nadia Formicola ◽  
Marjorie Heim ◽  
Jérémy Dufourt ◽  
Anne-Sophie Lancelot ◽  
Akira Nakamura ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Dynamic Networks ◽  
Regulatory Rna ◽  
Drosophila Brain ◽  
Resolution Imaging ◽  
Self Association ◽  
Rnp Granules ◽  
External Stimuli ◽  
Spatiotemporal Control

Ribonucleoprotein (RNP) granules are dynamic condensates enriched in regulatory RNA binding proteins (RBPs) and RNAs under tight spatiotemporal control. Extensive recent work has investigated the molecular principles underlying RNP granule assembly, unraveling that they form through the self-association of RNP components into dynamic networks of interactions. How endogenous RNP granules respond to external stimuli to regulate RNA fate is still largely unknown. Here, we demonstrate through high-resolution imaging of intactDrosophilabrains that Tyramine induces a reversible remodeling of somatic RNP granules characterized by the decondensation of granule-enriched RBPs (e.g. Imp/ZBP1/IGF2BP) and helicases (e.g. Me31B/DDX-6/Rck). Furthermore, our functional analysis reveals that Tyramine signals both through its receptor TyrR and through the calcium-activated kinase CamkII to trigger RNP component decondensation. Finally, we uncover that RNP granule remodeling is accompanied by the rapid and specific translational activation of associated mRNAs. Thus, this work sheds new light on the mechanisms controlling cue-induced rearrangement of physiological RNP condensates.

scholarly journals The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009775
Author(s):  
Mennatallah M. Y. Albarqi ◽  
Sean P. Ryder
Keyword(s):  
Cell Fate ◽  
Expression Pattern ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Control Cell ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Messenger Rnas ◽  
Allelic Series ◽  
Embryo Viability

RNA regulation is essential to successful reproduction. Messenger RNAs delivered from parent to progeny govern early embryonic development. RNA-binding proteins (RBPs) are the key effectors of this process, regulating the translation and stability of parental transcripts to control cell fate specification events prior to zygotic gene activation. The KH-domain RBP MEX-3 is conserved from nematode to human. It was first discovered in Caenorhabditis elegans, where it is essential for anterior cell fate and embryo viability. Here, we show that loss of the endogenous mex-3 3´UTR disrupts its germline expression pattern. An allelic series of 3´UTR deletion variants identify repressing regions of the UTR and demonstrate that repression is not precisely coupled to reproductive success. We also show that several RBPs regulate mex-3 mRNA through its 3´UTR to define its unique germline spatiotemporal expression pattern. Additionally, we find that both poly(A) tail length control and the translation initiation factor IFE-3 contribute to its expression pattern. Together, our results establish the importance of the mex-3 3´UTR to reproductive health and its expression in the germline. Our results suggest that additional mechanisms control MEX-3 function when 3´UTR regulation is compromised.

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