Gene Regulation at the RNA Layer: RNA Binding Proteins in Intercellular Signaling Networks

2003 ◽  
Vol 2003 (179) ◽  
pp. re6-re6 ◽  
Author(s):  
P. Lasko
Keyword(s):  
Gene Regulation ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Signaling Networks ◽  
Intercellular Signaling

scholarly journals RBPMetaDB: A comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins

2018 ◽  
Author(s):  
Jin Li ◽  
Su-Ping Deng ◽  
Jacob Vieira ◽  
James Thomas ◽  
Valerio Costa ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Dna Binding ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Experimental Studies ◽  
Easy Access ◽  
Rna Seq ◽  
Mrna Stabilization

AbstractRNA-binding proteins may play a critical role in gene regulation in various diseases or biological processes by controlling post-transcriptional events such as polyadenylation, splicing, and mRNA stabilization via binding activities to RNA molecules. Due to the importance of RNA-binding proteins in gene regulation, a great number of studies have been conducted, resulting in a large amount of RNA-Seq datasets. However, these datasets usually do not have structured organization of metadata, which limits their potentially wide use. To bridge this gap, the metadata of a comprehensive set of publicly available mouse RNA-Seq datasets with perturbed RNA-binding proteins were collected and integrated into a database called RBPMetaDB. This database contains 278 mouse RNA-Seq datasets for a comprehensive list of 163 RNA-binding proteins. These RNA-binding proteins account for only ∼10% of all known RNA-binding proteins annotated in Gene Ontology, indicating that most are still unexplored using high-throughput sequencing. This negative information provides a great pool of candidate RNA-binding proteins for biologists to conduct future experimental studies. In addition, we found that DNA-binding activities are significantly enriched among RNA-binding proteins in RBPMetaDB, suggesting that prior studies of these DNA- and RNA-binding factors focus more on DNA-binding activities instead of RNA-binding activities. This result reveals the opportunity to efficiently reuse these data for investigation of the roles of their RNA-binding activities. A web application has also been implemented to enable easy access and wide use of RBPMetaDB. It is expected that RBPMetaDB will be a great resource for improving understanding of the biological roles of RNA-binding proteins.Database URL: http://rbpmetadb.yubiolab.org

Plant PUF RNA-binding proteins: A wealth of diversity for post-transcriptional gene regulation

Plant Science ◽  
2020 ◽  
Vol 297 ◽  
pp. 110505
Author(s):  
Chris R. Joshna ◽  
Pritha Saha ◽  
Dilini Atugala ◽  
Gordon Chua ◽  
Douglas G. Muench
Keyword(s):  
Gene Regulation ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Transcriptional Gene Regulation

scholarly journals RNA-binding proteins and gene regulation in myogenesis

2011 ◽  
Vol 32 (11) ◽  
pp. 652-658 ◽  
Author(s):  
Luciano H. Apponi ◽  
Anita H. Corbett ◽  
Grace K. Pavlath
Keyword(s):  
Gene Regulation ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins

scholarly journals RNA-binding proteins and post-transcriptional gene regulation

FEBS Letters ◽  
2008 ◽  
Vol 582 (14) ◽  
pp. 1977-1986 ◽  
Author(s):  
Tina Glisovic ◽  
Jennifer L. Bachorik ◽  
Jeongsik Yong ◽  
Gideon Dreyfuss
Keyword(s):  
Gene Regulation ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Transcriptional Gene Regulation

scholarly journals Combinatorial Genetics of RNA Binding Proteins for Lifespan Regulation in C. elegans

2019 ◽  
Vol 4 (Spring 2019) ◽  
Author(s):  
Nikita Tapiawala
Keyword(s):  
Gene Regulation ◽  
Aging Process ◽  
Transcriptional Control ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
C Elegans ◽  
Experimental Laboratory ◽  
Control Post ◽  
Insight Into

RNA binding proteins control post-transcriptional aspects of gene regulation. While transcriptional control over the aging process has been well-established, less is known about post-transcriptional control over the aging process. We have used CRISPR/Cas9 genetics to study combinations of RNA binding proteins in C. elegan, a transparent nematode or roundworm one millimeter in length, and their role in aging. The manner in which the research was conducted was through experimental laboratory work in which the lifespan of the nematodes was monitored until their death. The three mutations affecting RNA binding proteins that assays were performed with are exc-7, fox-1, and mbl-1. We found that double mutants have stronger effects on lifespan than single mutants. Thus, RNA binding protein mutations, although separate, appeared to be functionally connected. These observations, though being considered in C. elegans, could have a substantive impact on the study of gene regulation in humans and in turn, provide insight into the human aging processes.

scholarly journals S1-Domain RNA-Binding Protein (CvfD) Is a New Post-Transcriptional Regulator That Mediates Cold Sensitivity, Phosphate Transport, and Virulence in Streptococcus pneumoniae D39

2020 ◽  
Author(s):  
Dhriti Sinha ◽  
Jiaqi J. Zheng ◽  
Ho-Ching Tiffany Tsui ◽  
John D. Richardson ◽  
Nicholas R. De Lay ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Binding Protein ◽  
Phosphate Transport ◽  
Cold Sensitivity ◽  
Rna Biology ◽  
Transcriptional Gene Regulation ◽  
Pleiotropic Regulator

ABSTRACTPost-transcriptional gene regulation often involves RNA-binding proteins that modulate mRNA translation and/or stability either directly through protein-RNA interactions or indirectly by facilitating the annealing of small regulatory RNAs (sRNAs). The human pathogen Streptococcus pneumoniae D39 (pneumococcus) does not encode homologs to RNA-binding proteins known to be involved in promoting sRNA stability and function, such as Hfq or ProQ, even though it contains genes for at least 112 sRNAs. However, the pneumococcal genome contains genes for other RNA-binding proteins, including at least six S1-domain proteins; ribosomal protein S1 (rpsA), polynucleotide phosphorylase (pnpA), RNase R (rnr), and three proteins of unknown functions. Here, we characterize the function of one of these conserved, yet uncharacterized S1-domain proteins, SPD_1366, which we have renamed CvfD (Conserved virulence factor D), since loss of this protein results in an attenuation of virulence in a murine pneumonia model. We report that deletion of cvfD impacts expression of 144 transcripts including the pst1 operon, encoding the phosphate transport system 1 in S. pneumoniae. We further show that CvfD post-transcriptionally regulates the PhoU2 master regulator of the pneumococcal dual phosphate transport system by binding phoU2 mRNA and impacting PhoU2 translation. CvfD not only controls expression of phosphate transporter genes, but also functions as a pleiotropic regulator that impacts cold sensitivity and the expression of sRNAs and genes involved in diverse cellular functions, including manganese uptake and zinc efflux. Together, our data show that CvfD exerts a broad impact on pneumococcal physiology and virulence, partly by post-transcriptional gene regulation.SIGNIFICANCERecent advances have led to the identification of numerous sRNAs in the major human respiratory pathogen, S. pneumoniae. However, little is known about the functions of most sRNAs or RNA-binding proteins involved in RNA biology in pneumococcus. In this paper, we characterize the phenotypes and one target of the S1-domain RNA-binding protein CvfD, a homolog of “general-stress protein 13” identified, but not extensively characterized in other Firmicute species. Pneumococcal CvfD is a broadly pleiotropic regulator, whose absence results in misregulation of divalent cation homeostasis, reduced translation of the PhoU2 master regulator of phosphate uptake, altered metabolism and sRNA amounts, cold sensitivity, and attenuation of virulence. These findings underscore the critical roles of RNA biology in pneumococcal physiology and virulence.

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