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Virology Oct 2013Papillomavirus gene expression is strictly linked to the differentiation state of the infected cell and is highly regulated at the level of transcription and RNA... (Review)
Review
Papillomavirus gene expression is strictly linked to the differentiation state of the infected cell and is highly regulated at the level of transcription and RNA processing. All papillomaviruses make extensive use of alternative mRNA polyadenylation and splicing to control gene expression. This chapter contains a compilation of all known alternatively spliced papillomavirus mRNAs and it summarizes our current knowledge of viral RNA elements, and viral and cellular factors that control papillomavirus mRNA processing.
Topics: 3' Untranslated Regions; Gene Expression Regulation, Viral; Humans; Keratinocytes; Papillomaviridae; Polyadenylation; Protein Binding; Protein Biosynthesis; RNA Splice Sites; RNA Splicing; RNA, Messenger; RNA, Viral; Regulatory Sequences, Ribonucleic Acid; Transcription, Genetic
PubMed: 23706315
DOI: 10.1016/j.virol.2013.04.034 -
FEMS Microbiology Reviews May 2015Regulatory RNAs play versatile roles in bacteria in the coordination of gene expression during various physiological processes, especially during stress adaptation.... (Review)
Review
Regulatory RNAs play versatile roles in bacteria in the coordination of gene expression during various physiological processes, especially during stress adaptation. Photosynthetic bacteria use sunlight as their major energy source. Therefore, they are particularly vulnerable to the damaging effects of excess light or UV irradiation. In addition, like all bacteria, photosynthetic bacteria must adapt to limiting nutrient concentrations and abiotic and biotic stress factors. Transcriptome analyses have identified hundreds of potential regulatory small RNAs (sRNAs) in model cyanobacteria such as Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, and in environmentally relevant genera such as Trichodesmium, Synechococcus and Prochlorococcus. Some sRNAs have been shown to actually contain μORFs and encode short proteins. Examples include the 40-amino-acid product of the sml0013 gene, which encodes the NdhP subunit of the NDH1 complex. In contrast, the functional characterization of the non-coding sRNA PsrR1 revealed that the 131 nt long sRNA controls photosynthetic functions by targeting multiple mRNAs, providing a paradigm for sRNA functions in photosynthetic bacteria. We suggest that actuatons comprise a new class of genetic elements in which an sRNA gene is inserted upstream of a coding region to modify or enable transcription of that region.
Topics: Bacterial Proteins; Cyanobacteria; Environment; Gene Expression Regulation, Bacterial; Photosynthesis; RNA, Bacterial; Regulatory Sequences, Ribonucleic Acid; Stress, Physiological; Transcriptome
PubMed: 25934122
DOI: 10.1093/femsre/fuv017 -
The Journal of International Advanced... Jul 2023We evaluated and compared the role of endoplasmic reticulum stress in chronic otitis media with cholesteatoma and chronic otitis media without cholesteatoma.
BACKGROUND
We evaluated and compared the role of endoplasmic reticulum stress in chronic otitis media with cholesteatoma and chronic otitis media without cholesteatoma.
METHODS
The messenger ribonucleic acid expression of endoplasmic reticulum stress was measured and compared between chronic otitis media with cholesteatoma and chronic otitis media without cholesteatoma according to the presence or absence of bacteria, type of hearing loss, ossicle destruction, and facial canal dehiscence.
RESULTS
The expression of immunoglobulin heavy chain-binding protein messenger ribonucleic acid was higher in the chronic otitis media without cholesteatoma group than in the chronic otitis media with cholesteatoma group, and Protein kinase RNA (PKR)-like endoplasmic reticulum kinase and activating transcription factor 6 messenger ribonucleic acid expression were higher in the chronic otitis media with cholesteatoma group than in the chronic otitis media without cholesteatoma group.
CONCLUSION
Endoplasmic reticulum stress messenger ribonucleic acids were expressed in both chronic otitis media with cholesteatoma and chronic otitis media without cholesteatoma. The levels of expression of endoplasmic reticulum stress messenger ribonucleic acids differed according to clinical features, suggesting that different endoplasmic reticulum stress pathways are involved in the pathophysiology of different types of chronic otitis media.
Topics: Humans; Cholesteatoma, Middle Ear; Otitis Media; RNA, Messenger; Chronic Disease; RNA; Endoplasmic Reticulum Stress
PubMed: 37528590
DOI: 10.5152/iao.2023.21182 -
Genome Research Oct 2015The regulatory potential of RNA has never ceased to amaze: from RNA catalysis, to RNA-mediated splicing, to RNA-based silencing of an entire chromosome during dosage... (Review)
Review
The regulatory potential of RNA has never ceased to amaze: from RNA catalysis, to RNA-mediated splicing, to RNA-based silencing of an entire chromosome during dosage compensation. More recently, thousands of long noncoding RNA (lncRNA) transcripts have been identified, the majority with unknown function. Thus, it is tempting to think that these lncRNAs represent a cadre of new factors that function through ribonucleic mechanisms. Some evidence points to several lncRNAs with tantalizing physiological contributions and thought-provoking molecular modalities. However, dissecting the RNA biology of lncRNAs has been difficult, and distinguishing the independent contributions of functional RNAs from underlying DNA elements, or the local act of transcription, is challenging. Here, we aim to survey the existing literature and highlight future approaches that will be needed to link the RNA-based biology and mechanisms of lncRNAs in vitro and in vivo.
Topics: Animals; Humans; RNA; RNA, Catalytic; RNA, Long Noncoding; Regulatory Sequences, Ribonucleic Acid
PubMed: 26430155
DOI: 10.1101/gr.191122.115 -
Cold Spring Harbor Perspectives in... Feb 2011A general approach for modeling the architecture of large and structured RNA molecules is described. The method exploits the modularity and the hierarchical folding of... (Review)
Review
A general approach for modeling the architecture of large and structured RNA molecules is described. The method exploits the modularity and the hierarchical folding of RNA architecture that is viewed as the assembly of preformed double-stranded helices defined by Watson-Crick base pairs and RNA modules maintained by non-Watson-Crick base pairs. Despite the extensive molecular neutrality observed in RNA structures, specificity in RNA folding is achieved through global constraints like lengths of helices, coaxiality of helical stacks, and structures adopted at the junctions of helices. The Assemble integrated suite of computer tools allows for sequence and structure analysis as well as interactive modeling by homology or ab initio assembly with possibilities for fitting within electronic density maps. The local key role of non-Watson-Crick pairs guides RNA architecture formation and offers metrics for assessing the accuracy of three-dimensional models in a more useful way than usual root mean square deviation (RMSD) values.
Topics: Base Sequence; Models, Molecular; Nucleic Acid Conformation; RNA; RNA-Binding Proteins; Regulatory Sequences, Ribonucleic Acid; Sequence Alignment; Software; Species Specificity
PubMed: 20504963
DOI: 10.1101/cshperspect.a003632 -
Wiley Interdisciplinary Reviews. RNA 2010The outcome of an inflammatory response depends upon the coordinated regulation of a variety of both pro-inflammatory and anti-inflammatory cytokines and other proteins.... (Review)
Review
The outcome of an inflammatory response depends upon the coordinated regulation of a variety of both pro-inflammatory and anti-inflammatory cytokines and other proteins. Regulation of these inflammation mediators can occur at multiple levels, including transcription, mRNA translation, post-translational modifications, and mRNA degradation. Post-transcriptional regulation has been shown to play an important role in controlling the expression of these mediators, allowing for normal initiation and resolution of the inflammatory response. Many inflammatory mediators have unstable mRNAs due, in part, to the presence of AU-rich elements in their 3'-untranslated regions. Increasing numbers of RNA-binding proteins have been identified that can bind to these AU-rich elements and then regulate the stability and/or translation of the mRNA. This review summarizes current knowledge about the role of several RNA-binding proteins that act through AU-rich elements to post-transcriptionally regulate the biosynthesis of proteins involved in inflammation.
Topics: 3' Untranslated Regions; Animals; Cytokines; Gene Expression Regulation; Humans; Inflammation; RNA; RNA Processing, Post-Transcriptional; RNA-Binding Proteins; Regulatory Sequences, Ribonucleic Acid
PubMed: 21956907
DOI: 10.1002/wrna.1 -
Trends in Cancer Apr 2019The 5' and 3' untranslated regions (UTRs) regulate crucial aspects of post-transcriptional gene regulation that are necessary for the maintenance of cellular... (Review)
Review
The 5' and 3' untranslated regions (UTRs) regulate crucial aspects of post-transcriptional gene regulation that are necessary for the maintenance of cellular homeostasis. When these processes go awry through mutation or misexpression of certain regulatory elements, the subsequent deregulation of oncogenic gene expression can drive or enhance cancer pathogenesis. Although the number of known cancer-related mutations in UTR regulatory elements has recently increased markedly as a result of advances in whole-genome sequencing, little is known about how the majority of these genetic aberrations contribute functionally to disease. In this review we explore the regulatory functions of UTRs, how they are co-opted in cancer, new technologies to interrogate cancerous UTRs, and potential therapeutic opportunities stemming from these regions.
Topics: 3' Untranslated Regions; 5' Untranslated Regions; Animals; Binding Sites; Gene Expression Regulation, Neoplastic; Genetic Association Studies; Genetic Predisposition to Disease; Humans; Internal Ribosome Entry Sites; MicroRNAs; Neoplasms; Polyadenylation; Protein Biosynthesis; RNA, Messenger; Regulatory Sequences, Ribonucleic Acid; Untranslated Regions
PubMed: 30961831
DOI: 10.1016/j.trecan.2019.02.011 -
Current Opinion in Genetics &... Aug 2011Neurons are exquisitely polarized cells that extend intricate axonal and dendritic arbors. Developmental cues guide axons and dendrites into circuits by inducing rapid... (Review)
Review
Neurons are exquisitely polarized cells that extend intricate axonal and dendritic arbors. Developmental cues guide axons and dendrites into circuits by inducing rapid changes in local protein expression and cytoskeletal structure. Neurons can transduce these signals through local mRNA regulation. Here, we review the latest insights regarding post-transcriptional control of gene expression through mRNA transport and local protein synthesis in developing neurons. We focus on local mRNA regulation during axon growth and guidance, dendrite morphogenesis, and synapse formation and refinement. Dysregulated mRNA transport and translation in neurological disorders are also discussed. The collection of molecules and mechanisms reviewed includes sequence-specific RNA binding proteins, microtubule motors and adaptors, microRNAs, translation initiation factors, and the receptor-mediated signaling that modulates these molecules.
Topics: Animals; Gene Expression Regulation, Developmental; Neurons; RNA Processing, Post-Transcriptional; RNA, Messenger; Regulatory Sequences, Ribonucleic Acid; Synapses
PubMed: 21530231
DOI: 10.1016/j.gde.2011.04.002 -
Biomolecules Feb 2017Liquid chromatography, coupled with tandem mass spectrometry, has become one of the most popular methods for the analysis of post-transcriptionally modified transfer... (Review)
Review
Liquid chromatography, coupled with tandem mass spectrometry, has become one of the most popular methods for the analysis of post-transcriptionally modified transfer ribonucleic acids (tRNAs). Given that the information collected using this platform is entirely determined by the mass of the analyte, it has proven to be the gold standard for accurately assigning nucleobases to the sequence. For the past few decades many labs have worked to improve the analysis, contiguous to instrumentation manufacturers developing faster and more sensitive instruments. With biological discoveries relating to ribonucleic acid happening more frequently, mass spectrometry has been invaluable in helping to understand what is happening at the molecular level. Here we present a brief overview of the methods that have been developed and refined for the analysis of modified tRNAs by liquid chromatography tandem mass spectrometry.
Topics: Chromatography, Liquid; RNA; RNA Processing, Post-Transcriptional; RNA, Transfer; Tandem Mass Spectrometry
PubMed: 28241457
DOI: 10.3390/biom7010021 -
Tumour Biology : the Journal of the... Sep 2018Circular ribonucleic acids are non-coding ribonucleic acids that can be identified from genome sequencing studies. Although they can be readily detected, their...
Circular ribonucleic acids are non-coding ribonucleic acids that can be identified from genome sequencing studies. Although they can be readily detected, their regulation and functional role in human diseases such as cancer are unknown. Using a systematic approach, we analyzed ribonucleic acid-sequencing data from a well-characterized cohort of intrahepatic cholangiocarcinoma to identify genetic pathways related to circular ribonucleic acids. Although the expression of most circular ribonucleic acids was similar in both the cancer and non-cancer tissues, expression of circ2174 was significantly increased in cancer tissues. Network analysis of co-related genes identified several pathways associated with circ2174, and common regulatory mediators between genes in these pathways and circ2174. Among these, alterations in several genes involved in interleukin-16 signaling responses such Lck, interleukin-16, and macrophage inflammatory protein-1-beta were the most prominent. Octamer transcription factor (Oct)-2 was identified as a signal transducer that was common to both circ2174 and interleukin-16. Circ2174 has sequence complementarity to miR149 which can target Oct-2. These data suggest a mechanism whereby circ2174 can act as a sponge to regulate the expression of miR149, and thereby modulate Oct-2 and interleukin-16 signaling pathways in cholangiocarcinoma.
Topics: Cholangiocarcinoma; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Humans; Interleukin-16; MicroRNAs; Octamer Transcription Factor-2; RNA; RNA, Circular; Signal Transduction
PubMed: 30168369
DOI: 10.1177/1010428318795761