Optoribogenetic control of regulatory RNA molecules

2020 ◽  
Author(s):  
Angika Basant
Keyword(s):  
Regulatory Rna ◽  
Rna Molecules

scholarly journals MicroRNAs in central nervous system disorders: current advances in pathogenesis and treatment

2021 ◽  
Vol 57 (1) ◽  
Author(s):  
Mona Hussein ◽  
Rehab Magdy
Keyword(s):  
Neurological Disorders ◽  
Target Genes ◽  
Transcriptional Regulators ◽  
Therapeutic Strategies ◽  
Regulatory Rna ◽  
Altered Expression ◽  
Rna Molecules ◽  
Central Nervous System Disorders ◽  
Novel Targets ◽  
Lateral Sclerosis

AbstractMicroRNAs (miRNAs) are a class of short, non-coding, regulatory RNA molecules that function as post transcriptional regulators of gene expression. Altered expression of multiple miRNAs was found to be extensively involved in the pathogenesis of different neurological disorders including Alzheimer’s disease, Parkinson’s disease, stroke, epilepsy, multiple sclerosis, amyotrophic lateral sclerosis, and Huntington’s disease. miRNAs are implicated in the pathogenesis of excitotoxicity, apoptosis, oxidative stress, inflammation, neurogenesis, angiogenesis, and blood–brain barrier protection. Consequently, miRNAs can serve as biomarkers for different neurological disorders. In recent years, advances in the miRNA field led to identification of potentially novel prospects in the development of new therapies for incurable CNS disorders. MiRNA-based therapeutics include miRNA mimics and inhibitors that can decrease or increase the expression of target genes. Better understanding of the mechanisms by which miRNAs are implicated in the pathogenesis of neurological disorders may provide novel targets to researchers for innovative therapeutic strategies.

scholarly journals Cardiac-targeted delivery of regulatory RNA molecules and genes for the treatment of heart failure

2010 ◽  
Vol 86 (3) ◽  
pp. 353-364 ◽  
Author(s):  
W. Poller ◽  
R. Hajjar ◽  
H. P. Schultheiss ◽  
H. Fechner
Keyword(s):  
Heart Failure ◽  
Targeted Delivery ◽  
Regulatory Rna ◽  
Rna Molecules

Bioinformatics Methods for Studying MicroRNA and ARE-Mediated Regulation of Post-Transcriptional Gene Expression

2010 ◽  
Vol 1 (3) ◽  
pp. 97-112 ◽  
Author(s):  
Richipal Singh Bindra ◽  
Jason T. L. Wang ◽  
Paramjeet Singh Bagga
Keyword(s):  
Mirna Target ◽  
Target Prediction ◽  
Untranslated Regions ◽  
Regulatory Rna ◽  
Rna Motifs ◽  
Protein Coding ◽  
Rna Molecules ◽  
Cellular Processes ◽  
Target Sites ◽  
Transcriptional Gene Regulation

MicroRNAs (miRNAs) are short single-stranded RNA molecules with 21-22 nucleotides known to regulate post-transcriptional expression of protein-coding genes involved in most of the cellular processes. Prediction of miRNA targets is a challenging bioinformatics problem. AU-rich elements (AREs) are regulatory RNA motifs found in the 3’ untranslated regions (UTRs) of mRNAs, and they play dominant roles in the regulated decay of short-lived human mRNAs via specific interactions with proteins. In this paper, the authors review several miRNA target prediction tools and data sources, as well as computational methods used for the prediction of AREs. The authors discuss the connection between miRNA and ARE-mediated post-transcriptional gene regulation. Finally, a data mining method for identifying the co-occurrences of miRNA target sites in ARE containing genes is presented.

scholarly journals A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules

PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e55168 ◽  
Author(s):  
Zsolt Czimmerer ◽  
Julianna Hulvely ◽  
Zoltan Simandi ◽  
Eva Varallyay ◽  
Zoltan Havelda ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Regulatory Rna ◽  
Stem Loop ◽  
Rna Molecules ◽  
Loop Primer ◽  
Small Regulatory Rna ◽  
Pcr Assays

scholarly journals Regulatory RNA molecules

2006 ◽  
Vol 27 (3) ◽  
pp. 124
Author(s):  
Stephen M Kwong ◽  
Neville Firth
Keyword(s):  
Gene Regulation ◽  
Antisense Rna ◽  
Current Knowledge ◽  
Regulatory Rna ◽  
Rna Molecules ◽  
Genetic Elements ◽  
Regulatory Systems ◽  
Regulatory Rnas

Numerous examples of antisense RNA-mediated gene regulation have been found in bacteria. Such regulatory systems were first identified on accessory genetic elements such as plasmids, transposons and phages, and it is from these that most of our current knowledge of regulatory RNAs is drawn.

scholarly journals Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

2016 ◽  
Vol 80 (4) ◽  
pp. 1029-1057 ◽  
Author(s):  
Ruben A. T. Mars ◽  
Pierre Nicolas ◽  
Emma L. Denham ◽  
Jan Maarten van Dijl
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Regulation Of Gene Expression ◽  
Regulatory Rna ◽  
Gram Positive ◽  
Content Type ◽  
Rna Molecules ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
The Stability

SUMMARYBacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules includetrans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5′ untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such asEscherichia coliandSalmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacteriumBacillus subtilis. A recent study identified 1,583 putative regulatory RNAs inB. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation inB. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation inB. subtilismostly involves elements at the 5′ ends of mRNA molecules. These can include 5′ secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs inB. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions inB. subtilis.

scholarly journals Optoribogenetic control of regulatory RNA molecules

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sebastian Pilsl ◽  
Charles Morgan ◽  
Moujab Choukeife ◽  
Andreas Möglich ◽  
Günter Mayer
Keyword(s):  
Gene Expression ◽  
Protein Function ◽  
Mammalian Cells ◽  
Regulatory Rna ◽  
Rna Molecules ◽  
Cell State ◽  
Non Invasive ◽  
Micro Rnas ◽  
Short Hairpin ◽  
Regulatory Rnas

Abstract Short regulatory RNA molecules underpin gene expression and govern cellular state and physiology. To establish an alternative layer of control over these processes, we generated chimeric regulatory RNAs that interact reversibly and light-dependently with the light-oxygen-voltage photoreceptor PAL. By harnessing this interaction, the function of micro RNAs (miRs) and short hairpin (sh) RNAs in mammalian cells can be regulated in a spatiotemporally precise manner. The underlying strategy is generic and can be adapted to near-arbitrary target sequences. Owing to full genetic encodability, it establishes optoribogenetic control of cell state and physiology. The method stands to facilitate the non-invasive, reversible and spatiotemporally resolved study of regulatory RNAs and protein function in cellular and organismal environments.

Core regulatory RNA molecules identified in articular cartilage stem/progenitor cells during osteoarthritis progression

Epigenomics ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 669-684 ◽  
Author(s):  
Shuai Zhang ◽  
Qier An ◽  
Peilin Hu ◽  
Xiaomin Wu ◽  
Xiaohua Pan ◽  
...  
Keyword(s):  
Articular Cartilage ◽  
Progenitor Cells ◽  
Regulatory Rna ◽  
Rna Molecules ◽  
Osteoarthritis Progression

scholarly journals Crosstalk between MicroRNA and Oxidative Stress in Physiology and Pathology

2020 ◽  
Vol 21 (4) ◽  
pp. 1270 ◽  
Author(s):  
Antonella Fioravanti ◽  
Luigi Pirtoli ◽  
Antonio Giordano ◽  
Francesco Dotta
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Messenger Rna ◽  
Regulatory Rna ◽  
Regulate Gene Expression ◽  
Rna Molecules ◽  
And Oxidative Stress ◽  
Specific Sequences ◽  
Regulate Gene

MicroRNAs (miRNA), are short regulatory RNA molecules that regulate gene expression by binding specific sequences within target messenger RNA (mRNA) [...]

scholarly journals A Novel Fur- and Iron-Regulated Small RNA, NrrF, Is Required for Indirect Fur-Mediated Regulation of the sdhA and sdhC Genes in Neisseria meningitidis

2007 ◽  
Vol 189 (10) ◽  
pp. 3686-3694 ◽  
Author(s):  
J. R. Mellin ◽  
Sulip Goswami ◽  
Susan Grogan ◽  
Brian Tjaden ◽  
Caroline A. Genco
Keyword(s):  
Neisseria Meningitidis ◽  
Gene Transcription ◽  
Small Rna ◽  
Iron Homeostasis ◽  
A Priori ◽  
Regulatory Rna ◽  
Rna Molecules ◽  
Small Regulatory Rna ◽  
Regulator Protein ◽  
Microarray Studies

ABSTRACT Iron is both essential for bacterial growth and toxic at higher concentrations; thus, iron homeostasis is tightly regulated. In Neisseria meningitidis the majority of iron-responsive gene regulation is mediated by the ferric uptake regulator protein (Fur), a protein classically defined as a transcriptional repressor. Recently, however, microarray studies have identified a number of genes in N. meningitidis that are iron and Fur activated, demonstrating a new role for Fur as a transcriptional activator. Since Fur has been shown to indirectly activate gene transcription through the repression of small regulatory RNA molecules in other organisms, we hypothesized that a similar mechanism could account for Fur-dependent, iron-activated gene transcription in N. meningitidis. In this study, we used a bioinformatics approach to screen for the presence of Fur-regulated small RNA molecules in N. meningitidis MC58. This screen identified one small RNA, herein named NrrF (for neisserial regulatory RNA responsive to iron [Fe]), which was demonstrated to be both iron responsive and Fur regulated and which has a well-conserved orthologue in N. gonorrhoeae. In addition, this screen identified a number of other likely, novel small RNA transcripts. Lastly, we utilized a new bioinformatics approach to predict regulatory targets of the NrrF small RNA. This analysis led to the identification of the sdhA and sdhC genes, which were subsequently demonstrated to be under NrrF regulation in an nrrF mutant. This study is the first report of small RNAs in N. meningitidis and the first to use a bioinformatics approach to identify, a priori, regulatory targets of a small RNA.

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