scholarly journals A Complex Genome-MicroRNA Interplay in Human Mitochondria

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Santosh Shinde ◽  
Utpal Bhadra
Keyword(s):  
Noncoding Rna ◽  
Wide Spectrum ◽  
Luciferase Assay ◽  
Northern Analysis ◽  
Regulatory Rna ◽  
Cell Organelles ◽  
Small Regulatory Rna ◽  
Novel Mirna ◽  
Rhesus Genome ◽  
Human Mitochondrial Genome

Small noncoding regulatory RNA exist in wide spectrum of organisms ranging from prokaryote bacteria to humans. In human, a systematic search for noncoding RNA is mainly limited to the nuclear and cytosolic compartments. To investigate whether endogenous small regulatory RNA are present in cell organelles, human mitochondrial genome was also explored for prediction of precursor microRNA (pre-miRNA) and mature miRNA (miRNA) sequences. Six novel miRNA were predicted from the organelle genome by bioinformatics analysis. The structures are conserved in other five mammals including chimp, orangutan, mouse, rat, and rhesus genome. Experimentally, six human miRNA are well accumulated or deposited in human mitochondria. Three of them are expressed less prominently in Northern analysis. To ascertain their presence in human skeletal muscles, total RNA was extracted from enriched mitochondria by an immunomagnetic method. The expression of six novel pre-miRNA and miRNA was confirmed by Northern blot analysis; however, low level of remaining miRNA was found by sensitive Northern analysis. Their presence is further confirmed by real time RT-PCR. The six miRNA find their multiple targets throughout the human genome in three different types of software. The luciferase assay was used to confirm that MT-RNR2 gene was the potential target of hsa-miR-mit3 and hsa-miR-mit4.

LncRNA HCG18 suppresses CD8+ T cells to confer resistance to cetuximab in colorectal cancer via miR-20b-5p/PD-L1 axis

Epigenomics ◽  
2021 ◽  
Author(s):  
Yan-Jie Xu ◽  
Jie-Min Zhao ◽  
Xue-Feng Ni ◽  
Wei Wang ◽  
Wen-Wei Hu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cd8 T Cells ◽  
Noncoding Rna ◽  
Luciferase Assay ◽  
Immunoprecipitation Assay ◽  
Gene And Protein Expression ◽  
Proliferation And Apoptosis ◽  
Rna Immunoprecipitation ◽  
Relative Gene

Aim: We aimed to explore the effect of long noncoding RNA HCG18 in colorectal cancer (CRC). Materials & methods: Relative gene and protein expression were screened. Colony formation and flow cytometry assays were performed to determine proliferation and apoptosis. Dual luciferase assay and RNA immunoprecipitation assay were conducted to validate the interaction between indicated molecules. Xenograft in nude mice was applied to verify the conclusion in vivo. Results: HCG18 and PD-L1 were upregulated while miR-20b-5p was downregulated in CRC tissue. Functional analysis revealed that lncRNA HCG18 promoted proliferation, migration and resistance to cetuximab of CRC cells via miR-20b-5p/PD-L1 axis. Conclusion: HCG18 facilitated the progress of tumor, conferred to cetuximab resistance and suppressed CD8+ T cell via miR-20b-5p/PD-L1 axis.

scholarly journals The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

2014 ◽  
Vol 26 (9) ◽  
pp. 3661-3679 ◽  
Author(s):  
J. Georg ◽  
D. Dienst ◽  
N. Schurgers ◽  
T. Wallner ◽  
D. Kopp ◽  
...  
Keyword(s):  
Regulatory Rna ◽  
Small Regulatory Rna

scholarly journals LuxS-dependent AI-2 production is not involved in global regulation of natural product biosynthesis inPhotorhabdusandXenorhabdus

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3471 ◽  
Author(s):  
Antje K. Heinrich ◽  
Merle Hirschmann ◽  
Nick Neubacher ◽  
Helge B. Bode
Keyword(s):  
Regulatory System ◽  
Regulatory Rna ◽  
Insect Larvae ◽  
Phenotypic Differences ◽  
Global Regulators ◽  
Autoinducer 2 ◽  
Small Regulatory Rna ◽  
Mutant Strains ◽  
Different Strains

The Gram-negative bacteriaPhotorhabdusandXenorhabdusare known to produce a variety of different natural products (NP). These compounds play different roles since the bacteria live in symbiosis with nematodes and are pathogenic to insect larvae in the soil. Thus, a fine tuned regulatory system controlling NP biosynthesis is indispensable. Global regulators such as Hfq, Lrp, LeuO and HexA have been shown to influence NP production ofPhotorhabdusandXenorhabdus. Additionally, photopyrones as quorum sensing (QS) signals were demonstrated to be involved in the regulation of NP production inPhotorhabdus.In this study, we investigated the role of another possible QS signal, autoinducer-2 (AI-2), in regulation of NP production. The AI-2 synthase (LuxS) is widely distributed within the bacterial kingdom and has a dual role as a part of the activated methyl cycle pathway, as well as being responsible for AI-2 precursor production. We deletedluxSin three different entomopathogenic bacteria and compared NP levels in the mutant strains to the wild type (WT) but observed no difference to the WT strains. Furthermore, the absence of the small regulatory RNAmicA, which is encoded directly upstream ofluxS, did not influence NP levels. Phenotypic differences between theP. luminescens luxSdeletion mutant and an earlier describedluxSdeficient strain ofP. luminescenssuggested that two phenotypically different strains have evolved in different laboratories.

scholarly journals Long noncoding RNA KCNQ1OT1 targets miRNA let-7a-5p to regulate Osteoarthritis development and progression

2021 ◽  
Author(s):  
hafiza sobia ramzan ◽  
Kashif Aziz Ahmad
Keyword(s):  
Cell Viability ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Luciferase Assay ◽  
Common Disease ◽  
Functional Roles ◽  
Non Coding Rna ◽  
Proliferation And Apoptosis ◽  
Long Non Coding Rna

Background: Osteoarthritis (OA) is a common disease of the joints among old populace until today. The treatment possibilities and roles of miRNA and long non-coding RNA (lncRNA) in therapy of OA has previously been explored. However, the functional roles of Long noncoding RNA KCNQ1OT1 and miRNA let-7a-5p on Osteoarthritis development and progression remains unclear. This study aimed at investigating the influence of KCNQ1OT1 on let-7a-5p in moderation of OA development and advancement. Materials and Methods: RT-qPCR examined expression of KCNQ1OT1and let-7a-5p in cultured human primary chondrocyte cell lines. Cell transfection overexpressed or knocked down the genes and CCK-8 assay measured cell viability in the proliferation biomarkers Ki87 and PCNA. While caspase-8 and caspase-3 activity determined rate of apoptosis. Furthermore, luciferase assay analyzed the luciferase activity and western blotting analysis determined the protein expression of KCNQ1OT1 and let-7a-5p in proliferation and apoptosis biomarkers. Results: The results demonstrated that KCNQ1OT1 is upregulated in OA-mimic cells and promotes the cell viability. KCNQ1OT1 knockdown suppresses cell viability of OA cells. Furthermore KCNQ1OT1 directly binds the 3'-UTR of let-7a-5p to negatively regulate let-7a-5p expression and OA progression. While upregulated let-7a-5p abolishes the proliferation effect of KCNQ1OT1 in OA cells. Conclusion: In summary, our study provides further insights into the underlying molecular mechanisms of KCNQ1OT1 and let-7a-5p suggesting a novel therapeutic approach to OA

MiR-17 Knockdown Promotes Vascular Smooth Muscle Cell Phenotypic Modulation Through Upregulated Interferon Regulator Factor 9 Expression

2020 ◽  
Author(s):  
Wenyan Li ◽  
Ping Deng ◽  
Junhua Wang ◽  
Zhaofeng Li ◽  
Huming Zhang
Keyword(s):  
Smooth Muscle ◽  
Vascular Smooth Muscle ◽  
Smooth Muscle Cell ◽  
Muscle Cell ◽  
Vascular Smooth Muscle Cell ◽  
Noncoding Rna ◽  
Luciferase Assay ◽  
Marker Genes ◽  
Phenotypic Modulation ◽  
Rt Pcr

Abstract BACKGROUND MiR-17 is a small noncoding RNA that plays an important role in the development of tumorgenesis, which recently has emerged to be involved in regulation of inflammatory responses and angiogenesis. However, the effect and underlying mechanism of miR-17 on vascular smooth muscle cell (VSMC) phenotypic modulation have not been investigated. METHODS AND RESULTS In the current study, we observed that miR-17 expression tested by real-time polymerase chain reaction (RT-PCR) was downregulated in VSMCs administrated with platelet-derived growth factor-BB stimulation and carotid arteries subjected to wire injury, which were accompanied with decreased VSMC differentiation markers. Loss-of-function strategy demonstrated that miR-17 knockdown promoted VSMC phenotypic modulation characterized as decreased VSMC differentiation marker genes, increased proliferated and migrated capability of VSMC examined by RT-PCR and western blot analysis. Mechanistically, the bioinformatics analysis and luciferase assay demonstrated that miR-17 directly targeted Interferon Regulator Factor 9 (IRF9) and the upregulated IRF9 expression was responsible for the promoted effect miR-17 knockdown on VSMC phenotypic modulation. CONCLUSIONS Taken together, our results demonstrated that miR-17 knockdown accelerated VSMC phenotypic modulation partially through directly targeting to IRF9, which suggested that miR-17 may act as a novel therapeutic target for intimal hyperplasia management.

Optimization of phage λ promoter strength for synthetic small regulatory RNA-based metabolic engineering

2016 ◽  
Vol 21 (4) ◽  
pp. 483-490 ◽  
Author(s):  
Minhui Sung ◽  
Seung Min Yoo ◽  
Ren Jun ◽  
Jae Eun Lee ◽  
Sang Yup Lee ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Promoter Strength ◽  
Regulatory Rna ◽  
Small Regulatory Rna

scholarly journals The FasX Small Regulatory RNA Negatively Regulates the Expression of Two Fibronectin-Binding Proteins in Group A Streptococcus

2015 ◽  
Vol 197 (23) ◽  
pp. 3720-3730 ◽  
Author(s):  
Jessica L. Danger ◽  
Nishanth Makthal ◽  
Muthiah Kumaraswami ◽  
Paul Sumby
Keyword(s):  
Cell Surface ◽  
Virulence Factors ◽  
Binding Proteins ◽  
Mrna Translation ◽  
Regulatory Rna ◽  
Collagen Binding ◽  
Content Type ◽  
Small Regulatory Rna ◽  
Group A ◽  
Fibronectin Binding

ABSTRACTThe group AStreptococcus(GAS;Streptococcus pyogenes) causes more than 700 million human infections each year. The success of this pathogen can be traced in part to the extensive arsenal of virulence factors that are available for expression in temporally and spatially specific manners. To modify the expression of these virulence factors, GAS use both protein- and RNA-based regulators, with the best-characterized RNA-based regulator being the small regulatory RNA (sRNA) FasX. FasX is a 205-nucleotide sRNA that contributes to GAS virulence by enhancing the expression of the thrombolytic secreted virulence factor streptokinase and by repressing the expression of the collagen-binding cell surface pili. Here, we have expanded the FasX regulon, showing that this sRNA also negatively regulates the expression of the adhesion- and internalization-promoting, fibronectin-binding proteins PrtF1 and PrtF2. FasX posttranscriptionally regulates the expression of PrtF1/2 through a mechanism that involves base pairing to theprtF1andprtF2mRNAs within their 5′ untranslated regions, overlapping the mRNA ribosome-binding sites. Thus, duplex formation between FasX and theprtF1andprtF2mRNAs blocks ribosome access, leading to an inhibition of mRNA translation. Given that FasX positively regulates the expression of the spreading factor streptokinase and negatively regulates the expression of the collagen-binding pili and of the fibronectin-binding PrtF1/2, our data are consistent with FasX functioning as a molecular switch that governs the transition of GAS between the colonization and dissemination stages of infection.IMPORTANCEMore than half a million deaths each year are a consequence of infections caused by GAS. Insights into how this pathogen regulates the production of proteins during infection may facilitate the development of novel therapeutic or preventative regimens aimed at inhibiting this activity. Here, we have expanded insight into the regulatory activity of the GAS small RNA FasX. In addition to identifying that FasX reduces the abundance of the cell surface-located fibronectin-binding proteins PrtF1/2, fibronectin is present in high abundance in human tissues, and we have determined the mechanism behind this regulation. Importantly, as FasX is the only mechanistically characterized regulatory RNA in GAS, it serves as a model RNA in this and related pathogens.

scholarly journals miRNA-Disease Association Prediction with Collaborative Matrix Factorization

Complexity ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Zhen Shen ◽  
You-Hua Zhang ◽  
Kyungsook Han ◽  
Asoke K. Nandi ◽  
Barry Honig ◽  
...  
Keyword(s):  
Matrix Factorization ◽  
Noncoding Rna ◽  
Esophageal Neoplasms ◽  
Kidney Neoplasms ◽  
Disease Association ◽  
Computational Method ◽  
Experimental Identification ◽  
Novel Mirna ◽  
Disease Associations ◽  
High Prediction

As one of the factors in the noncoding RNA family, microRNAs (miRNAs) are involved in the development and progression of various complex diseases. Experimental identification of miRNA-disease association is expensive and time-consuming. Therefore, it is necessary to design efficient algorithms to identify novel miRNA-disease association. In this paper, we developed the computational method of Collaborative Matrix Factorization for miRNA-Disease Association prediction (CMFMDA) to identify potential miRNA-disease associations by integrating miRNA functional similarity, disease semantic similarity, and experimentally verified miRNA-disease associations. Experiments verified that CMFMDA achieves intended purpose and application values with its short consuming-time and high prediction accuracy. In addition, we used CMFMDA on Esophageal Neoplasms and Kidney Neoplasms to reveal their potential related miRNAs. As a result, 84% and 82% of top 50 predicted miRNA-disease pairs for these two diseases were confirmed by experiment. Not only this, but also CMFMDA could be applied to new diseases and new miRNAs without any known associations, which overcome the defects of many previous computational methods.

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