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MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression

Steven W. Paugh, David R. Coss, Ju Bao, Lucas T. Laudermilk, Christy R. Grace, Antonio M. Ferreira, M. Brett Waddell, Granger Ridout, Deanna Naeve, Michael Leuze, Philip F. LoCascio, John C. Panetta (+7 others)
2016 PLoS Computational Biology  
MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA) and typically down-regulating their stability  ...  , SPR) that purine or pyrimidine-rich microRNAs of appropriate length and sequence form triple-helical structures with purinerich sequences of duplex DNA, and identify microRNA sequences that favor triplex  ...  triplex binding sequences, indicating this as a potential mechanism via which microRNA can directly enhance gene expression.  ... 
doi:10.1371/journal.pcbi.1004744 pmid:26844769 pmcid:PMC4742280 fatcat:6ko4itlt5re5ph47xok4dngcdm

Functional Prediction of Candidate MicroRNAs for CRC Management Using in Silico Approach

Adewale Oluwaseun Fadaka, Ashley Pretorius, Ashwil Klein
2019 International Journal of Molecular Sciences  
Furthermore, due to the regulation of important genes in the CRC pathway and the enrichment of the microRNA with triplex binding sites, they may be a useful diagnostic biomarker for the disease subtype  ...  Three of the candidate microRNA were capable of forming multiple triplexes along with three of the target mRNAs.  ...  However, research has suggested the mechanism by which microRNA forms triplex with double-stranded DNA but their exact mechanism of interaction is less well understood [26, 27, 77] .  ... 
doi:10.3390/ijms20205190 pmid:31635135 pmcid:PMC6834124 fatcat:jcoj5doztjcpbpyfkqnsyzbdzy

Emerging roles and context of circular RNAs

Amaresh C. Panda, Ioannis Grammatikakis, Rachel Munk, Myriam Gorospe, Kotb Abdelmohsen
2016 Wiley Interdisciplinary Reviews - RNA  
Circular RNAs (CircRNAs) represent a large class of noncoding RNAs (ncRNAs) that have recently emerged as regulators of gene expression.  ...  The ensuing changes in gene expression patterns elicited by circRNAs are proposed to drive key cellular processes, such as cell proliferation, differentiation and survival, that govern health and disease  ...  CircRNAs in the nucleus may interact with the opposite strand of its genomic DNA via sequence complementarity which may form a DNA-RNA triple helix affecting DNA replication.  ... 
doi:10.1002/wrna.1386 pmid:27612318 pmcid:PMC5315638 fatcat:qnpgomhjafejje54whmk2jpobe

Potential of Peptide Nucleic Acids in Future Therapeutic Applications

Soheila Montazersaheb, Mohammad Saeid Hejazi, Hojjatollah Nozad Charoudeh
2018 Advanced Pharmaceutical Bulletin  
Peptide nucleic acids (PNA) are synthetic analog of DNA with a repeating N-(2-aminoethyl)-glycine peptide backbone connected to purine and pyrimidine nucleobases via a linker.  ...  toward PNA- based technology as a promising approach for gene alteration.  ...  Acknowledgments This review is a part of Ph.D thesis of Soheila Montazersaheb (Thesis No. : 102) at Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.  ... 
doi:10.15171/apb.2018.064 pmid:30607328 pmcid:PMC6311635 fatcat:ihgoqwym4fhktknxhdxxp6yc3e

Therapeutic Peptide Nucleic Acids: Principles, Limitations, and Opportunities

Elias Quijano, Raman Bahal, Adele Ricciardi, W Mark Saltzman, Peter M Glazer
2017 The Yale Journal of Biology and Medicine  
Since their invention in 1991, peptide nucleic acids (PNAs) have been used in a myriad of chemical and biological assays.  ...  This review focuses on recent advances in PNA therapeutic applications, in which chemical modifications are made to improve PNA function and nanoparticles are used to enhance PNA delivery.  ...  Figure 3 . 3 Canonical binding motifs of PNAs with double-stranded DNA. Adapted from [25] . Figure 4 . 4 Gene editing by triplex-forming oligonucleotides.  ... 
pmid:29259523 pmcid:PMC5733847 fatcat:stuawqgjcnhpxasplax64nlwya

RNA interference: The molecular immune system

Omar Bagasra, Kiley R. Prilliman
2004 Journal of Molecular Histology  
Introduction of double-stranded RNA (dsRNA) into cells expressing a homologous gene triggers RNA interference (RNAi), or RNA-based gene silencing (RBGS).  ...  In eukaryotes, dsRNA directed against a range of viruses (i.e., HIV-1, RSV, HPV, poliovirus and others) and endogenous genes can induce sequence-specific inhibition of gene expression.  ...  a mechanism by which eukaryotes are able to regulate gene expression, fight double-stranded RNA (dsRNA) viral infections, and protect their genomes from genetic parasites such as transposons (the DNA  ... 
doi:10.1007/s10735-004-2192-8 pmid:15614608 fatcat:cbnd4gwjivhchberlvwjdqtoea

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

Sarah Geisler, Jeff Coller
2013 Nature reviews. Molecular cell biology  
Early discoveries support a paradigm in which lncRNAs regulate transcription via chromatin modulation, but new functions are steadily emerging.  ...  While these new and enigmatic players in the complex transcriptional milieu are encoded by a significant proportion of the genome, their functions are mostly unknown.  ...  The authors regret that not all contributions of their colleagues could be discussed due to space constraints.  ... 
doi:10.1038/nrm3679 pmid:24105322 pmcid:PMC4852478 fatcat:kzpgwvlbh5aczhsdqqbvwm4oei

The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress

Hong Zhang, Huan Guo, Weiguo Hu, Wanquan Ji
2020 International Journal of Molecular Sciences  
Growing interest and recent evidence have identified long non-coding RNA (lncRNA) as the potential regulatory elements for eukaryotes.  ...  The knowledge gained from a deeper understanding of this colossal special group of plant lncRNAs will help in the biotechnological improvement of crops.  ...  Acknowledgments: We apologize in advance to all scientists whose research could not be cited because of space limitations.  ... 
doi:10.3390/ijms21082659 pmid:32290420 fatcat:5o7rovds4zgozk3elbfzlnh6ty

Effects of Replication and Transcription on DNA Structure-Related Genetic Instability

Guliang Wang, Karen Vasquez
2017 Genes  
For example, a single-stranded inverted repeat sequence can form Watson-Crick base-pairs between the self-complementary regions on the same strand to form hairpin or cruciform structures [15] ; an H-DNA  ...  A-DNA is a duplex structure that exits under dehydrating conditions such as crystal formation, with altered major and minor groove structures [6] .  ...  Although the same group reported that a third-strand TC (20) oligonucleotide in a triplex structure could be separated by the SV40 large T-antigen DNA helicase from a linearized double-stranded plasmid  ... 
doi:10.3390/genes8010017 pmid:28067787 pmcid:PMC5295012 fatcat:pu35wsk72nacrf66blw7ibozle

Genome Regulation by Long Noncoding RNAs

John L. Rinn, Howard Y. Chang
2012 Annual Review of Biochemistry  
The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis.  ...  An emerging theme from multiple model systems is that lncRNAs form extensive networks of ribonucleoprotein (RNP) complexes with numerous chromatin regulators and then target these enzymatic activities  ...  ACKNOWLEDGMENTS We apologize to colleagues whose work could not be discussed or cited owing to space limitations. J.L.R. is supported by National Institutes of Health (NIH) grants 1DP2OD00667-01  ... 
doi:10.1146/annurev-biochem-051410-092902 pmid:22663078 pmcid:PMC3858397 fatcat:ktyi4pycbzdcjlb2uzuyaark3e

Strategies to target long non-coding RNAs in cancer treatment: progress and challenges

Behdokht Fathi Dizaji
2020 Egyptian Journal of Medical Human Genetics  
Long non-coding RNAs are important regulators of gene expression and diverse biological processes.  ...  Their aberrant expression contributes to a verity of diseases including cancer development and progression, providing them with great potential to be diagnostic and prognostic biomarkers and therapeutic  ...  Using a small molecule microarray strategy, two ligands were detected, which specifically bind to the mouse Malat1 ENE triplex. They had~90% homology with human MALAT1 ENE triplex [101] .  ... 
doi:10.1186/s43042-020-00074-4 fatcat:fyenpemoend6nghutlosv4eetm

Cooperativity and Interdependency between RNA Structure and RNA–RNA Interactions

Ilias Skeparnias, Jinwei Zhang
2021 Non-Coding RNA  
These analyses highlight a reciprocal relationship that intimately links RNA structure formation with RNA–RNA interactions.  ...  Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation.  ...  The ribose 2 -hydroxyl imparts significant structural rigidity over DNA strands and enforces A-form geometry in both double-stranded RNAs (dsRNA) and RNA-DNA hybrids.  ... 
doi:10.3390/ncrna7040081 pmid:34940761 pmcid:PMC8704770 fatcat:dfiacfhs4vbena57a4mt2xbzsq

MYC and Chromatin

Lance R. Thomas, William P. Tansey
2015 Open Access Journal of Science and Technology  
They are aberrantly expressed in a majority of human malignancies, and derive their extraordinary oncogenic potential from the ability to control expression of genes linked to cell growth, proliferation  ...  Here, we review contemporary understanding of the MYC-chromatin connection, focusing on how the encasement of DNA into chromatin impacts expression of MYC genes, and how MYC responds to and modulates chromatin  ...  Such elements can form triplex H-DNA via interactions with each repeat, or G-quartets (G4-DNA) via interactions with G residues in each repeat-half.  ... 
doi:10.11131/2015/101124 fatcat:bht2qs6qb5b5lblcoycij5vasu

Nucleic Acids as Therapeutics [chapter]

Saraswat Pushpendra, Pareek Arvind, Bhandari Anil
2012 From Nucleic Acids Sequences to Molecular Medicine  
For antigene applications, oligonucleotides must enter the cell nucleus, form a triplex with the double-stranded genomic DNA, and inhibit the translation as well as the transcription process of the protein  ...  They function by binding to the target moiety through antisense sequence-specific hybridization and inactivating it by cleaving the phosphodiester backbone at a specific site.  ... 
doi:10.1007/978-3-642-27426-8_2 fatcat:efzcwpr44jfknhn5diza6xmrzi

RNA–protein interactions in human health and disease

Ahmad M. Khalil, John L. Rinn
2011 Seminars in Cell and Developmental Biology  
with the major promoter of DHFR and forming a DNA-RNA triplex.  ...  In contrast to transcription factors, which can recognize and bind to specific DNA sequences, the majority of chromatinmodifying complexes do not have DNA binding capacity.  ... 
doi:10.1016/j.semcdb.2011.02.016 pmid:21333748 pmcid:PMC3184770 fatcat:cwpzqjimibeuhppxev7l3h2cay
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