scholarly journals Regulation and imaging of gene expression via an RNA interference antagonistic biomimetic probe

2017 ◽  
Vol 8 (7) ◽  
pp. 4973-4977 ◽  
Author(s):  
Kai Zhang ◽  
Xue-Jiao Yang ◽  
Wei Zhao ◽  
Ming-Chen Xu ◽  
Jing-Juan Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Rna Interference ◽  
Living Cells

A versatile strategy is reported which permits gene regulation and imaging in living cells via an RNA interference antagonistic probe.

scholarly journals Epigenetic manipulation of gene expression

2005 ◽  
Vol 169 (6) ◽  
pp. 847-857 ◽  
Author(s):  
Rudy L. Juliano ◽  
Vidula R. Dixit ◽  
Hyunmin Kang ◽  
Tai Young Kim ◽  
Yuko Miyamoto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Rna Interference ◽  
Antisense Oligonucleotide ◽  
Significant Progress ◽  
Direct Experience ◽  
Key Features ◽  
Epigenetic Manipulation

Cell biologists have been afforded extraordinary new opportunities for experimentation by the emergence of powerful technologies that allow the selective manipulation of gene expression. Currently, RNA interference is very much in the limelight; however, significant progress has also been made with two other approaches. Thus, antisense oligonucleotide technology is undergoing a resurgence as a result of improvements in the chemistry of these molecules, whereas designed transcription factors offer a powerful and increasingly convenient strategy for either up- or down-regulation of targeted genes. This mini-review will highlight some of the key features of these three approaches to gene regulation, as well as provide pragmatic guidance concerning their use in cell biological experimentation based on our direct experience with each of these technologies. The approaches discussed here are being intensely pursued in terms of possible therapeutic applications. However, we will restrict our comments primarily to the cell culture situation, only briefly alluding to fundamental differences between utilization in animals versus cells.

scholarly journals RNA interference: what it is and what it does: A potent gene regulator

2004 ◽  
Vol 26 (5) ◽  
pp. 7-10
Author(s):  
Darcey Black ◽  
Sarah Newbury
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Rna Interference ◽  
Metabolic Pathways ◽  
Drug Targets ◽  
Human Cells ◽  
Potential Drug ◽  
Genetic Studies ◽  
Multicellular Organisms ◽  
Potential Drug Targets

RNA interference (RNAi) is a potent and specific way of down-regulating gene expression. It is effective in most multicellular organisms, and every gene in the genome can potentially be targeted, providing that the sequence of the gene is known. It has provided a breakthrough in the study of gene regulation, because the function of a gene can often be deduced by inhibiting its ex-pression. RNAi therefore provides a rapid way of studying the function of known genes in organisms where genetic studies are difficult. Since RNAi is effective in human cells, it is now being used in several ways. These include the elucidation of biochemical and metabolic pathways, validation of potential drug targets, and as a therapeutic in the treatment of disease.

scholarly journals Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene

2021 ◽  
Vol 22 (6) ◽  
pp. 3234
Author(s):  
Juhyun Lee ◽  
Si-Eun Sung ◽  
Janghyun Lee ◽  
Jin Young Kang ◽  
Joon-Hwa Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Nmr Spectroscopy ◽  
Bacillus Cereus ◽  
Base Pair ◽  
Noncoding Rna ◽  
Hydrogen Exchange ◽  
Magnesium Ion ◽  
Fluoride Ion ◽  
Base Pair Opening

Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.

scholarly journals CFTR Cooperative Cis-Regulatory Elements in Intestinal Cells

2021 ◽  
Vol 22 (5) ◽  
pp. 2599
Author(s):  
Mégane Collobert ◽  
Ozvan Bocher ◽  
Anaïs Le Nabec ◽  
Emmanuelle Génin ◽  
Claude Férec ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cystic Fibrosis ◽  
Gene Regulation ◽  
Genetic Diseases ◽  
Regulatory Elements ◽  
Cftr Gene ◽  
Intestinal Cells ◽  
Cooperative Effects ◽  
Cis Acting ◽  
Study Techniques

About 8% of the human genome is covered with candidate cis-regulatory elements (cCREs). Disruptions of CREs, described as “cis-ruptions” have been identified as being involved in various genetic diseases. Thanks to the development of chromatin conformation study techniques, several long-range cystic fibrosis transmembrane conductance regulator (CFTR) regulatory elements were identified, but the regulatory mechanisms of the CFTR gene have yet to be fully elucidated. The aim of this work is to improve our knowledge of the CFTR gene regulation, and to identity factors that could impact the CFTR gene expression, and potentially account for the variability of the clinical presentation of cystic fibrosis as well as CFTR-related disorders. Here, we apply the robust GWAS3D score to determine which of the CFTR introns could be involved in gene regulation. This approach highlights four particular CFTR introns of interest. Using reporter gene constructs in intestinal cells, we show that two new introns display strong cooperative effects in intestinal cells. Chromatin immunoprecipitation analyses further demonstrate fixation of transcription factors network. These results provide new insights into our understanding of the CFTR gene regulation and allow us to suggest a 3D CFTR locus structure in intestinal cells. A better understand of regulation mechanisms of the CFTR gene could elucidate cases of patients where the phenotype is not yet explained by the genotype. This would thus help in better diagnosis and therefore better management. These cis-acting regions may be a therapeutic challenge that could lead to the development of specific molecules capable of modulating gene expression in the future.

scholarly journals Recent Advances in the Development of Exogenous dsRNA for the Induction of RNA Interference in Cancer Therapy

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 701
Author(s):  
Tatiana S. Golubeva ◽  
Viktoria A. Cherenko ◽  
Konstantin E. Orishchenko
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Molecular Biology ◽  
Gene Silencing ◽  
Regulation Of Gene Expression ◽  
Research Area ◽  
Disease Treatment ◽  
Practical Applications ◽  
Agricultural Plants ◽  
Insect Reproduction

Selective regulation of gene expression by means of RNA interference has revolutionized molecular biology. This approach is not only used in fundamental studies on the roles of particular genes in the functioning of various organisms, but also possesses practical applications. A variety of methods are being developed based on gene silencing using dsRNA—for protecting agricultural plants from various pathogens, controlling insect reproduction, and therapeutic techniques related to the oncological disease treatment. One of the main problems in this research area is the successful delivery of exogenous dsRNA into cells, as this can be greatly affected by the localization or origin of tumor. This overview is dedicated to describing the latest advances in the development of various transport agents for the delivery of dsRNA fragments for gene silencing, with an emphasis on cancer treatment.

Pursuing gene regulation 'logic' via RNA interference and chromatin immunoprecipitation

2006 ◽  
Vol 7 (7) ◽  
pp. 692-697 ◽  
Author(s):  
Caiyi C Li ◽  
Vladimir R Ramirez-Carrozzi ◽  
Stephen T Smale
Keyword(s):  
Gene Regulation ◽  
Rna Interference ◽  
Chromatin Immunoprecipitation
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