Enhancers predominantly regulate gene expression in vivo via transcription initiation

2019 ◽  
Author(s):  
Clarice Hong
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Regulate Gene Expression ◽  
Regulate Gene

scholarly journals Enhancers Predominantly Regulate Gene Expression in vivo Via Transcription Initiation

2019 ◽  
Author(s):  
Martin Stephen Charles Larke ◽  
Takayuki Nojima ◽  
Jelena Telenius ◽  
Jacqueline A. Sharpe ◽  
Jacqueline A. Sloane-Stanley ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Regulate Gene Expression ◽  
Regulate Gene

scholarly journals Enhancers predominantly regulate gene expression during differentiation via transcription initiation

2021 ◽  
Vol 81 (5) ◽  
pp. 983-997.e7 ◽  
Author(s):  
Martin S.C. Larke ◽  
Ron Schwessinger ◽  
Takayuki Nojima ◽  
Jelena Telenius ◽  
Robert A. Beagrie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Regulate Gene Expression ◽  
Regulate Gene

Epigenetherapy, a new concept

2011 ◽  
Vol 2 (3) ◽  
pp. 127-134
Author(s):  
Tiia Husso ◽  
Mikko P. Turunen ◽  
Nigel Parker ◽  
Seppo Ylä-Herttuala
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Basic Research ◽  
Clinical Applications ◽  
Regulate Gene Expression ◽  
Endogenous Gene ◽  
Rna Molecules ◽  
Regulate Gene

AbstractSmall RNAs have been shown to regulate gene transcription by interacting with the promoter region and modifying the histone code. The exact mechanism of function is still unclear but the feasibility to activate or repress endogenous gene expression with small RNA molecules has already been demonstrated in vitro and in vivo. In traditional gene therapy non-mutated or otherwise useful genes are inserted into patient's cells to treat a disease. In epigenetherapy the action of small RNAs is utilized by delivering only the small RNAs to patient's cells where they then regulate gene expression by epigenetic mechanisms. This method could be widely useful not only for basic research but also for clinical applications of small RNAs.

Use of Synchronous Site-Specific Recombination in Vivo to Regulate Gene Expression

1984 ◽  
Vol 2 (12) ◽  
pp. 1045-1049 ◽  
Author(s):  
K. Backman ◽  
M. J. O'Connor ◽  
A. Maruya ◽  
M. Erfle
Keyword(s):  
Gene Expression ◽  
Site Specific ◽  
Regulate Gene Expression ◽  
Site Specific Recombination ◽  
Regulate Gene

Gene expression regulation in trypanosomatids

2011 ◽  
Vol 51 ◽  
pp. 31-46 ◽  
Author(s):  
Javier G. De Gaudenzi ◽  
Griselda Noé ◽  
Vanina A. Campo ◽  
Alberto C. Frasch ◽  
Alejandro Cassola
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Leishmania Major ◽  
Gene Expression Regulation ◽  
Mrna Translation ◽  
Regulate Gene Expression ◽  
Ribonucleoprotein Complexes ◽  
Micro Organisms ◽  
Regulate Gene

Trypanosomatids are protozoan micro-organisms that cause serious health problems in humans and domestic animals. In addition to their medical relevance, these pathogens have novel biological structures and processes. From nuclear DNA transcription to mRNA translation, trypanosomes use unusual mechanisms to control gene expression. For example, transcription by RNAPII (RNA polymerase II) is polycistronic, and only a few transcription initiation sites have been identified so far. The sequences present in the polycistronic units code for proteins having unrelated functions, that is, not involved in a similar metabolic pathway. Owing to these biological constraints, these micro-organisms regulate gene expression mostly by post-transcriptional events. Consequently, the function of proteins that recognize RNA elements preferentially at the 3′ UTR (untranslated region) of transcripts is central. It was recently shown that mRNP (messenger ribonucleoprotein) complexes are organized within post-transcriptional operons to co-ordinately regulate gene expression of functionally linked transcripts. In the present chapter we will focus on particular characteristics of gene expression in the so-called TriTryp parasites: Trypanosoma cruzi, Trypanosoma brucei and Leishmania major.

scholarly journals Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter-protein

2020 ◽  
Author(s):  
Clara D. Wang ◽  
Rachel Mansky ◽  
Hannah LeBlanc ◽  
Chandra M. Gravel ◽  
Katherine E. Berry
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Regulate Gene Expression ◽  
E Coli ◽  
Binding Energetics ◽  
Response To Stress ◽  
First Time ◽  
Regulate Gene

ABSTRACTNon-coding RNAs regulate gene expression in every domain of life. In bacteria, small RNAs (sRNAs) regulate gene expression in response to stress and are often assisted by RNA-chaperone proteins, such as Hfq. We have recently developed a bacterial three-hybrid (B3H) assay that detects the strong binding interactions of certain E. coli sRNAs with proteins Hfq and ProQ. Despite the promise of this system, the signal-to-noise has made it challenging to detect weaker interactions. In this work, we use Hfq-sRNA interactions as a model system to optimize the B3H assay, so that weaker RNA-protein interactions can be more reliably detected. We find that the concentration of the RNA-DNA adapter is an important parameter in determining the signal in the system, and have modified the plasmid expressing this component to tune its concentration to optimal levels. In addition, we have systematically perturbed the binding affinity of Hfq-RNA interactions to define, for the first time, the relationship between B3H signal and in vitro binding energetics. The new pAdapter construct presented here substantially expands the range of detectable interactions in the B3H assay, broadening its utility. This improved assay will increase the likelihood of identifying novel protein-RNA interactions with the B3H system, and will facilitate exploration of the binding mechanisms of these interactions.

scholarly journals Drosophila fabp  is a retinoid-inducible gene required for Rhodopsin-1 homeostasis and photoreceptor survival

2021 ◽  
Author(s):  
Hyung Don Ryoo ◽  
Huai-Wei Huang
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Fatty Acid Binding ◽  
Regulate Gene Expression ◽  
Protein Levels ◽  
Expression Of Genes ◽  
Light Loss ◽  
Regulate Gene ◽  
Inducible Gene

Retinoids act as chromophore co-factors for light-detecting rhodopsin proteins. In vertebrates, retinoids also actively regulate gene expression. Whether retinoids regulate gene expression in  Drosophila for a specific biological function remains unclear. Here, we report that  Drosophila fatty acid binding protein ( fabp ) is a retinoid-inducible gene required for Rhodopsin-1 (Rh1) protein homeostasis and photoreceptor survival. Specifically, we performed a photoreceptor-specific gene expression profiling study in flies bearing a misfolding-prone Rhodopsin-1 (Rh1) mutant,  ninaE G69D , which serves as a  Drosophila  model for Retinitis Pigmentosa.  ninaE G69D photoreceptors showed increased expression of genes that control Rh1 protein levels, along with a poorly characterized gene, fabp . We found that in vivo  fabp  expression was reduced when the retinoids were deprived through independent methods. Conversely,  fabp  mRNA was induced when we challenged cultured  Drosophila cells with retinoic acid. In flies reared under light, loss of  fabp  caused an accumulation of Rh1 proteins in cytoplasmic vesicles.  fabp  mutants exhibited light-dependent retinal degeneration, a phenotype also found in other mutants that block light-activated Rh1 degradation. These observations indicate that a retinoid-inducible gene expression program regulates  fabp  that is required forRh1 proteostasis and photoreceptor survival.

scholarly journals In Vivo Behavior of the Tandem Glycine Riboswitch in Bacillus subtilis

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Arianne M. Babina ◽  
Nicholas E. Lea ◽  
Michelle M. Meyer
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Regulate Gene Expression ◽  
Binding Domains ◽  
Expression Platform ◽  
The Impact ◽  
Organismal Fitness ◽  
Regulate Gene

ABSTRACT In many bacterial species, the glycine riboswitch is composed of two homologous ligand-binding domains (aptamers) that each bind glycine and act together to regulate the expression of glycine metabolic and transport genes. While the structure and molecular dynamics of the tandem glycine riboswitch have been the subject of numerous in vitro studies, the in vivo behavior of the riboswitch remains largely uncharacterized. To examine the proposed models of tandem glycine riboswitch function in a biologically relevant context, we characterized the regulatory activity of mutations to the riboswitch structure in Bacillus subtilis using β-galactosidase assays. To assess the impact disruptions to riboswitch function have on cell fitness, we introduced these mutations into the native locus of the tandem glycine riboswitch within the B. subtilis genome. Our results indicate that glycine does not need to bind both aptamers for regulation in vivo and mutations perturbing riboswitch tertiary structure have the most severe effect on riboswitch function and gene expression. We also find that in B. subtilis, the glycine riboswitch-regulated gcvT operon is important for glycine detoxification. IMPORTANCE The glycine riboswitch is a unique cis-acting mRNA element that contains two tandem homologous glycine-binding domains that act on a single expression platform to regulate gene expression in response to glycine. While many in vitro experiments have characterized the tandem architecture of the glycine riboswitch, little work has investigated the behavior of this riboswitch in vivo. In this study, we analyzed the proposed models of tandem glycine riboswitch regulation in the context of its native locus within the Bacillus subtilis genome and examined how disruptions to glycine riboswitch function impact organismal fitness. Our work offers new insights into riboswitch function in vivo and reinforces the potential of riboswitches as novel antimicrobial targets. IMPORTANCE The glycine riboswitch is a unique cis-acting mRNA element that contains two tandem homologous glycine-binding domains that act on a single expression platform to regulate gene expression in response to glycine. While many in vitro experiments have characterized the tandem architecture of the glycine riboswitch, little work has investigated the behavior of this riboswitch in vivo. In this study, we analyzed the proposed models of tandem glycine riboswitch regulation in the context of its native locus within the Bacillus subtilis genome and examined how disruptions to glycine riboswitch function impact organismal fitness. Our work offers new insights into riboswitch function in vivo and reinforces the potential of riboswitches as novel antimicrobial targets.

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