scholarly journals Synthesis and in vitro assessment of chemically modified siRNAs targeting BCL2 that contain 2′-ribose and triazole-linked backbone modifications

MedChemComm ◽  
2015 ◽  
Vol 6 (6) ◽  
pp. 1210-1215 ◽  
Author(s):  
Gordon Hagen ◽  
Brandon J. Peel ◽  
John Samis ◽  
Jean-Paul Desaulniers
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chemically Modified ◽  
Naturally Occurring ◽  
In Vitro Assessment ◽  
Transcriptional Gene Regulation ◽  
Deleterious Genes

Short-interfering RNAs (siRNAs) are naturally occurring biomolecules used for post-transcriptional gene regulation, and therefore hold promise as a future therapeutic by silencing gene expression of overexpressed deleterious genes.

Post-transcriptional gene regulation in chondrocytes

2010 ◽  
Vol 38 (6) ◽  
pp. 1627-1631 ◽  
Author(s):  
Simon R. Tew ◽  
Peter D. Clegg
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Articular Chondrocytes ◽  
Transcriptional Level ◽  
Control Of Gene Expression ◽  
Health And Disease ◽  
Unexplored Area ◽  
Steady State Levels ◽  
Transcriptional Gene Regulation

The control of gene expression in articular chondrocytes is an essential factor in maintaining the homoeostasis of extracellular matrix synthesis and turnover necessary in healthy articular cartilage. Although much is known of how steady-state levels of gene expression and rates of transcription are altered, there has been a poorer understanding of gene control at the post-transcriptional level and its relevance to cartilage health and disease. Now, an emerging picture is developing of the importance of this tier of gene regulation, driven by in vitro studies and mouse genetic models. This level of cellular regulation represents an as yet unexplored area of potential intervention for the treatment of degenerative cartilage disorders such as osteoarthritis.

scholarly journals Variation in the Group B Streptococcus CsrRS Regulon and Effects on Pathogenicity

2008 ◽  
Vol 190 (6) ◽  
pp. 1956-1965 ◽  
Author(s):  
Sheng-Mei Jiang ◽  
Nadeeza Ishmael ◽  
Julie Dunning Hotopp ◽  
Manuela Puliti ◽  
Luciana Tissi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Virulence Factors ◽  
Group B Streptococcus ◽  
Regulatory System ◽  
Systemic Infection ◽  
Global Gene Expression ◽  
Pathogenic Potential ◽  
Group B

ABSTRACT CsrRS (or CovRS) is a two-component regulatory system that controls expression of multiple virulence factors in the important human pathogen group B Streptococcus (GBS). We now report global gene expression studies in GBS strains 2603V/R and 515 and their isogenic csrR and csrS mutants. Together with data reported previously for strain NEM316, the results reveal a conserved 39-gene CsrRS regulon. In vitro phosphorylation-dependent binding of recombinant CsrR to promoter regions of both positively and negatively regulated genes suggests that direct binding of CsrR can mediate activation as well as repression of target gene expression. Distinct patterns of gene regulation in csrR versus csrS mutants in strain 2603V/R compared to 515 were associated with different hierarchies of relative virulence of wild-type, csrR, and csrS mutants in murine models of systemic infection and septic arthritis. We conclude that CsrRS regulates a core group of genes including important virulence factors in diverse strains of GBS but also displays marked variability in the repertoire of regulated genes and in the relative effects of CsrS signaling on CsrR-mediated gene regulation. Such variation is likely to play an important role in strain-specific adaptation of GBS to particular host environments and pathogenic potential in susceptible hosts.

scholarly journals Gene expression profiling of acute type A aortic dissection combined with in vitro assessment†

2017 ◽  
Vol 52 (4) ◽  
pp. 810-817 ◽  
Author(s):  
Naoyuki Kimura ◽  
Kyoko Futamura ◽  
Mamoru Arakawa ◽  
Naoko Okada ◽  
Fabian Emrich ◽  
...  
Keyword(s):  
Gene Expression ◽  
Aortic Dissection ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Type A ◽  
Acute Type ◽  
Type A Aortic Dissection ◽  
In Vitro Assessment

scholarly journals Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model

2021 ◽  
Author(s):  
Genevieve Housman ◽  
Emilie Briscoe ◽  
Yoav Gilad
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Bone Cells ◽  
Cell Types ◽  
Differentially Expressed ◽  
Functional Genomic ◽  
Cell Culture Model ◽  
Culture Model ◽  
Study Gene Regulation

AbstractThe evolution of complex skeletal traits in primates was likely influenced by both genetic and environmental factors. Because skeletal tissues are notoriously challenging to study using functional genomic approaches, they remain poorly characterized even in humans, let alone across multiple species. The challenges involved in obtaining functional genomic data from the skeleton, combined with the difficulty of obtaining such tissues from nonhuman apes, motivated us to consider an alternative in vitro system with which to comparatively study gene regulation in skeletal cell types. Specifically, we differentiated six human and six chimpanzee induced pluripotent stem cell lines (iPSCs) into mesenchymal stem cells (MSCs) and subsequently into osteogenic cells (bone cells). We validated differentiation using standard methods and collected single-cell RNA sequencing data from over 100,000 cells across multiple samples and replicates at each stage of differentiation. While most genes that we examined display conserved patterns of expression across species, hundreds of genes are differentially expressed (DE) between humans and chimpanzees within and across stages of osteogenic differentiation. Some of these interspecific DE genes show functional enrichments relevant in skeletal tissue trait development. Moreover, topic modeling indicates that interspecific gene programs become more pronounced as cells mature. Overall, we propose that this in vitro model can be used to identify interspecific regulatory differences that may have contributed to skeletal trait differences between species.Author SummaryPrimates display a range of skeletal morphologies and susceptibilities to skeletal diseases, but the molecular basis of these phenotypic differences is unclear. Studies of gene expression variation in primate skeletal tissues are extremely restricted due to the ethical and practical challenges associated with collecting samples. Nevertheless, the ability to study gene regulation in primate skeletal tissues is crucial for understanding how the primate skeleton has evolved. We therefore developed a comparative primate skeletal cell culture model that allows us to access a spectrum of human and chimpanzee cell types as they differentiate from stem cells into bone cells. While most gene expression patterns are conserved across species, we also identified hundreds of differentially expressed genes between humans and chimpanzees within and across stages of differentiation. We also classified cells by osteogenic stage and identified additional interspecific differentially expressed genes which may contribute to skeletal trait differences. We anticipate that this model will be extremely useful for exploring questions related to gene regulation variation in primate bone biology and development.

Gene Regulation during the Erythrocytic Differentiation of Embryonic Stem Cells.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4255-4255
Author(s):  
Ewa Carrier ◽  
Shermila Kausal ◽  
Anand S. Srivastava
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Growth Factors ◽  
Es Cells ◽  
Embryonic Stem ◽  
Globin Genes ◽  
Rt Pcr ◽  
Expression Studies ◽  
Gene Expression Studies

Abstract We have studied the in vitro differentiation of murine embryonic stem cells (ES cells) towards erythropoiesis and expression of genes during this process. It has been reported that dexamethasone directs ES cells towards erythrocytic differentiation but the mechanism of gene regulation induced by dexamethasone is not well understood. We hypothesized that dexamethasone induces upregulation of erythropoietic genes such as GATA-1, FLK-1, EPO-R and directs ES cells towards erythropoietic differentiation. Murine ES cells (129 CCE) obtained from Dr. Nagy laboratory, Canada (Nagy et al., Histochem Cell Biol., 2001; 115:49–58) were subjected to the in vitro primary hematopoietic differentiation media containing methylcellulose, IMDM, IL -3, IL-6 and SCF (stem cell factor) without LIF (leukemia inhibitory factor) to promote embryoid body (EB) formation. Total RNA was collected on day 3, 5 and 9 EBs for gene expression studies using RT-PCR. On day 9 EBs were subjected to secondary differentiation using three different cytokines and growth factors combination 1) SCF, EPO, dexamethasone, IGF, 2) SCF, IL-3, IL-6, TPO, 3) SCF IL-3, IL-6, TPO, EPO. Total RNA from day12 of secondary differentiated ES cells was collected to study cytokines and growth factors dependent erythrocytic differentiation and gene regulation, using RT-PCR. Our results demonstrate upregulation of Gata-1, Flk-1, HoxB-4, Epo-R and globin genes (α-globin, BH-1 globin, β-major globin, e -globin and z-globin) in the 9 days old EBs, whereas, RNA collected from 5 days old EBs showed expression of HoxB-4, e-globin, γ-globin, BH1-globin and FLK-1. Three days old EBs showed only HoxB-4 and FLK-1 gene expression and lack of expression of globin genes, indicating that erythtropoiesis-specific genes activate later. Gene expression studies of RNA collected from secondary differentiated ES cells and media containing dexamethasone showed downregulation of GATA-3 and upregulation of GATA-1, Flk-1 and Epo-R in comparison to the two other cytokines and growth factors media combination. These results confirm our hypothesis that dexamethasome induces erythropoiesis by down regulating GATA -3 and upregulating erythropoietic-related genes such as GATA-1, Flk-1 and Epo-R. The morphological characteristics of cells after secondary differentiation showed enhanced production of erythrocytic precursors in dexamethasone containing media, which corresponded with molecular studies. Further studies will address the role of wnt/β-catenin and E-cadherin in this process.

scholarly journals Characterization of Engineered PreQ1 Riboswitches for Inducible Gene Regulation in Mycobacteria

2017 ◽  
Vol 199 (6) ◽  
Author(s):  
Erik R. Van Vlack ◽  
Shana Topp ◽  
Jessica C. Seeliger
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Fluorescent Protein ◽  
Lactobacillus Rhamnosus ◽  
Content Type ◽  
Naturally Occurring ◽  
Binding Event ◽  
Steady State Model ◽  
Green Fluorescent ◽  
Inducible Gene

ABSTRACT We report here the behavior of naturally occurring and rationally engineered preQ1 riboswitches and their application to inducible gene regulation in mycobacteria. Because mycobacteria lack preQ1 biosynthetic genes, we hypothesized that preQ1 could be used as an exogenous nonmetabolite ligand to control riboswitches in mycobacteria. Selected naturally occurring preQ1 riboswitches were assayed and successfully drove preQ1-dependent repression of a green fluorescent protein reporter in Mycobacterium smegmatis. Using structure-based design, we engineered three preQ1 riboswitches from Thermoanaerobacter tencongensis, Bacillus subtilis, and Lactobacillus rhamnosus toward achieving higher response ratios and increased repression. Assuming a steady-state model, variants of the T. tencongensis riboswitch most closely followed the predicted trends. Unexpectedly, the preQ1 dose response was best described by a model with a second, independent preQ1 binding site. This behavior was general to the preQ1 riboswitch family, since the wild type and rationally designed mutants of riboswitches from all three bacteria behaved analogously. Across all variants, the response ratios, which describe expression in the absence versus the presence of preQ1, ranged from <2 to ∼10, but repression in all cases was incomplete up to 1 mM preQ1. By reducing the transcript expression level, we obtained a preQ1 riboswitch variant appropriate for inducible knockdown applications. We further showed that the preQ1 response is reversible, is titratable, and can be used to control protein expression in mycobacteria within infected macrophages. By engineering naturally occurring preQ1 riboswitches, we have not only extended the tools available for inducible gene regulation in mycobacteria but also uncovered new behavior of these riboswitches. IMPORTANCE Riboswitches are elements found in noncoding regions of mRNA that regulate gene expression, typically in response to an endogenous metabolite. Riboswitches have emerged as important tools for inducible gene expression in diverse organisms. We noted that mycobacteria lack the biosynthesis genes for preQ1, a ligand for riboswitches from diverse bacteria. Predicting that preQ1 is not present in mycobacteria, we showed that it controls optimized riboswitches appropriate for gene knockdown applications. Further, the riboswitch response is subject to a second independent preQ1 binding event that has not been previously documented. By engineering naturally occurring riboswitches, we have uncovered a new behavior, with implications for riboswitch function in its native context, and extended the tools available for inducible gene regulation in mycobacteria.

scholarly journals MLL-mediated transcriptional gene regulation investigated by gene expression profiling

Oncogene ◽  
2003 ◽  
Vol 22 (23) ◽  
pp. 3655-3668 ◽  
Author(s):  
Dorothe Schraets ◽  
Tanja Lehmann ◽  
Theo Dingermann ◽  
Rolf Marschalek
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Transcriptional Gene Regulation
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