scholarly journals Antigene-block strategy: Effective regulation of gene expression by 2′,4′-BNA-modified TFOs with an additional stem-loop structure

2005 ◽  
Vol 49 (1) ◽  
pp. 335-336 ◽  
Author(s):  
Naoto Tsuda ◽  
Ayumi Matsumoto ◽  
Aya Ito ◽  
Tomomi Uneda ◽  
Atsuhiro Tanabe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure

scholarly journals The perplexities of ZC3H12A self-mRNA regulation

2016 ◽  
Vol 63 (3) ◽  
Author(s):  
Mateusz Wawro ◽  
Jakub Kochan ◽  
Aneta Kasza
Keyword(s):  
Gene Expression ◽  
Biological Activity ◽  
Transcriptional Regulation ◽  
Untranslated Region ◽  
Regulation Of Gene Expression ◽  
Loop Structure ◽  
Stem Loop ◽  
Mrna Regulation ◽  
Stem Loop Structure ◽  
Post Transcriptional Regulation

The mechanisms regulating transcripts turnover are key processes in the regulation of gene expression. The list of proteins involved in mRNAs degradation is still growing, however, the details of RNase-mRNAs interaction are not fully understood. ZC3H12A is a recently discovered inflammation-related RNase engaged in the control of proinflammatory cytokines transcripts turnover. ZC3H12A regulates also its own transcript half-live. We studied the details of this regulation. Our results confirm the importance of the 3’UTR in ZC3H12A-dependent ZC3H12A mRNA degradations. We compared mouse and human stem‑loop structures present in this region and discovered that human conserved stem-loop structure is not sufficient for ZC3H12A-dependent degradation. However, this structure is important for ZC3H12A mRNA post-transcriptional regulation. Our studies emphasize the importance of surroundings of the identified stem-loop structure for its biological activity. Removing of this region together with stem-loop structure greatly inhibits ZC3H12A regulation of the investigated 3’-untranslated region (3’UTR).

scholarly journals Functional Genetic Elements for Controlling Gene Expression inCupriavidus necatorH16

2018 ◽  
Vol 84 (19) ◽  
Author(s):  
Swathi Alagesan ◽  
Erik K. R. Hanko ◽  
Naglis Malys ◽  
Muhammad Ehsaan ◽  
Klaus Winzer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dynamic Range ◽  
Loop Structure ◽  
Stem Loop ◽  
Control Of Gene Expression ◽  
Content Type ◽  
Genetic Elements ◽  
Stem Loop Structure ◽  
Inducible Systems ◽  
The Impact

ABSTRACTA robust and predictable control of gene expression plays an important role in synthetic biology and biotechnology applications. Development and quantitative evaluation of functional genetic elements, such as constitutive and inducible promoters as well as ribosome binding sites (RBSs), are required. In this study, we designed, built, and tested promoters and RBSs for controlling gene expression in the model lithoautotrophCupriavidus necatorH16. A series of variable-strength, insulated, constitutive promoters exhibiting predictable activity within a >700-fold dynamic range was compared to the native PphaC, with the majority of promoters displaying up to a 9-fold higher activity. Positively (AraC/ParaBAD-l-arabinose and RhaRS/PrhaBAD-l-rhamnose) and negatively (AcuR/PacuRI-acrylate and CymR/Pcmt-cumate) regulated inducible systems were evaluated. By supplying different concentrations of inducers, a >1,000-fold range of gene expression levels was achieved. Application of inducible systems for controlling expression of the isoprene synthase geneispSled to isoprene yields that exhibited a significant correlation to the reporter protein synthesis levels. The impact of designed RBSs and other genetic elements, such as mRNA stem-loop structure and A/U-rich sequence, on gene expression was also evaluated. A second-order polynomial relationship was observed between the RBS activities and isoprene yields. This report presents quantitative data on regulatory genetic elements and expands the genetic toolbox ofC. necator.IMPORTANCEThis report provides tools for robust and predictable control of gene expression in the model lithoautotrophC. necatorH16. To address a current need, we designed, built, and tested promoters and RBSs for controlling gene expression inC. necatorH16. To answer a question on how existing and newly developed inducible systems compare, two positively (AraC/ParaBAD-l-arabinose and RhaRS/PrhaBAD-l-rhamnose) and two negatively (AcuR/PacuRI-acrylate and CymR/Pcmt-cumate) regulated inducible systems were quantitatively evaluated and their induction kinetics analyzed. To establish if gene expression can be further improved, the effect of genetic elements, such as mRNA stem-loop structure and A/U-rich sequence, on gene expression was evaluated. Using isoprene production as an example, the study investigated if and to what extent chemical compound yield correlates to the level of gene expression of product-synthesizing enzyme.

968: Gelsolin Gene Silencing Involving Unusual Chromatin Structures and a Novel Stem Loop Structure of the Promoter Region in Human Bladder Cancer

2004 ◽  
Vol 171 (4S) ◽  
pp. 256-257
Author(s):  
Kazunori Haga ◽  
Ataru Sazawa ◽  
Toru Harabayashi ◽  
Nobuo Shinohara ◽  
Minoru Nomoto ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Gene Silencing ◽  
Promoter Region ◽  
Loop Structure ◽  
Human Bladder Cancer ◽  
Human Bladder ◽  
Stem Loop ◽  
Stem Loop Structure

Detection and sequence analysis of an imperfect stem-loop structure in cis activating gene element from SV40PolyA

2011 ◽  
Vol 33 (4) ◽  
pp. 337-346
Author(s):  
Hong-Gang WANG ◽  
Huan MA ◽  
Zhu LI ◽  
Bin ZHANG ◽  
Xiang-Yang JING ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
In Cis ◽  
Gene Element

scholarly journals Identification and in Silico Characterization of Novel and Conserved MicroRNAs in Methyl Jasmonate-Stimulated Scots Pine (Pinus sylvestris L.) Needles

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 384
Author(s):  
Baiba Krivmane ◽  
Ilze Šņepste ◽  
Vilnis Šķipars ◽  
Igor Yakovlev ◽  
Carl Gunnar Fossdal ◽  
...  
Keyword(s):  
Methyl Jasmonate ◽  
Scots Pine ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Stem Loop ◽  
Protein Coding ◽  
Stem Loop Structure ◽  
In Silico Characterization ◽  
Potential Precursor

MicroRNAs (miRNAs) are non-protein coding RNAs of ~20–24 nucleotides in length that play an important role in many biological and metabolic processes, including the regulation of gene expression, plant growth and developmental processes, as well as responses to stress and pathogens. The aim of this study was to identify and characterize novel and conserved microRNAs expressed in methyl jasmonate-treated Scots pine needles. In addition, potential precursor sequences and target genes of the identified miRNAs were determined by alignment to the Pinus unigene set. Potential precursor sequences were identified using the miRAtool, conserved miRNA precursors were also tested for the ability to form the required stem-loop structure, and the minimal folding free energy indexes were calculated. By comparison with miRBase, 4975 annotated sequences were identified and assigned to 173 miRNA groups, belonging to a total of 60 conserved miRNA families. A total of 1029 potential novel miRNAs, grouped into 34 families were found, and 46 predicted precursor sequences were identified. A total of 136 potential target genes targeted by 28 families were identified. The majority of previously reported highly conserved plant miRNAs were identified in this study, as well as some conserved miRNAs previously reported to be monocot specific. No conserved dicot-specific miRNAs were identified. A number of potential gymnosperm or conifer specific miRNAs were found, shared among a range of conifer species.

scholarly journals Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting

2021 ◽  
Vol 14 (2) ◽  
pp. 121
Author(s):  
André Miranda ◽  
Tiago Santos ◽  
Eric Largy ◽  
Carla Cruz
Keyword(s):  
Loop Structure ◽  
Binding Properties ◽  
Stem Loop ◽  
Affinity Ligand ◽  
Stem Loop Structure ◽  
Topology Maintenance ◽  
G Quadruplex ◽  
Dimeric Form ◽  
Biophysical Techniques ◽  
Melting Experiments

We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K+ promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.

scholarly journals Role of a Stem-Loop Structure inHelicobacter pylori cagATranscript Stability

2018 ◽  
Vol 87 (2) ◽  
Author(s):  
John T. Loh ◽  
Aung Soe Lin ◽  
Amber C. Beckett ◽  
Mark S. McClain ◽  
Timothy L. Cover
Keyword(s):  
Steady State ◽  
Untranslated Region ◽  
Loop Structure ◽  
Stem Loop ◽  
Content Type ◽  
Transcript Stability ◽  
Protein Levels ◽  
Caga Protein ◽  
Stem Loop Structure ◽  
Steady State Levels

ABSTRACTHelicobacter pyloriCagA is a secreted effector protein that contributes to gastric carcinogenesis. Previous studies showed that there is variation amongH. pyloristrains in the steady-state levels of CagA and that a strain-specific motif downstream of thecagAtranscriptional start site (the +59 motif) is associated with both high levels of CagA and premalignant gastric histology. ThecagA5′ untranslated region contains a predicted stem-loop-forming structure adjacent to the +59 motif. In the current study, we investigated the effect of the +59 motif and the adjacent stem-loop oncagAtranscript levels andcagAmRNA stability. Using site-directed mutagenesis, we found that mutations predicted to disrupt the stem-loop structure resulted in decreased steady-state levels of both thecagAtranscript and the CagA protein. Additionally, these mutations resulted in a decreasedcagAmRNA half-life. Mutagenesis of the +59 motif without altering the stem-loop structure resulted in reduced steady-statecagAtranscript and CagA protein levels but did not affectcagAtranscript stability.cagAtranscript stability was not affected by increased sodium chloride concentrations, an environmental factor known to augmentcagAtranscript levels and CagA protein levels. These results indicate that both a predicted stem-loop structure and a strain-specific +59 motif in thecagA5′ untranslated region influence the levels ofcagAexpression.

scholarly journals Mechanism of Rep-Mediated Adeno-Associated Virus Origin Nicking

2000 ◽  
Vol 74 (17) ◽  
pp. 7762-7771 ◽  
Author(s):  
J. Rodney Brister ◽  
Nicholas Muzyczka
Keyword(s):  
Specific Activity ◽  
Dna Helicase ◽  
Loop Structure ◽  
Stem Loop ◽  
Adeno Associated Virus ◽  
Stem Loop Structure ◽  
Virus Origin ◽  
Rep Proteins ◽  
Sequence Elements ◽  
Origin Function

ABSTRACT The single-stranded adeno-associated virus type 2 (AAV) genome is flanked by terminal repeats (TRs) that fold back on themselves to form hairpinned structures. During AAV DNA replication, the TRs are nicked by the virus-encoded Rep proteins at the terminal resolution site (trs). This origin function apparently requires three sequence elements, the Rep binding element (RBE), a small palindrome that comprises a single tip of an internal hairpin within the TR (RBE′), and the trs. Previously, we determined the sequences at the trs required for Rep-mediated cleavage and demonstrated that the trs endonuclease reaction occurs in two discrete steps. In the first step, the Rep DNA helicase activity unwinds the TR, thereby extruding a stem-loop structure at thetrs. In the second step, Rep transesterification activity cleaves the trs. Here we investigate the contribution of the RBE and RBE′ during this process. Our data indicate that Rep is tethered to the RBE in a specific orientation duringtrs nicking. This orientation appears to align Rep on the AAV TR, allowing specific nucleotide contacts with the RBE′ and directing nicking to the trs. Accordingly, alterations in the polarity or position of the RBE relative to the trsgreatly inhibit Rep nicking. Substitutions within the RBE′ also reduce Rep specific activity, but to a lesser extent. Interestingly, Rep interactions with the RBE and RBE′ during nicking seem to be functionally distinct. Rep contacts with the RBE appear necessary for both the DNA helicase and trs cleavage steps of the endonuclease reaction. On the other hand, RBE′ contacts seem to be required primarily for TR unwinding and formation of thetrs stem-loop structure, not cleavage. Together, these results suggest a model of Rep interaction with the AAV TR during origin nicking through a tripartite cleavage signal comprised of the RBE, the RBE′, and the trs.

Sign in / Sign up

Export Citation Format

Share Document