scholarly journals The role of G-quadruplex/i-motif secondary structures as cis-acting regulatory elements

2010 ◽  
Vol 82 (8) ◽  
pp. 1609-1621 ◽  
Author(s):  
Samantha Kendrick ◽  
Laurence H. Hurley
Keyword(s):  
Secondary Structure ◽  
Small Molecules ◽  
Dynamic Equilibrium ◽  
Double Helix ◽  
Regulatory Elements ◽  
Cis Acting ◽  
Secondary Structure Formation ◽  
G Quadruplex ◽  
Intracellular Proteins

The nature of DNA has captivated scientists for more than 50 years. The discovery of the double-helix model of DNA by Watson and Crick in 1953 not only established the primary structure of DNA, but also provided the mechanism behind DNA function. Since then, researchers have continued to further the understanding of DNA structure and its pivotal role in transcription. The demonstration of DNA secondary structure formation has allowed for the proposal that the dynamics of DNA itself can function to modulate transcription. This review presents evidence that DNA can exist in a dynamic equilibrium between duplex and secondary conformations. In addition, data demonstrating that intracellular proteins as well as small molecules can shift this equilibrium in either direction to alter gene transcription will be discussed, with a focus on the modulation of proto-oncogene expression.

scholarly journals Novel sequence variations in LAMA2 and SGCG genes modulating cis-acting regulatory elements and RNA secondary structure

2010 ◽  
Vol 33 (1) ◽  
pp. 190-197 ◽  
Author(s):  
Olfa Siala ◽  
Ikhlass Hadj Salem ◽  
Abdelaziz Tlili ◽  
Imen Ammar ◽  
Hanen Belguith ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Regulatory Elements ◽  
Cis Acting ◽  
Sequence Variations

scholarly journals Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1669
Author(s):  
Angelo De Paolis ◽  
Sofia Caretto ◽  
Angela Quarta ◽  
Gian-Pietro Di Sansebastiano ◽  
Irene Sbrocca ◽  
...  
Keyword(s):  
Artemisia Annua ◽  
Antimalarial Activity ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome ◽  
Rapid Amplification

Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.

scholarly journals Beyond G-Quadruplexes—The Effect of Junction with Additional Structural Motifs on Aptamers Properties

2021 ◽  
Vol 22 (18) ◽  
pp. 9948
Author(s):  
Weronika Kotkowiak ◽  
Anna Pasternak
Keyword(s):  
Nucleic Acid ◽  
Regulatory Elements ◽  
Research Area ◽  
Structural Elements ◽  
Molecular Tools ◽  
Nucleic Acid Structure ◽  
G Quadruplex ◽  
Target Molecules ◽  
Acid Structure

G-quadruplexes constitute an important type of nucleic acid structure, which can be found in living cells and applied by cell machinery as pivotal regulatory elements. Importantly, robust development of SELEX technology and modern, nucleic acid-based therapeutic strategies targeted towards various molecules have also revealed a large group of potent aptamers whose structures are grounded in G-quadruplexes. In this review, we analyze further extension of tetraplexes by additional structural elements and investigate whether G-quadruplex junctions with duplex, hairpin, triplex, or second G-quadruplex motifs are favorable for aptamers stability and biological activity. Furthermore, we indicate the specific and pivotal role of the G-quadruplex domain and the additional structural elements in interactions with target molecules. Finally, we consider the potency of G-quadruplex junctions in future applications and indicate the emerging research area that is still waiting for development to obtain highly specific and effective nucleic acid-based molecular tools.

scholarly journals Exon B of human surfactant protein A2 mRNA, alone or within its surrounding sequences, interacts with 14-3-3; role of cis-elements and secondary structure

2013 ◽  
Vol 304 (11) ◽  
pp. L722-L735 ◽  
Author(s):  
Georgios T. Noutsios ◽  
Patricia Silveyra ◽  
Faizah Bhatti ◽  
Joanna Floros
Keyword(s):  
Secondary Structure ◽  
Mass Spectroscopy ◽  
Splice Variant ◽  
Protein A ◽  
Surfactant Protein ◽  
Regulatory Elements ◽  
Cytoskeletal Proteins ◽  
Cis Elements ◽  
Specific Manner

Human surfactant protein A, an innate immunity molecule, is encoded by two genes: SFTPA1 (SP-A1) and SFTPA2 (SP-A2). The 5′ untranslated (5′UTR) splice variant of SP-A2 (ABD), but not of SP-A1 (AD), contains exon B (eB), which is an enhancer for transcription and translation. We investigated whether eB contains cis-regulatory elements that bind trans-acting factors in a sequence-specific manner as well as the role of the eB mRNA secondary structure. Binding of cytoplasmic NCI-H441 proteins to wild-type eB, eB mutant, AD, and ABD 5′UTR mRNAs were studied by RNA electromobility shift assays (REMSAs). The bound proteins were identified by mass spectroscopy and specific antibodies (Abs). We found that 1) proteins bind eB mRNA in a sequence-specific manner, with two cis-elements identified within eB to be important; 2) eB secondary structure is necessary for binding; 3) mass spectroscopy and specific Abs in REMSAs identified 14-3-3 proteins to bind (directly or indirectly) eB and the natural SP-A2 (ABD) splice variant but not the SP-A1 (AD) splice variant; 4) other ribosomal and cytoskeletal proteins, and translation factors, are also present in the eB mRNA-protein complex; 5) knockdown of 14-3-3 β/α isoform resulted in a downregulation of SP-A2 expression. In conclusion, proteins including the 14-3-3 family bind two cis-elements within eB of hSP-A2 mRNA in a sequence- and secondary structure-specific manner. Differential regulation of SP-A1 and SP-A2 is mediated by the 14-3-3 protein family as well as by a number of other proteins that bind UTRs with or without eB mRNA.

scholarly journals Genome-Wide Analysis of SRNF Genes in Gossypium hirsutum Reveals the Role of GhSRNF18 in Primary Root Growth

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Yu ◽  
Shuojun Zhang ◽  
Hailun Liu ◽  
Yufei Wang ◽  
Yiting Wei ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Plant Species ◽  
Primary Root ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cis Acting ◽  
Over Expression ◽  
Root Morphogenesis

Root systems are instrumental for water and nutrient uptake and the anchorage of plants in the soil. Root regulating GL2-interacting repressors (GIRs) contain a Short RING-like Zinc-Finger (SRNF) domain, but there has been no comprehensive characterization about this gene family in any plant species. Here, we renamed the GIR-like proteins as SRNF proteins due to their conserved domain and identified 140 SRNF genes from 16 plant species including 24 GhSRNF genes in Gossypium hirsutum. Phylogenetic analysis of the SRNFs revealed both similarities and divergences between five subfamilies. Notably, synteny analysis revealed that polyploidization and whole-genome duplication contribute to the expansion of the GhSRNF gene family. Various cis-acting regulatory elements were shown to be pertinent to light, phytohormone, defense responsive, and meristem regulation. Furthermore, GhSRNF2/15 were predominantly expressed in root, whereas the expression of GhSRNF18 is positively correlated with the primary root (PR) length in G. hirsutum, quantified by quantitative real-time PCR (qRT-PCR). Over-expression of GhSRNF18 in Arabidopsis and virus-induced gene silencing (VIGS) of GhSRNF18 in G. hirsutum has revealed the role of GhSRNF18 in PR growth. The over-expression of GhSRNF18 in Arabidopsis resulted in an increase of meristematic activities and auxin accumulations in PRs, which were consistent with the transcriptomic data. Our results suggested that GhSRNF18 positively regulates PR growth. This study increased our understanding of the SRNF gene family in plants and provided a novel rationale for the further investigation of cotton root morphogenesis regulated by the GhSRNFs.

The role of positive charges on G-quadruplex binding small molecules: Learning from bisaryldiketene derivatives

2013 ◽  
Vol 1830 (11) ◽  
pp. 5006-5013 ◽  
Author(s):  
Shuo-Bin Chen ◽  
Qiu-Xia Shi ◽  
Dan Peng ◽  
Si-Yuan Huang ◽  
Tian-Miao Ou ◽  
...  
Keyword(s):  
Small Molecules ◽  
G Quadruplex

scholarly journals Deciphering the Role of various cis-acting regulatory elements in controlling SamDC gene expression in Rice

2014 ◽  
Vol 9 (3) ◽  
pp. e28391 ◽  
Author(s):  
Supratim Basu ◽  
Aryadeep Roychoudhury ◽  
Dibyendu N Sengupta
Keyword(s):  
Gene Expression ◽  
Regulatory Elements ◽  
Cis Acting

scholarly journals Modelling the impact of magnesium ions concentration on the folding of the SAM-II riboswitch

2021 ◽  
Author(s):  
Osama Alaidi
Keyword(s):  
Small Molecules ◽  
Messenger Rna ◽  
Regulatory Elements ◽  
Vital Role ◽  
Magnesium Ions ◽  
Bacterial Gene ◽  
Titration Curves ◽  
Adenosyl Methionine ◽  
The Impact

ABSTRACTRiboswitches are regulatory elements present in bacterial messenger RNA acting as sensors of small molecules and consequently playing a vital role in bacterial gene regulation. The SAM-II riboswitch is a class of riboswitches, that recognizes S-adenosyl methionine. It has been previously illustrated that the presence of Mg2+ ions stabilizes the pre-existing minor state of the riboswitch, which is structurally characterised by having a nucleated pseudoknot, leading to the increase of its probability. In this study, an analytical equilibrium model is developed to describe the impact of Mg2+ ions concentration on the folding of the SAM-II riboswitch, linking RNA folding and tertiary interactions energetics to ligand binding, and, hence enabling quantitative predictions. The method was used to study the role of the P1 helix sequence in determining the fraction of binding competent conformers of the SAM-II riboswitch, by simulating the Mg2+ titration curves of various mutants.Graphical abstract

scholarly journals G-quadruplex located in the 5′UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance

2019 ◽  
Vol 47 (19) ◽  
pp. 10247-10266 ◽  
Author(s):  
Rachel Jodoin ◽  
Julie C Carrier ◽  
Nathalie Rivard ◽  
Martin Bisaillon ◽  
Jean-Pierre Perreault
Keyword(s):  
Colorectal Cancer ◽  
Secondary Structure ◽  
Cancer Cells ◽  
Mrna Translation ◽  
Regulatory Elements ◽  
Protein Isoforms ◽  
Initiation Of Translation ◽  
G Quadruplex ◽  
Colorectal Cancer Cells ◽  
Independent Translation

Abstract The anti-apoptotic BAG-1 protein isoforms are known to be overexpressed in colorectal tumors and are considered to be potential therapeutic targets. The isoforms are derived from alternative translation initiations occuring at four in-frame start codons of a single mRNA transcript. Its 5′UTR also contains an internal ribosome entry site (IRES) regulating the cap-independent translation of the transcript. An RNA G-quadruplex (rG4) is located at the 5′end of the BAG-1 5′UTR, upstream of the known cis-regulatory elements. Herein, we observed that the expression of BAG-1 isoforms is post-transcriptionally regulated in colorectal cancer cells and tumors, and that stabilisation of the rG4 by small molecules ligands reduces the expression of endogenous BAG-1 isoforms. We demonstrated a critical role for the rG4 in the control of both cap-dependent and independent translation of the BAG-1 mRNA in colorectal cancer cells. Additionally, we found an upstream ORF that also represses BAG-1 mRNA translation. The structural probing of the complete 5′UTR showed that the rG4 acts as a steric block which controls the initiation of translation at each start codon of the transcript and also maintains the global 5′UTR secondary structure required for IRES-dependent translation.

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