RNA:DNA triple helices: from peculiar structures to pervasive chromatin regulators

2021 ◽  
Author(s):  
Andreas Adam Greifenstein ◽  
SoYoung Jo ◽  
Holger Bierhoff

Abstract The genomes of complex eukaryotes largely contain non-protein-coding DNA, which is pervasively transcribed into a plethora of non-coding RNAs (ncRNAs). The functional importance of many of these ncRNAs has been investigated in the last two decades, revealing their crucial and multifaceted roles in chromatin regulation. A common mode of action of ncRNAs is the recruitment of chromatin modifiers to specific regions in the genome. Whereas many ncRNA–protein interactions have been characterised in detail, binding of ncRNAs to their DNA target sites is much less understood. Recently developed RNA-centric methods have mapped the genome-wide distribution of ncRNAs, however, how ncRNAs achieve locus-specificity remains mainly unresolved. In terms of direct RNA–DNA interactions, two kinds of triple-stranded structures can be formed: R-loops consisting of an RNA:DNA hybrid and a looped out DNA strand, and RNA:DNA triple helices (triplexes), in which the RNA binds to the major groove of the DNA double helix by sequence-specific Hoogsteen base pairing. In this essay, we will review the current knowledge about RNA:DNA triplexes, summarising triplex formation rules, detection methods, and ncRNAs reported to engage in triplexes. While the functional characterisation of RNA:DNA triplexes is still anecdotal, recent advances in high-throughput and computational analyses indicate their widespread distribution in the genome. Thus, we are witnessing a paradigm shift in the appreciation of RNA:DNA triplexes, away from exotic structures towards a prominent mode of ncRNA–chromatin interactions.

2004 ◽  
Vol 69 (4) ◽  
pp. 715-747 ◽  
Author(s):  
Miroslav Fojta

This review is devoted to applications of mercury electrodes in the electrochemical analysis of nucleic acids and in studies of DNA structure and interactions. At the mercury electrodes, nucleic acids yield faradaic signals due to redox processes involving adenine, cytosine and guanine residues, and tensammetric signals due to adsorption/desorption of polynucleotide chains at the electrode surface. Some of these signals are highly sensitive to DNA structure, providing information about conformation changes of the DNA double helix, formation of DNA strand breaks as well as covalent or non-covalent DNA interactions with small molecules (including genotoxic agents, drugs, etc.). Measurements at mercury electrodes allow for determination of small quantities of unmodified or electrochemically labeled nucleic acids. DNA-modified mercury electrodes have been used as biodetectors for DNA damaging agents or as detection electrodes in DNA hybridization assays. Mercury film and solid amalgam electrodes possess similar features in the nucleic acid analysis to mercury drop electrodes. On the contrary, intrinsic (label-free) DNA electrochemical responses at other (non-mercury) solid electrodes cannot provide information about small changes of the DNA structure. A review with 188 references.


2009 ◽  
Vol 42 (1) ◽  
pp. 41-81 ◽  
Author(s):  
Tali E. Haran ◽  
Udayan Mohanty

AbstractShort runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.


2019 ◽  
Author(s):  
Hazal B. Kose ◽  
Sherry Xie ◽  
George Cameron ◽  
Melania S. Strycharska ◽  
Hasan Yardimci

AbstractThe DNA double helix is unwound by the Cdc45/Mcm2-7/GINS (CMG) complex at the eukaryotic replication fork. While isolated CMG unwinds duplex DNA very slowly, its fork unwinding rate is stimulated by an order of magnitude by single-stranded DNA binding protein, RPA. However, the molecular mechanism by which RPA enhances CMG helicase activity remained elusive. Here, we demonstrate that engagement of CMG with parental double-stranded DNA (dsDNA) at the replication fork impairs its helicase activity, explaining the slow DNA unwinding by isolated CMG. Using single-molecule and ensemble biochemistry, we show that binding of RPA to the excluded DNA strand prevents duplex engagement by the helicase and speeds up CMG-mediated DNA unwinding. When stalled due to dsDNA interaction, DNA rezipping-induced helicase backtracking re-establishes productive helicase-fork engagement underscoring the significance of plasticity in helicase action. Together, our results elucidate the dynamics of CMG at the replication fork and reveal how other replisome components can mediate proper DNA engagement by the replicative helicase to achieve efficient fork progression.


2021 ◽  
Author(s):  
Sandrine Lagarrigue ◽  
Matthias Lorthiois ◽  
Fabien Degalez ◽  
David Gilot ◽  
Thomas Derrien

AbstractAnimal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.


Author(s):  
Sumire Inaga ◽  
Hitoshi Osatake ◽  
Akihiro lino ◽  
Keiichi Tanaka

So far, the ultrastructure of DNA strand and nucleosome had been observed mainly by transmission electron microscopy with some techniques (thin-sectioning, spreading method, replica method and so on). Among them, the freeze-etching replica method gave high magnified images of DNA double helix (Ruben et al., 1989). Further, scanning tunneling microscopy also elucidated the images of major and minor grooves in a helical DNA duplex. Though scanning electron microscopy (SEM) was also applied for observing chromatin structures, it had been difficult to observe clearly such small materials. Because, the resolution of SEM was too poor to investigate such fine structures. The obstruction of resolution, however, was overcome by the development of an ultrahigh resolution SEM (UHS-T1, Tanaka et al., 1985). Using the SEM, we could successfully observed naked DNA strands and nucleosomes of chicken erythrocyte nuclei without any metal-coating.Preparations were made by the microspreading procedure basically according to the method of Seki et al.


Author(s):  
Martin Meagher ◽  
Madison N. Spence ◽  
Eric J. Enemark

Cells strongly regulate DNA replication to ensure genomic stability and prevent several diseases, including cancers. Eukaryotes and archaea strictly control DNA-replication initiation by the regulated loading of hexameric minichromosome maintenance (MCM) rings to encircle both strands of the DNA double helix followed by regulated activation of the loaded rings such that they then encircle one DNA strand while excluding the other. Both steps involve an open/closed ring transformation, allowing DNA strands to enter or exit. Here, the crystal structure of a dimer of the N-terminal domain of Sulfolobus solfataricus MCM with an intersubunit interface that is more extensive than in closed-ring structures, while including common interactions to enable facile interconversion, is presented. It is shown that the identified interface could stabilize open MCM rings by compensating for lost interactions at an open neighbor interface and that the prior open-ring cryo-EM structure of MCM loading has a similar extended interface adjacent to its open interface.


2021 ◽  
Vol 2 (2) ◽  
pp. 177-183
Author(s):  
András Kotschy

Összefoglaló. A betegségek mögött meghúzódó biokémiai, sejtbiológiai változások molekuláris szintű megértése a korszerű gyógyszerkutatás alapját képezi. A kiválasztott biológiai célpont, leggyakrabban egy fehérje, működésének gátlásától vagy fokozásától azt reméljük, hogy elősegíti a gyógyulást. A hagyományos gyógyszerkutatási megközelítések molekuláris alapját a kiválasztott fehérjével való közvetlen kölcsönhatás jelentette. Ugyanakkor a sejten belüli molekuláris biológiai folyamatok részletesebb megértése több új megközelítést nyitott a gyógyszerkutatás számára. A közlemény ezeket a gyógyszerkutatási irányzatokat mutatja be, külön kitérve biztonságosságukra. Summary. Human diseases originate from and are accompanied by changes in the biochemistry of cells. The molecular level understanding of these deviations from normal functioning is key to the curing of the diseases, therefore a principal objective of drug discovery. The key-lock principle postulated by Emil Fischer serves well the understanding of most enzymatic processes and has been helping researchers both in academia and industry to discover new drugs. The binding of a small molecule to the target protein and inhibiting or activating its function is the basis for the efficient functioning of a long list of current drugs. Sometimes the desired biological effect comes from the selective action on a single protein, in other instances it is the combined effect on the working of several proteins. The appropriate selectivity profile is key to the safety and efficiency of the drug in both cases. The completion of the Human Genome Project, in parallel with a significant improvement in the performance of the analytical instrumentation, increased our molecular and systemic level understanding of diseases immensely. Analysis of the differences between healthy and diseased cells and tissues led to the identification of new targets, a lot of which are not classical enzymes but proteins exerting their effect through molecular interactions with other proteins or nucleic acids. Although these proteins were considered undruggable some decades ago, their disease modifying potential led to the discovery of new approaches and modalities to target them. The inhibition of protein-protein interactions, for example, requires the selective targeting of hydrophobic surfaces, sometimes with very high affinity. Drug candidates acting through this molecular mechanism are typically beyond the size of classical drugs that might complicate their development. Besides interacting directly with the protein of interest we might also impact its working through manipulating its quantity within the cell. Interference with the proteasomal degradation of cellular proteins, blocking its working, or hijacking it to selectively increase the degradation of our protein of choice are promising new modalities that are transitioning from research into clinical practice. Alternatively, one might also interfere with the transcriptional machinery. Selective blocking of the messenger RNA responsible for carrying the sequence information of the targeted protein by using so called antisense oligonucleotides, small interfering RNAs, or micro RNAs can result in a decreased synthesis of the protein. Appropriately designed oligonucleotides can also enhance protein synthesis or lead to an alteration of the sequence to synthesize for a given protein. Finally, we might also target the epigenetic regulatory machinery, which is in charge of unpacking the DNA double helix from its storage form and making it available for transcription. This interference typically leads to a more complex change, the parallel modulation of the level of several proteins at the same time.


Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.


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