RNA-cDNA hybrids mediate transposition via different mechanisms

Abstract Retrotransposons can represent half of eukaryotic genomes. Retrotransposon dysregulation destabilizes genomes and has been linked to various human diseases. Emerging regulators of retromobility include RNA–DNA hybrid-containing structures known as R-loops. Accumulation of these structures at the transposons of yeast 1 (Ty1) elements has been shown to increase Ty1 retromobility through an unknown mechanism. Here, via a targeted genetic screen, we identified the rnh1Δ rad27Δ yeast mutant, which lacked both the Ty1 inhibitor Rad27 and the RNA–DNA hybrid suppressor Rnh1. The mutant exhibited elevated levels of Ty1 cDNA-associated RNA–DNA hybrids that promoted Ty1 mobility. Moreover, in this rnh1Δ rad27Δ mutant, but not in the double RNase H mutant rnh1Δ rnh201Δ, RNA–DNA hybrids preferentially existed as duplex nucleic acid structures and increased Ty1 mobility in a Rad52-dependent manner. The data indicate that in cells lacking RNA–DNA hybrid and Ty1 repressors, elevated levels of RNA-cDNA hybrids, which are associated with duplex nucleic acid structures, boost Ty1 mobility via a Rad52-dependent mechanism. In contrast, in cells lacking RNA–DNA hybrid repressors alone, elevated levels of RNA-cDNA hybrids, which are associated with triplex nucleic acid structures, boost Ty1 mobility via a Rad52-independent process. We propose that duplex and triplex RNA–DNA hybrids promote transposon mobility via Rad52-dependent or -independent mechanisms.

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Sphingosine 1-phosphate stimulates Na+/H+ exchange in thyroid FRTL-5 cells

AJP Cell Physiology ◽

10.1152/ajpcell.1997.272.3.c1052 ◽

1997 ◽

Vol 272 (3) ◽

pp. C1052-C1057 ◽

Cited By ~ 12

Author(s):

K. Tornquist

Keyword(s):

Phosphatidic Acid ◽

Phospholipase D ◽

Mechanism Of Action ◽

Cell Types ◽

Dependent Manner ◽

Tetraacetic Acid ◽

Sphingosine 1 Phosphate ◽

Dose Dependent ◽

Dependent Mechanism ◽

In Cells

Sphingosine derivatives are potent mitogens in several cell types. Many mitogens activate the Na+/H+ exchange, although the interrelationships between Na+/H+ exchange and mitogenesis are unclear. The present investigation in thyroid FRTL-5 cells shows that sphingosine 1-phosphate (SPP) activates Na+/H+ exchange in a dose-dependent manner in acid-loaded cells. The effect of SPP was abolished in a Na+-free buffer and by pretreatment of the cells with ethylisopropylamiloride. SPP did not affect basal intracellular pH (pHi). SPP stimulated the release of sequestered Ca2+ and a substantial entry of Ca2+. The effect of SPP on pH(i) was abolished in cells incubated in a Ca2+-free buffer, and in cells loaded with the intracellular Ca2+ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid. Furthermore, the effect of SPP was abolished in pertussis toxin (PTX)-treated cells. PTX decreased Ca2+ entry only, without affecting the release from intracellular stores. Phosphatidic acid (PA) did not activate Na+/H+ exchange, suggesting that the effect of SPP was not mediated via activation of phospholipase D and the production of PA. Thus one mechanism of action of SPP in FRTL-5 cells appears to be to activate Na+/H+ exchange. This action is mediated via a G protein-dependent mechanism and requires an increase in intracellular free Ca2+.

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Association of Rad9 with Double-Strand Breaks through a Mec1-Dependent Mechanism

Molecular and Cellular Biology ◽

10.1128/mcb.24.8.3277-3285.2004 ◽

2004 ◽

Vol 24 (8) ◽

pp. 3277-3285 ◽

Cited By ~ 44

Author(s):

Takahiro Naiki ◽

Tatsushi Wakayama ◽

Daisuke Nakada ◽

Kunihiro Matsumoto ◽

Katsunori Sugimoto

Keyword(s):

Dna Damage ◽

Double Strand Breaks ◽

Dna Damage Checkpoint ◽

Dependent Manner ◽

Wild Type ◽

Strand Breaks ◽

Dependent Mechanism ◽

In Cells

ABSTRACT Rad9 is required for the activation of DNA damage checkpoint pathways in budding yeast. Rad9 is phosphorylated after DNA damage in a Mec1- and Tel1-dependent manner and subsequently interacts with Rad53. This Rad9-Rad53 interaction has been suggested to trigger the activation and phosphorylation of Rad53. Here we show that Mec1 controls the Rad9 accumulation at double-strand breaks (DSBs). Rad9 was phosphorylated after DSB induction and associated with DSBs. However, its phosphorylation and association with DSBs were significantly decreased in cells carrying a mec1Δ or kinase-negative mec1 mutation. Mec1 phosphorylated the S/TQ motifs of Rad9 in vitro, the same motifs that are phosphorylated after DNA damage in vivo. In addition, multiple mutations in the Rad9 S/TQ motifs resulted in its defective association with DSBs. Phosphorylation of Rad9 was partially defective in cells carrying a weak mec1 allele (mec1-81), whereas its association with DSBs occurred efficiently in the mec1-81 mutants, as found in wild-type cells. However, the Rad9-Rad53 interaction after DSB induction was significantly decreased in mec1-81 mutants, as it was in mec1Δ mutants. Deletion mutation in RAD53 did not affect the association of Rad9 with DSBs. Our results suggest that Mec1 promotes association of Rad9 with sites of DNA damage, thereby leading to full phosphorylation of Rad9 and its interaction with Rad53.

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Characterization of Gazdar murine sarcoma virus by nucleic acid hybridization and analysis of viral expression in cells.

Journal of Virology ◽

10.1128/jvi.24.2.551-556.1977 ◽

1977 ◽

Vol 24 (2) ◽

pp. 551-556 ◽

Cited By ~ 6

Author(s):

R H Pang ◽

L A Phillips ◽

D K Haapala

Keyword(s):

Nucleic Acid ◽

Nucleic Acid Hybridization ◽

Viral Expression ◽

Murine Sarcoma Virus ◽

Sarcoma Virus ◽

Murine Sarcoma ◽

In Cells

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Role of leukemia inhibitor factor (LIF) in decidualisation of murine uterine stromal cells in vitro

Journal of Endocrinology ◽

10.1677/joe.0.1810477 ◽

2004 ◽

Vol 181 (3) ◽

pp. 477-492 ◽

Cited By ~ 19

Author(s):

AA Fouladi Nashta ◽

CV Andreu ◽

N Nijjar ◽

JK Heath ◽

SJ Kimber

Keyword(s):

In Vitro Culture ◽

Stromal Cells ◽

Control Level ◽

Calf Serum ◽

Prostaglandin E ◽

Dependent Manner ◽

Alp Activity ◽

Dose Dependent ◽

In Cells

Decidualisation of uterine stromal cells is a prerequisite for implantation of the embryo in mice. Here we have used an in vitro culture system in which stromal cells decidualise as indicated by a number of markers, including an increase in alkaline phosphatase (ALP) activity. The latter was used as a quantitative marker of decidualisation in the presence of low (2%) fetal calf serum. Prostaglandin E(2) (PGE(2)), which is known to induce decidualisation, increased ALP activity, and this effect was blocked in a dose-dependent manner by indomethacin. Leukemia inhibitory factor (LIF) was then examined, but it had no effect on PGE(2) secretion. However, LIF suppressed ALP activity in a dose-dependent manner in the presence of 2% serum, while an inhibitor of LIF that competes for binding to its receptor reversed the effect of LIF and increased ALP activity above the control level. In serum-free cultures, stromal cells differentiated rapidly, and no differences were observed between LIF-treated and untreated cultures. Stromal cells produce LIF during in vitro culture, and this peaked at 48 h. Freshly collected stromal cells from both day-2 and -4 pregnant mice expressed mRNA for the LIF receptor, and the transcript level was higher in cells isolated on day 4. However, no differences were observed in the relative levels of transcripts in cells from day 2 and day 4 after culture, nor were there differences between the LIF-treated cultures and controls. Therefore, in this study, we have shown that LIF suppresses decidualisation of murine uterine stromal cells in the presence of serum, this is not due to the regulation of PGE(2) secretion by stromal cells.

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Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

Analytical and Bioanalytical Chemistry ◽

10.1007/s00216-021-03309-4 ◽

2021 ◽

Author(s):

Noemi Bellassai ◽

Roberta D’Agata ◽

Giuseppe Spoto

Keyword(s):

Nucleic Acid ◽

Structural Properties ◽

Molecular Beacon ◽

Dna Origami ◽

Molecular Beacons ◽

Conformational Polymorphism ◽

Functional Systems ◽

Similarities And Differences ◽

Nucleic Acid Structures ◽

Nucleic Acid Sequences

AbstractNucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

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Overlapping but distinct: a new model for G-quadruplex biochemical specificity

Nucleic Acids Research ◽

10.1093/nar/gkab037 ◽

2021 ◽

Author(s):

Martin Volek ◽

Sofia Kolesnikova ◽

Katerina Svehlova ◽

Pavel Srb ◽

Ráchel Sgallová ◽

...

Keyword(s):

Nucleic Acid ◽

Drug Design ◽

Solution Structure ◽

Biochemical Data ◽

Biological Regulation ◽

New Model ◽

G Quadruplex ◽

Range Of Functions ◽

Nucleic Acid Structures ◽

Sequence Requirements

Abstract G-quadruplexes are noncanonical nucleic acid structures formed by stacked guanine tetrads. They are capable of a range of functions and thought to play widespread biological roles. This diversity raises an important question: what determines the biochemical specificity of G-quadruplex structures? The answer is particularly important from the perspective of biological regulation because genomes can contain hundreds of thousands of G-quadruplexes with a range of functions. Here we analyze the specificity of each sequence in a 496-member library of variants of a reference G-quadruplex with respect to five functions. Our analysis shows that the sequence requirements of G-quadruplexes with these functions are different from one another, with some mutations altering biochemical specificity by orders of magnitude. Mutations in tetrads have larger effects than mutations in loops, and changes in specificity are correlated with changes in multimeric state. To complement our biochemical data we determined the solution structure of a monomeric G-quadruplex from the library. The stacked and accessible tetrads rationalize why monomers tend to promote a model peroxidase reaction and generate fluorescence. Our experiments support a model in which the sequence requirements of G-quadruplexes with different functions are overlapping but distinct. This has implications for biological regulation, bioinformatics, and drug design.

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