scholarly journals Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions

2020 ◽  
Vol 85 (1) ◽  
pp. e00110-20
Author(s):  
Lucie Poggi ◽  
Guy-Franck Richard
Keyword(s):  
Genetic Instability ◽  
Developmental Disorders ◽  
Double Helix ◽  
Fragile Sites ◽  
Trinucleotide Repeats ◽  
Molecular Evidence ◽  
Dna Structures ◽  
Alternative Structures

SUMMARYDuplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences in vitro. However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function in vivo or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures in vivo and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.

scholarly journals Radiofrequency Irradiation Modulates TRPV1-Related Burning Sensation in Rosacea

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1424
Author(s):  
Seyeon Oh ◽  
Myeongjoo Son ◽  
Joonhong Park ◽  
Donghwan Kang ◽  
Kyunghee Byun
Keyword(s):  
Burning Sensation ◽  
In Vivo Model ◽  
Molecular Evidence ◽  
Exposed Skin ◽  
Heat Treated ◽  
Vitro Model ◽  
Effective Use ◽  
Inflammatory Molecules

Rosacea is a skin inflammatory condition that is accompanied by not only redness and flushing but also unseen symptoms, such as burning, stinging, and itching. TRPV1 expression in UVB-exposed skin can lead to a painful burning sensation. Upregulated TRPV1 expression helps release neuropeptides, including calcitonin gene-related peptide, pituitary adenylate cyclase-activating polypeptide, and vasoactive intestinal peptide, which can activate macrophage and inflammatory molecules. In this study, we found that radiofrequency (RF) irradiation reduced TRPV1 activation and neuropeptide expression in a UVB-exposed in vivo model and UVB- or heat-treated in an in vitro model. RF irradiation attenuated neuropeptide-induced macrophage activation and inflammatory molecule expression. Interestingly, the burning sensation in the skin of UVB-exposed mice and patients with rosacea was significantly decreased by RF irradiation. These results can provide experimental and molecular evidence on the effective use of RF irradiation for the burning sensation in patients with rosacea.

scholarly journals DisA Limits RecG Activities at Stalled or Reversed Replication Forks

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1357
Author(s):  
Rubén Torres ◽  
Carolina Gándara ◽  
Begoña Carrasco ◽  
Ignacio Baquedano ◽  
Silvia Ayora ◽  
...  
Keyword(s):  
Atp Hydrolysis ◽  
Holliday Junctions ◽  
Genome Integrity ◽  
Stable Complex ◽  
Dna Unwinding ◽  
Replication Forks ◽  
Dna Structures ◽  
Checkpoint Protein

The DNA damage checkpoint protein DisA and the branch migration translocase RecG are implicated in the preservation of genome integrity in reviving haploid Bacillus subtilis spores. DisA synthesizes the essential cyclic 3′, 5′-diadenosine monophosphate (c‑di-AMP) second messenger and such synthesis is suppressed upon replication perturbation. In vitro, c-di-AMP synthesis is suppressed when DisA binds DNA structures that mimic stalled or reversed forks (gapped forks or Holliday junctions [HJ]). RecG, which does not form a stable complex with DisA, unwinds branched intermediates, and in the presence of a limiting ATP concentration and HJ DNA, it blocks DisA-mediated c-di-AMP synthesis. DisA pre-bound to a stalled or reversed fork limits RecG-mediated ATP hydrolysis and DNA unwinding, but not if RecG is pre-bound to stalled or reversed forks. We propose that RecG-mediated fork remodeling is a genuine in vivo activity, and that DisA, as a molecular switch, limits RecG-mediated fork reversal and fork restoration. DisA and RecG might provide more time to process perturbed forks, avoiding genome breakage.

scholarly journals MiR-204 is responsible for inherited retinal dystrophy associated with ocular coloboma

2015 ◽  
Vol 112 (25) ◽  
pp. E3236-E3245 ◽  
Author(s):  
Ivan Conte ◽  
Kristen D. Hadfield ◽  
Sara Barbato ◽  
Sabrina Carrella ◽  
Mariateresa Pizzo ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
Retinal Pigment ◽  
Retinal Dystrophy ◽  
In Vitro Assays ◽  
Heterozygous Mutation ◽  
Seed Region ◽  
Medaka Fish ◽  
Inherited Retinal Dystrophies

Ocular developmental disorders, including the group classified as microphthalmia, anophthalmia, and coloboma (MAC) and inherited retinal dystrophies, collectively represent leading causes of hereditary blindness. Characterized by extreme genetic and clinical heterogeneity, the separate groups share many common genetic causes, in particular relating to pathways controlling retinal and retinal pigment epithelial maintenance. To understand these shared pathways and delineate the overlap between these groups, we investigated the genetic cause of an autosomal dominantly inherited condition of retinal dystrophy and bilateral coloboma, present in varying degrees in a large, five-generation family. By linkage analysis and exome sequencing, we identified a previously undescribed heterozygous mutation, n.37C > T, in the seed region of microRNA-204 (miR-204), which segregates with the disease in all affected individuals. We demonstrated that this mutation determines significant alterations of miR-204 targeting capabilities via in vitro assays, including transcriptome analysis. In vivo injection, in medaka fish (Oryzias latipes), of the mutated miR-204 caused a phenotype consistent with that observed in the family, including photoreceptor alterations with reduced numbers of both cones and rods as a result of increased apoptosis, thereby confirming the pathogenic effect of the n.37C > T mutation. Finally, knockdown assays in medaka fish demonstrated that miR-204 is necessary for normal photoreceptor function. Overall, these data highlight the importance of miR-204 in the regulation of ocular development and maintenance and provide the first evidence, to our knowledge, of its contribution to eye disease, likely through a gain-of-function mechanism.

scholarly journals In vitro and In vivo Molecular Evidence for Better Therapeutic Efficacy of ABT-627 and Taxotere Combination in Prostate Cancer

2007 ◽  
Vol 67 (8) ◽  
pp. 3818-3826 ◽  
Author(s):  
Sanjeev Banerjee ◽  
Maha Hussain ◽  
Zhiwei Wang ◽  
Allen Saliganan ◽  
Mingxin Che ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Therapeutic Efficacy ◽  
Molecular Evidence

scholarly journals Helicases FANCJ, RTEL1 and BLM Act on Guanine Quadruplex DNA in Vivo

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 870 ◽  
Author(s):  
Peter Lansdorp ◽  
Niek van Wietmarschen
Keyword(s):  
Gene Expression ◽  
Genome Stability ◽  
Cell Function ◽  
Historical Context ◽  
Telomere Maintenance ◽  
Dna Structures ◽  
G4 Dna ◽  
Guanine Quadruplex

Guanine quadruplex (G4) structures are among the most stable secondary DNA structures that can form in vitro, and evidence for their existence in vivo has been steadily accumulating. Originally described mainly for their deleterious effects on genome stability, more recent research has focused on (potential) functions of G4 structures in telomere maintenance, gene expression, and other cellular processes. The combined research on G4 structures has revealed that properly regulating G4 DNA structures in cells is important to prevent genome instability and disruption of normal cell function. In this short review we provide some background and historical context of our work resulting in the identification of FANCJ, RTEL1 and BLM as helicases that act on G4 structures in vivo. Taken together these studies highlight important roles of different G4 DNA structures and specific G4 helicases at selected genomic locations and telomeres in regulating gene expression and maintaining genome stability.

187 Phenotype switch of human fibroblasts into trophoblastic cells

2019 ◽  
Vol 31 (1) ◽  
pp. 218
Author(s):  
S. Arcuri ◽  
E. F. M. Manzoni ◽  
F. Gandolfi ◽  
T. A. L. Brevini
Keyword(s):  
Developmental Disorders ◽  
Human Fibroblasts ◽  
Normal Karyotype ◽  
Small Cells ◽  
Specific Gene ◽  
Trophoblast Cells ◽  
Human Trophoblast ◽  
Trophoblastic Cells

The first differentiation event in mammalian embryos is the formation of the trophectoderm, which is crucial for implantation of the blastocyst and gives rise to specialised populations of trophoblast cells in the definitive placenta. However, our understanding of these early differentiation events is limited, particularly in humans, because of ethical and legal restrictions on the isolation and manipulation of human embryogenesis. Here we describe experiments aimed at converting human fibroblasts into trophoblastic cells, using 5-azacytidine (5-aza-CR) to erase the original phenotype and a cocktail containing bone morphogenic protein 4 (BMP4) and inhibitors of the activin/nodal/ERK signalling pathways, to drive trophoblastic differentiation. The method required 3 main steps: (1) preparation of mouse embryonic fibroblasts (MEF) monolayer, and culture and collection of MEF conditioned medium (CM); (2) culture of human fibroblasts, obtained from a skin biopsy, and epigenetic erasure with 5-aza-CR for 18 h; (3) use of CM, with BMP4 (50 ng mL−1), PD0325901 (1 µM), CHIR99021 (1 µM), and PD173074 (0.1 µM) to differentiate erased human fibroblasts to trophoblast cells. Morphology changes were monitored along the process. In the initial phase of differentiation, a mixture of cell types appeared, including small cells growing in clusters and giant cells possessing very large nuclei. After 2 weeks of culture, cells displayed a distinct trophoblast-like morphology and showed the presence of typical clustering/lacunae monolayer patterning. Cells continued to proliferate and maintained a normal karyotype. BMP4-mediated differentiation was also assessed by quantitative RT-PCR using primers specific for 2 trophoblast markers: keratin 7 (KRT7) and caudal type homeobox 2 (CDX2), that are absent in the original fibroblasts. Their expression appeared by Day 3 of induction and was strong and steady throughout the process, confirming that the acquisition of a trophoblast-like morphology was supported by the activation of trophoblast-specific gene transcription. The results demonstrate the possibility of obtaining trophoblast-like cells through the conversion of human fibroblasts and confirm the involvement of BMP4-together with the inhibition of the activin/nodal/ERK signalling pathway-to activate early trophoblast differentiation in vitro. The challenge for future experiments will be to determine the precise role of BMP signals in human trophoblast definition in vivo, which, to our knowledge, has not been elucidated yet. The method here described is efficient and reproducible and has the advantage of utilising easily accessible cells as a starting population. It can be used for a variety of applications, including drug discovery and stem cell research, as well as to implement studies on the pathogenesis of developmental disorders with trophoblast defects. This research was supported by Carraresi Foundation. Authors are members of the COST Actions CA16119 and CM1406.

scholarly journals The Functional Consequences of Eukaryotic Topoisomerase 1 Interaction with G-Quadruplex DNA

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 193
Author(s):  
Alexandra Berroyer ◽  
Nayun Kim
Keyword(s):  
Topoisomerase I ◽  
Genome Instability ◽  
Strand Break ◽  
Dna Topology ◽  
Single Strand Break ◽  
Dna Structures ◽  
G4 Dna ◽  
G Quadruplex

Topoisomerase I in eukaryotic cells is an important regulator of DNA topology. Its catalytic function is to remove positive or negative superhelical tension by binding to duplex DNA, creating a reversible single-strand break, and finally religating the broken strand. Proper maintenance of DNA topological homeostasis, in turn, is critically important in the regulation of replication, transcription, DNA repair, and other processes of DNA metabolism. One of the cellular processes regulated by the DNA topology and thus by Topoisomerase I is the formation of non-canonical DNA structures. Non-canonical or non-B DNA structures, including the four-stranded G-quadruplex or G4 DNA, are potentially pathological in that they interfere with replication or transcription, forming hotspots of genome instability. In this review, we first describe the role of Topoisomerase I in reducing the formation of non-canonical nucleic acid structures in the genome. We further discuss the interesting recent discovery that Top1 and Top1 mutants bind to G4 DNA structures in vivo and in vitro and speculate on the possible consequences of these interactions.

Biallelic mutations in the TOGARAM1 gene cause a novel primary ciliopathy

2020 ◽  
pp. jmedgenet-2020-106833
Author(s):  
Valeria Morbidoni ◽  
Emanuele Agolini ◽  
Kevin C Slep ◽  
Luca Pannone ◽  
Daniela Zuccarello ◽  
...  
Keyword(s):  
Sensory Neurons ◽  
Developmental Disorders ◽  
Cleft Lip ◽  
Cleft Lip And Palate ◽  
Missense Variant ◽  
Causative Role ◽  
Biallelic Mutations ◽  
The Impact

BackgroundDysfunction in non-motile cilia is associated with a broad spectrum of developmental disorders characterised by clinical heterogeneity. While over 100 genes have been associated with primary ciliopathies, with wide phenotypic overlap, some patients still lack a molecular diagnosis.ObjectiveTo investigate and functionally characterise the molecular cause of a malformation disorder observed in two sibling fetuses characterised by microphthalmia, cleft lip and palate, and brain anomalies.MethodsA trio-based whole exome sequencing (WES) strategy was used to identify candidate variants in the TOGARAM1 gene. In silico, in vitro and in vivo (Caenorhabditis elegans) studies were carried out to explore the impact of mutations on protein structure and function, and relevant biological processes.ResultsTOGARAM1 encodes a member of the Crescerin1 family of proteins regulating microtubule dynamics. Its orthologue in C. elegans, che-12, is expressed in a subset of sensory neurons and localises in the dendritic cilium where it is required for chemosensation. Nematode lines harbouring the corresponding missense variant in TOGARAM1 were generated by CRISPR/Cas9 technology. Although chemotaxis ability on a NaCl gradient was not affected, che-12 point mutants displayed impaired lipophilic dye uptake, with shorter and altered cilia in sensory neurons. Finally, in vitro analysis of microtubule polymerisation in the presence of wild-type or mutant TOG2 domain revealed a faster polymerisation associated with the mutant protein, suggesting aberrant tubulin binding.ConclusionsOur data are in favour of a causative role of TOGARAM1 variants in the pathogenesis of this novel disorder, connecting this gene with primary ciliopathy.

Recombinant mammalian DNA methyltransferase activity on model transcriptional gene silencing short RNA–DNA heteroduplex substrates

2010 ◽  
Vol 432 (2) ◽  
pp. 323-332 ◽  
Author(s):  
Jason P. Ross ◽  
Isao Suetake ◽  
Shoji Tajima ◽  
Peter L. Molloy
Keyword(s):  
Gene Silencing ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Double Helix ◽  
In Vitro Assays ◽  
Enzyme Analysis ◽  
Transcriptional Gene Silencing ◽  
Restriction Enzyme Analysis

The biochemical mechanism of short RNA-induced TGS (transcriptional gene silencing) in mammals is unknown. Two competing models exist; one suggesting that the short RNA interacts with a nascent transcribed RNA strand (RNA–RNA model) and the other implying that short RNA forms a heteroduplex with DNA from the unwound double helix, an R-loop structure (RNA–DNA model). Likewise, the requirement for DNA methylation to enact TGS is still controversial. In vitro assays using purified recombinant murine Dnmt (DNA methyltransferase) 1-dN (where dN indicates an N-terminal truncation), 3a and 3b enzymes and annealed oligonucleotides were designed to question whether Dnmts methylate DNA in a RNA–DNA heteroduplex context and whether a RNA–DNA heteroduplex R-loop is a good substrate for Dnmts. Specifically, model synthetic oligonucleotides were used to examine methylation of single-stranded oligonucleotides, annealed oligonucleotide duplexes, RNA–DNA heteroduplexes, DNA bubbles and R-loops. Dnmt methylation activity on the model substrates was quantified with initial velocity assays, novel ARORA (annealed RNA and DNA oligonucleotide-based methylation-sensitive restriction enzyme analysis), tBS (tagged-bisulfite sequencing) and the quantitative PCR-based method MethylQuant. We found that RNA–DNA heteroduplexes and R-loops are poor substrates for methylation by both the maintenance (Dnmt1) and de novo (Dnmt3a and Dnmt3b) Dnmts. These results suggest the proposed RNA/DNA model of TGS in mammals is unlikely. Analysis of tagged-bisulfite genomic sequencing led to the unexpected observation that Dnmt1-dN can methylate cytosines in a non-CpG context in DNA bubbles. This may have relevance in DNA replication and silencing of transcriptionally active loci in vivo.

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