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Nucleic Acids Research Feb 2022Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures...
Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect gene expression, DNA methylation, replication fork progression and genome stability. When and how G4 structures form and are resolved remains unclear. Here we report the use of Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping native G4 in mammalian cell lines at high resolution and low background. Mild native conditions used for the procedure retain more G4 structures and provide a higher signal-to-noise ratio than ChIP-based methods. We determine the G4 landscape of mouse embryonic stem cells (ESC), observing widespread G4 formation at active promoters, active and poised enhancers. We discover that the presence of G4 motifs and G4 structures distinguishes active and primed enhancers in mouse ESCs. Upon differentiation to neural progenitor cells (NPC), enhancer G4s are lost. Further, performing R-loop CUT&Tag, we demonstrate the genome-wide co-occurrence of single-stranded DNA, G4s and R loops at promoters and enhancers. We confirm that G4 structures exist independent of ongoing transcription, suggesting an intricate relationship between transcription and non-canonical DNA structures.
Topics: Animals; DNA; G-Quadruplexes; Genomic Instability; Mammals; Mice; R-Loop Structures; RNA
PubMed: 34792172
DOI: 10.1093/nar/gkab1073 -
Endocrine Reviews May 2021In the mid- to late 1970s, recombinant deoxyribonucleic acid methods for cloning and expressing genes in E. coli were under intense development. The important question...
In the mid- to late 1970s, recombinant deoxyribonucleic acid methods for cloning and expressing genes in E. coli were under intense development. The important question had become: Can humans design and chemically synthesize novel genes that function in bacteria? This question was answered in 1978 and in 1979 with the successful expression in E. coli of 2 mammalian hormones, first somatostatin and then human insulin. The successful production of human insulin in bacteria provided, for the first time, a practical, scalable source of human insulin and resulted in the approval, in 1982, of human insulin for the treatment of diabetics. In this short review, I give my personal view of how the making, cloning, and expressing of human insulin genes was accomplished by a team of scientists led by Keiichi Itakura, Herbert W. Boyer, and myself.
Topics: Cloning, Molecular; DNA, Recombinant; Escherichia coli; Humans; Insulin; Insulin, Regular, Human
PubMed: 33340315
DOI: 10.1210/endrev/bnaa029 -
Frontiers in Endocrinology 2023Normal levels of reactive oxygen species (ROS) play an important role in regulating follicular growth, angiogenesis and sex hormone synthesis in ovarian tissue. When the... (Review)
Review
Normal levels of reactive oxygen species (ROS) play an important role in regulating follicular growth, angiogenesis and sex hormone synthesis in ovarian tissue. When the balance between ROS and antioxidants is disrupted, however, it can cause serious consequences of oxidative stress (OS), and the quantity and quality of oocytes will decline. Therefore, this review discusses the interrelationship between OS and premature ovarian insufficiency (POI), the potential mechanisms and the methods by which antioxidants can improve POI through controlling the level of OS. We found that OS can mediate changes in genetic materials, signal pathways, transcription factors and ovarian microenvironment, resulting in abnormal apoptosis of ovarian granulosa cells (GCs) and abnormal meiosis as well as decreased mitochondrial Deoxyribonucleic Acid(mtDNA) and other changes, thus accelerating the process of ovarian aging. However, antioxidants, mesenchymal stem cells (MSCs), biological enzymes and other antioxidants can delay the disease process of POI by reducing the ROS level .
Topics: Female; Humans; Antioxidants; Reactive Oxygen Species; Menopause, Premature; Primary Ovarian Insufficiency; Oxidative Stress; DNA, Mitochondrial
PubMed: 37600717
DOI: 10.3389/fendo.2023.1172481 -
Molecular Cell Feb 2023The protection of DNA replication forks under stress is essential for genome maintenance and cancer suppression. One mechanism of fork protection involves an elevation...
The protection of DNA replication forks under stress is essential for genome maintenance and cancer suppression. One mechanism of fork protection involves an elevation in intracellular Ca ([Ca]), which in turn activates CaMKK2 and AMPK to prevent uncontrolled fork processing by Exo1. How replication stress triggers [Ca] elevation is unclear. Here, we report a role of cytosolic self-DNA (cytosDNA) and the ion channel TRPV2 in [Ca] induction and fork protection. Replication stress leads to the generation of ssDNA and dsDNA species that, upon translocation into cytoplasm, trigger the activation of the sensor protein cGAS and the production of cGAMP. The subsequent binding of cGAMP to STING causes its dissociation from TRPV2, leading to TRPV2 derepression and Ca release from the ER, which in turn activates the downstream signaling cascade to prevent fork degradation. This Ca-dependent genome protection pathway is also activated in response to replication stress caused by oncogene activation.
Topics: DNA; DNA Replication; DNA, Single-Stranded; Membrane Proteins; Nucleotidyltransferases; Signal Transduction; TRPV Cation Channels
PubMed: 36696898
DOI: 10.1016/j.molcel.2022.12.034 -
Frontiers in Bioscience (Landmark... Apr 2021Being polymorphic, deoxyribonucleic acid is worthy of raise a variety of structure like right-handed B to left-handed Z conformation. In left-handed contour of DNA... (Comparative Study)
Comparative Study Review
Being polymorphic, deoxyribonucleic acid is worthy of raise a variety of structure like right-handed B to left-handed Z conformation. In left-handed contour of DNA consecutive nucleotides substitute between syn-arrangement and anti-arrangement, through the chain. 2D gel electrophoresis comprising d(PCpG)n of topo isomers of a plasmid inserts d(pCpG)n, in this 'n' ranges among 8 to 21, indicate the change of B-Z DNA. The high denseness of salt is required for conversion of B configuration d(CG)n toward Z configuration. The rate of B to Z transition is measured by "Cytosine Analogues" and "Fluorescence Spectroscopy". h-ZαADAR1 that a Z-DNA's binding domain, binds and stabilizes one part in Z configuration and therefore the remaining half in B deoxyribonucleic acid configuration. At halfway point, it creates B-Z junction. "Stacking" is the main reason for the B-Z DNA junction construction. Upregulation of ADAM-12, related with Z-DNA is said to a cause for cancer, arthritis, and hypertrophy. Z-DNA forming sequence (ZFS) conjointly generates massive - scale deletion in cells from mammals.
Topics: Alzheimer Disease; Autoimmune Diseases; Biophysics; Cytosine; DNA; DNA, Z-Form; Genome, Human; Humans; Nucleic Acid Conformation; Protein Binding; Protein Domains
PubMed: 34027648
DOI: 10.52586/4922 -
Current Biology : CB Nov 2022Emilie Didaskalou and colleagues introduce the analysis of DNA form environmental samples.
Emilie Didaskalou and colleagues introduce the analysis of DNA form environmental samples.
Topics: DNA, Environmental; DNA
PubMed: 36413963
DOI: 10.1016/j.cub.2022.09.052 -
Molecules (Basel, Switzerland) Feb 2020Deoxyribonucleic acid (DNA) serves not only as a genetic information carrier but also as an excellent material for programmable nanoscale assembly [...].
Deoxyribonucleic acid (DNA) serves not only as a genetic information carrier but also as an excellent material for programmable nanoscale assembly [...].
Topics: DNA; Nanostructures; Nanotechnology
PubMed: 32028556
DOI: 10.3390/molecules25030639 -
Nature Reviews. Microbiology Aug 2022Bacteria are continuously exposed to numerous endogenous and exogenous DNA-damaging agents. To maintain genome integrity and ensure cell survival, bacteria have evolved... (Review)
Review
Bacteria are continuously exposed to numerous endogenous and exogenous DNA-damaging agents. To maintain genome integrity and ensure cell survival, bacteria have evolved several DNA repair pathways to correct different types of DNA damage and non-canonical bases, including strand breaks, nucleotide modifications, cross-links, mismatches and ribonucleotide incorporations. Recent advances in genome-wide screens, the availability of thousands of whole-genome sequences and advances in structural biology have enabled the rapid discovery and characterization of novel bacterial DNA repair pathways and new enzymatic activities. In this Review, we discuss recent advances in our understanding of base excision repair and nucleotide excision repair, and we discuss several new repair processes including the EndoMS mismatch correction pathway and the MrfAB excision repair system.
Topics: Bacteria; DNA; DNA Damage; DNA Repair; DNA, Bacterial
PubMed: 35210609
DOI: 10.1038/s41579-022-00694-0 -
Nucleic Acids Research Jun 2021Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases... (Review)
Review
Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.
Topics: DNA; Genes, Synthetic; Information Storage and Retrieval
PubMed: 33836076
DOI: 10.1093/nar/gkab230 -
Biophysical Journal Aug 2021Our goal is to review the main theoretical models used to calculate free energy changes associated with common, torsion-induced conformational changes in DNA and provide... (Review)
Review
Our goal is to review the main theoretical models used to calculate free energy changes associated with common, torsion-induced conformational changes in DNA and provide the resulting equations hoping to facilitate quantitative analysis of both in vitro and in vivo studies. This review begins with a summary of work regarding the energy change of the negative supercoiling-induced B- to L-DNA transition, followed by a discussion of the energetics associated with the transition to Z-form DNA. Finally, it describes the energy changes associated with the formation of DNA curls and plectonemes, which can regulate DNA-protein interactions and promote cross talk between distant DNA elements, respectively. The salient formulas and parameters for each scenario are summarized in table format to facilitate comparison and provide a concise, user-friendly resource.
Topics: DNA; DNA, Superhelical; DNA, Z-Form; Models, Theoretical; Nucleic Acid Conformation; Thermodynamics
PubMed: 33974883
DOI: 10.1016/j.bpj.2021.05.002