DNA-Topology Simplification by Topoisomerases [PDF]
Molecules, 2021 The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies
Andreas Hanke +2 more
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Effects of DNA Topology on Transcription from rRNA Promoters in Bacillus subtilis. [PDF]
Microorganisms, 2021 The expression of rRNA is one of the most energetically demanding cellular processes and, as such, it must be stringently controlled. Here, we report that DNA topology, i.e., the level of DNA supercoiling, plays a role in the regulation of Bacillus ...
Sudzinová P +5 more
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Top1-PARP1 association and beyond: from DNA topology to break repair. [PDF]
NAR Cancer, 2021 Selective trapping of human topoisomerase 1 (Top1) on the DNA (Top1 cleavage complexes; Top1cc) by specific Top1-poisons triggers DNA breaks and cell death. Poly(ADP-ribose) polymerase 1 (PARP1) is an early nick sensor for trapped Top1cc. New mechanistic
Chowdhuri SP, Das BB.
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Revised role for Hfq bacterial regulator on DNA topology. [PDF]
Sci Rep, 2018 Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNA.
Malabirade A +9 more
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Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays. [PDF]
J Biol Chem, 2019 The length of linker DNA that separates nucleosomes is highly variable, but its mechanistic role in modulating chromatin structure and functions remains unknown.
Bass MV +4 more
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DNA topology in chromatin is defined by nucleosome spacing. [PDF]
Sci Adv, 2017 Nucleosome spacing variations cause topological polymorphism of chromatin that can affect DNA supercoiling and transcription. In eukaryotic nucleosomes, DNA makes ~1.7 superhelical turns around histone octamer.
Nikitina T +3 more
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Controlling the topology of mammalian mitochondrial DNA
Open Biology, 2021 The genome of mitochondria, called mtDNA, is a small circular DNA molecule present at thousands of copies per human cell. MtDNA is packaged into nucleoprotein complexes called nucleoids, and the density of mtDNA packaging affects mitochondrial gene ...
Katja E. Menger +3 more
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Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression. [PDF]
Mol MicrobiolDNA in bacterial chromosomes is organized into higher‐order structures by DNA‐binding proteins called nucleoid‐associated proteins (NAPs) or bacterial chromatin proteins (BCPs). BCPs often bind to or near DNA loci transcribed by RNA polymerase (RNAP) and
Hustmyer CM, Landick R.
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The Effect of DNA Topology on Observed Rates of R-Loop Formation and DNA Strand Cleavage by CRISPR Cas12a. [PDF]
Genes (Basel), 2019 Here we explored the mechanism of R-loop formation and DNA cleavage by type V CRISPR Cas12a (formerly known as Cpf1). We first used a single-molecule magnetic tweezers (MT) assay to show that R-loop formation by Lachnospiraceae bacterium ND2006 Cas12a is
van Aelst K +3 more
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A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2. [PDF]
PLoS Genetics, 2012 DNA topology has fundamental control over the ability of transcription factors to access their target DNA sites at gene promoters. However, the influence of DNA topology on protein-DNA and protein-protein interactions is poorly understood.
Andrew D S Cameron, Charles J Dorman
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