Helical repeat of DNA in solution.

Wang, James C.

doi:10.1073/pnas.76.1.200

Cited by 449 publications

(206 citation statements)

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“…The sine wave pattern of integration near the Sap1 motif could be indicative of integration occurring as a result of helical distortion induced by Sap1 binding. The peaks of integration within these sine waves occur in 10-bp intervals, the approximate length of a DNA helical turn (Wang et al 1979). Perhaps the binding of a Sap1 dimer to the DNA results in conformational changes at regular intervals along the DNA helix, which makes certain regions of each helical turn more amenable to Tf1 insertion.…”

Section: Discussionmentioning

confidence: 99%

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

et al. 2015

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Transposable elements (TEs) constitute a substantial fraction of the eukaryotic genome and, as a result, have a complex relationship with their host that is both adversarial and dependent. To minimize damage to cellular genes, TEs possess mechanisms that target integration to sequences of low importance. However, the retrotransposon Tf1 of Schizosaccharomyces pombe integrates with a surprising bias for promoter sequences of stress-response genes. The clustering of integration in specific promoters suggests that Tf1 possesses a targeting mechanism that is important for evolutionary adaptation to changes in environment. We report here that Sap1, an essential DNA-binding protein, plays an important role in Tf1 integration. A mutation in Sap1 resulted in a 10-fold drop in Tf1 transposition, and measures of transposon intermediates support the argument that the defect occurred in the process of integration. Published ChIP-Seq data on Sap1 binding combined with high-density maps of Tf1 integration that measure independent insertions at single-nucleotide positions show that 73.4% of all integration occurs at genomic sequences bound by Sap1. This represents high selectivity because Sap1 binds just 6.8% of the genome. A genome-wide analysis of promoter sequences revealed that Sap1 binding and amounts of integration correlate strongly. More important, an alignment of the DNA-binding motif of Sap1 revealed integration clustered on both sides of the motif and showed high levels specifically at positions +19 and 29. These data indicate that Sap1 contributes to the efficiency and position of Tf1 integration. KEYWORDS Sap1; Tf1; integration; transposition; Schizosaccharomyces pombe R ETROTRANSPOSONS are pervasive among eukaryotes and, in many cases, account for a substantial portion of the host genome (Moore et al. 2004;Scheifele et al. 2009;Levin and Moran 2011). The ability of these elements to selectively integrate into specific target sequences has been paramount to their success because the employment of specific targeting mechanisms has allowed these retrotransposons to propagate within host genomes without disrupting genes and compromising the host's survival (Levin and Moran 2011). The long terminal repeat (LTR) retrotransposons Ty1, Ty3, and Ty5 of Saccharomyces cerevisiae avoid causing damage to the host by targeting noncoding genomic regions; Ty1 and Ty3 integrate upstream of RNA polemerase III-transcribed genes, while Ty5 integrates into heterochromatin (Chalker and Sandmeyer 1990;1992;Ji et al. 1993;Kirchner et al. 1995;Devine and Boeke 1996;Zou et al. 1996;Zou and Voytas 1997;Yieh et al. 2000;Sandmeyer 2003;Lesage and Todeschini 2005).In Schizosaccharomyces pombe, the LTR retrotransposon Tf1 has a unique targeting mechanism that directs integration to promoters of RNA polymerase II-transcribed genes with a bias for the promoters of stress-response genes (Behrens et al. 2000;Singleton and Levin 2002;Bowen et al. 2003;Leem et al. 2008;Guo and Levin 2010). Surprisingly, insertion of Tf1 into promoters rarel...

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Section: Discussionmentioning

confidence: 99%

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

et al. 2015

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“…4C). Given that 10.4 bp corresponds to one full DNA helical turn, decreasing the spacing by 5 bp (i.e., half a helical turn) brings the two nucleosomes closer together in terms of base pair distance, but now places them toward opposite sides of the DNA and hence further apart overall (8,25,26) (Fig. 4C).…”

Section: Significancementioning

confidence: 99%

Nucleosomal arrangement affects single-molecule transcription dynamics

Fitz

Shin

Ehrlich

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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In eukaryotes, gene expression depends on chromatin organization. However, how chromatin affects the transcription dynamics of individual RNA polymerases has remained elusive. Here, we use dual trap optical tweezers to study single yeast RNA polymerase II (Pol II) molecules transcribing along a DNA template with two nucleosomes. The slowdown and the changes in pausing behavior within the nucleosomal region allow us to determine a drift coefficient, χ , which characterizes the ability of the enzyme to recover from a nucleosomal backtrack. Notably, χ can be used to predict the probability to pass the first nucleosome. Importantly, the presence of a second nucleosome changes χ in a manner that depends on the spacing between the two nucleosomes, as well as on their rotational arrangement on the helical DNA molecule. Our results indicate that the ability of Pol II to pass the first nucleosome is increased when the next nucleosome is turned away from the first one to face the opposite side of the DNA template. These findings help to rationalize how chromatin arrangement affects Pol II transcription dynamics.T o accommodate the massive amount of genetic material within the nucleus, DNA is packaged into chromatin. The level of chromatin compaction determines the accessibility of the underlying DNA, which in turn impacts gene expression (1). The first step in gene expression is transcription, where RNA polymerase II (Pol II) processively moves along the DNA template to generate an RNA copy. However, how chromatin impacts the translocation dynamics of individual RNA polymerases has remained unclear.The fundamental unit of chromatin is a single nucleosome, which consists of 147 bp of DNA wrapped ∼ 1.7 times around a histone octamer (2). In vitro experiments have revealed that a single nucleosome exhibits a significant mechanical barrier to the transcribing Pol II (3-7). Using optical tweezers, it was shown that a nucleosome both decreases the rate of forward translocation and increases polymerase pausing and backtracking (3, 5). These changes have been suggested to depend on the unwrapping dynamics of the nucleosome itself, which are governed by nucleosomal properties such as the histones' modification state as well as the underlying DNA sequence (3, 5).In vivo, the process of chromatin transcription is far more complex. Chromatin accessibility is affected by many accessory factors that facilitate the progression of RNA polymerases through nucleosomal obstacles (1). A central outstanding question is to what extent the nucleosomal arrangement affects Pol II transcription behavior. This arrangement might be particularly important in budding yeast, an organism with a compact genome with short internucleosomal distances (8-11).Here, we study the impact of the arrangement of two nucleosomes on the nucleosomal transcription performance of individual molecules of Pol II. We use dual-trap optical tweezers in a single-molecule approach to follow single enzymes of Pol II as they progress through a dinucleosomal array (3, 5). Specifi...

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“…Because the natural equilibrium length for a single turn of DNA appears to be close to 10.5 base pairs 26,27 , and because DNA backbones are not symmetrically spaced around the helix (there is a major and minor groove), designs of such two dimensional DNA nanostructures (which must use integral numbers of DNA bases) invariably incorporate features that should cause strain. That is, the design assumes a DNA geometry slightly different than that of a single isolated helix with 10.5 bases per turn with 'normal' major/minor groove angles.…”

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confidence: 99%

Folding DNA to create nanoscale shapes and patterns

Rothemund

2006

Nature

6,440

6,222

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Supplementary Note S1: Design of DNA origamiThe program used for designing DNA origami, multishapes.m, may be downloaded from:http://www.dna.caltch.edu/SupplementaryMaterial/ Below is a description of how design proceeds using this program. It is not meant to be a manual but rather to show the level of abstraction at which the origami are designed, and to show the various types of diagrams that the program can draw to aid in design. If scaffolded DNA origami becomes widely used, a better CAD design tool will have to be written. Given a desired shape (for example the red outline in Fig. 1a) design of a DNA origami to approximate it proceeds in five phases (two manual design steps and three passes of the program):1. Generation of a block diagram. By hand, a rough geometric model is generated. It is comprised of rectangular blocks in which each block is taken to be one turn of DNA wide and one DNA helix plus the interhelix gap in height. (Such a block diagram sloppily overestimates the height of a structure by one inter-helix gap.) An example block diagram is in Supplementary Fig. S1 step 1.This step is performed with an eye towards the next step (generation of a folding path), in some cases the block diagram is conceived almost simultaneously with the folding path. The phase of the underlying periodic crossover lattice is chosen as well; generally this phasing is chosen so that seams and long edges of the shape align with columns of periodic crossovers. For blocks on the edge of the diagram, it is useful to keep track of the relationship of such blocks to the underlying crossover lattice. For an origami with 1.5-turn spacing between crossovers there are 3 possible offsets that an edge may have with respect to the underlying lattice-call them 0, +1 and -1 (Origami with 2.5 turn spacing have 5 possible offsets). For designs with a central seam, blocks on edges of offset 0 are colored red and blocks on edges of offset +1 and -1 are colored yellow and orange, depending on whether they occur to the left or right of the central seam. At this point the placement of seams may already be apparent; if so, half-blocks are used along seams. Adjacent half-blocks involved in the same scaffold crossover are colored the same (one of either green or purple) but adjacent half-blocks that participate in different crossovers are given different colors.2. Generation of a folding path, by raster fill, through the block diagram. For a given shape there are many compatible raster fill patterns; currently the raster fill pattern must be hand-designed. For any helical domain in which the scaffold is to start and end on the same side of the helix (top or bottom), an integral number of turns (blocks) is traversed. For any helical domain in which the scaffold starts and ends on opposite sides sides of the helix, the scaffold traverses an odd number of half-turns (half-blocks). An example folding path is in Supplementary Fig. S1 step 2.3. Generation of a first pass design based on the block diagram and folding path. The lengths of various heli...

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Helical repeat of DNA in solution.

Cited by 449 publications

References 12 publications

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

Nucleosomal arrangement affects single-molecule transcription dynamics

Folding DNA to create nanoscale shapes and patterns

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