scholarly journals Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

2017 ◽  
Vol 292 (18) ◽  
pp. 7607-7618 ◽  
Author(s):  
Aleksandre Japaridze ◽  
Sylvain Renevey ◽  
Patrick Sobetzko ◽  
Liubov Stoliar ◽  
William Nasser ◽  
...  
Keyword(s):  
Long Range ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Sequence Motif ◽  
Structural Differentiation ◽  
Ample Evidence ◽  
Organizational Principle ◽  
Nucleoprotein Complexes

Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT-rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS-binding sequences in the assembly of long-range nucleoprotein structures remains unknown. In this study, by using high-resolution atomic force microscopy combined with biochemical assays, we explored the formation of H-NS nucleoprotein complexes on circular DNA molecules having different arrangements of identical sequences containing high-affinity H-NS-binding sites. We provide the first experimental evidence that variable sequence arrangements result in various three-dimensional nucleoprotein structures that differ in their shape and the capacity to constrain supercoils and compact the DNA. We believe that the DNA sequence-directed versatile assembly of periodic higher-order structures reveals a general organizational principle that can be exploited for knowledge-based design of long-range nucleoprotein complexes and purposeful manipulation of the bacterial chromatin architecture.

scholarly journals The role of CTCF in regulating nuclear organization

2008 ◽  
Vol 205 (4) ◽  
pp. 747-750 ◽  
Author(s):  
Adam Williams ◽  
Richard A. Flavell
Keyword(s):  
Long Range ◽  
Dna Sequences ◽  
Spatial Organization ◽  
Zinc Finger Protein ◽  
Nuclear Organization ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Binding Factor ◽  
Long Range Interactions ◽  
Regulatory Functions

The spatial organization of the genome is thought to play an important part in the coordination of gene regulation. New techniques have been used to identify specific long-range interactions between distal DNA sequences, revealing an ever-increasing complexity to nuclear organization. CCCTC-binding factor (CTCF) is a versatile zinc finger protein with diverse regulatory functions. New data now help define how CTCF mediates both long-range intrachromosomal and interchromosomal interactions, and highlight CTCF as an important factor in determining the three-dimensional structure of the genome.

scholarly journals L1 and B1 repeats blueprint the spatial organization of chromatin

2019 ◽  
Author(s):  
J. Yuyang Lu ◽  
Lei Chang ◽  
Tong Li ◽  
Ting Wang ◽  
Yafei Yin ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Mammalian Cells ◽  
Spatial Organization ◽  
Genome Structure ◽  
Three Dimensional ◽  
Order Structure ◽  
Basic Principles ◽  
Heterochromatin Protein ◽  
3D Genome ◽  
Genomic Repeats

SUMMARYDespite extensive mapping of three-dimensional (3D) chromatin structures, the basic principles underlying genome folding remain unknown. Here, we report a fundamental role for L1 and B1 retrotransposons in shaping the macroscopic 3D genome structure. Homotypic clustering of B1 and L1 repeats in the nuclear interior or at the nuclear and nucleolar peripheries, respectively, segregates the genome into mutually exclusive nuclear compartments. This spatial segregation of L1 and B1 is conserved in mouse and human cells, and occurs dynamically during establishment of the 3D chromatin structure in early embryogenesis and the cell cycle. Depletion of L1 transcripts drastically disrupts the spatial distributions of L1- and B1-rich compartments. L1 transcripts are strongly associated with L1 DNA sequences and induce phase separation of the heterochromatin protein HP1α. Our results suggest that genomic repeats act as the blueprint of chromatin macrostructure, thus explaining the conserved higher-order structure of chromatin across mammalian cells.

Patchiness and correlations in DNA sequences

Science ◽  
1993 ◽  
Vol 259 (5095) ◽  
pp. 677-680 ◽  
Author(s):  
S Karlin ◽  
V Brendel
Keyword(s):  
Random Walk ◽  
Stochastic Processes ◽  
Long Range ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Sequence Variation ◽  
Long Range Correlations ◽  
Fractal Models ◽  
Dna Sequence Variation

The highly nonrandom character of genomic DNA can confound attempts at modeling DNA sequence variation by standard stochastic processes (including random walk or fractal models). In particular, the mosaic character of DNA consisting of patches of different composition can fully account for apparent long-range correlations in DNA.

scholarly journals DNA sequence encodes the position of DNA supercoils

2017 ◽  
Author(s):  
Sung Hyun Kim ◽  
Mahipal Ganji ◽  
Jaco van der Torre ◽  
Elio Abbondanzieri ◽  
Cees Dekker
Keyword(s):  
Dna Sequence ◽  
Single Molecule ◽  
Dna Sequences ◽  
Structural Information ◽  
Three Dimensional ◽  
Decisive Role ◽  
Dimensional Structure ◽  
Transcription Start Sites ◽  
Cellular Processes

AbstractThe three-dimensional structure of DNA is increasingly understood to play a decisive role in gene regulation and other vital cellular processes, which has triggered an explosive growth of research on the spatial architecture of the genome. Many studies focus on the role of various DNA-packaging proteins, crowding, and confinement in organizing chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we use a fluorescence-based single-molecule technique to visualize plectonemes, the extended intertwined DNA loops that form upon twisting DNA. Remarkably, we find that the underlying DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific positions. We explore a variety of DNA sequences to determine what features influence pinning, and we develop a physical model that predicts the level of plectoneme pinning in excellent agreement with the data. The intrinsic curvature measured over a range of ~70 base pairs is found to be the key property governing the supercoiled structure of DNA. Our model predicts that plectonemes are likely to localize directly upstream of prokaryotic transcription start sites, and this prediction is experimentally verifiedin vitro.Our results reveal a hidden code in DNA that helps to spatially organize the genome.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Three-Dimensional Structure of Cloned T3 Connector Protein at 1.6nm Resolution

1990 ◽  
Vol 48 (1) ◽  
pp. 282-283
Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa
Keyword(s):  
Dna Sequences ◽  
Expression Vector ◽  
Three Dimensional ◽  
Deae Cellulose ◽  
Dna Packaging ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Freezing And Thawing ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.

scholarly journals DNA thermodynamics shape chromosome organization and topology

2013 ◽  
Vol 41 (2) ◽  
pp. 548-553 ◽  
Author(s):  
Andrew A. Travers ◽  
Georgi Muskhelishvili
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Chromosome Organization ◽  
Topological Properties ◽  
Genetic Organization ◽  
And Topology ◽  
Dna Translocases

How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.

scholarly journals Applying Learning Analytics to Detect Sequences of Actions and Common Errors in a Geometry Game

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1025
Author(s):  
Manuel J. Gomez ◽  
José A. Ruipérez-Valiente ◽  
Pedro A. Martínez ◽  
Yoon Jeon Kim
Keyword(s):  
Learning Analytics ◽  
Process Mining ◽  
Three Dimensional ◽  
Noncognitive Skills ◽  
Assessment Data ◽  
Ample Evidence ◽  
Clear Sense ◽  
Games For Learning ◽  
The U.S

Games have become one of the most popular activities across cultures and ages. There is ample evidence that supports the benefits of using games for learning and assessment. However, incorporating game activities as part of the curriculum in schools remains limited. Some of the barriers for broader adoption in classrooms is the lack of actionable assessment data, the fact that teachers often do not have a clear sense of how students are interacting with the game, and it is unclear if the gameplay is leading to productive learning. To address this gap, we seek to provide sequence and process mining metrics to teachers that are easily interpretable and actionable. More specifically, we build our work on top of Shadowspect, a three-dimensional geometry game that has been developed to measure geometry skills as well other cognitive and noncognitive skills. We use data from its implementation across schools in the U.S. to implement two sequence and process mining metrics in an interactive dashboard for teachers. The final objective is to facilitate that teachers can understand the sequence of actions and common errors of students using Shadowspect so they can better understand the process, make proper assessment, and conduct personalized interventions when appropriate.

scholarly journals An application of slow feature analysis to the genetic sequences of coronaviruses and influenza viruses

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Anastasios A. Tsonis ◽  
Geli Wang ◽  
Lvyi Zhang ◽  
Wenxu Lu ◽  
Aristotle Kayafas ◽  
...  
Keyword(s):  
Mathematical Method ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Transmission Rate ◽  
Complex Structure ◽  
Mortality Rates ◽  
Influenza Viruses ◽  
Feature Analysis ◽  
Slow Feature Analysis ◽  
Genetic Sequences

Abstract Background Mathematical approaches have been for decades used to probe the structure of DNA sequences. This has led to the development of Bioinformatics. In this exploratory work, a novel mathematical method is applied to probe the DNA structure of two related viral families: those of coronaviruses and those of influenza viruses. The coronaviruses are SARS-CoV-2, SARS-CoV-1, and MERS. The influenza viruses include H1N1-1918, H1N1-2009, H2N2-1957, and H3N2-1968. Methods The mathematical method used is the slow feature analysis (SFA), a rather new but promising method to delineate complex structure in DNA sequences. Results The analysis indicates that the DNA sequences exhibit an elaborate and convoluted structure akin to complex networks. We define a measure of complexity and show that each DNA sequence exhibits a certain degree of complexity within itself, while at the same time there exists complex inter-relationships between the sequences within a family and between the two families. From these relationships, we find evidence, especially for the coronavirus family, that increasing complexity in a sequence is associated with higher transmission rate but with lower mortality. Conclusions The complexity measure defined here may hold a promise and could become a useful tool in the prediction of transmission and mortality rates in future new viral strains.

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