scholarly journals Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

2017 ◽  
Author(s):  
Michael R. Stadler ◽  
Jenna E. Haines ◽  
Michael B. Eisen
Keyword(s):  
Drosophila Melanogaster ◽  
High Resolution ◽  
Polytene Chromosomes ◽  
Three Dimensional ◽  
Order Structure ◽  
Chromatin Conformation ◽  
Insulator Proteins ◽  
Self Association ◽  
The One ◽  
Genomic Regions

AbstractEvidence has emerged in recent years linking insulators and the proteins that bind them to the higher order structure of animal chromatin, but the precise nature of this relationship and the manner by which insulators influence chromatin structure have remained elusive. Here we present high-resolution genome-wide chromatin conformation capture (Hi-C) data from early Drosophila melanogaster embryos that allow us to map three-dimensional interactions to 500 base pairs. We observe a complex, nested pattern of regions of chromatin self-association, and use a combination of computational and manual annotation to identify boundaries between these topological associated domains (TADs). We demonstrate that, when mapped at high resolution, boundaries resemble classical insulators: short (500 - 1000 bp) genomic regions that are sensitive to DNase digestion and strongly bound by known insulator proteins. Strikingly, we show that for regions where the banding pattern of polytene chromosomes has been mapped to genomic position at comparably high resolution, there is a perfect correspondence between polytene banding and our chromatin conformation maps, with boundary insulators forming the interband regions that separate compacted bands that correspond to TADs. We propose that this precise, high-resolution relationship between insulators and TADs on the one hand and polytene bands and interbands on the other extends across the genome, and suggest a model in which the decompaction of insulator regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains.

scholarly journals Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Michael R Stadler ◽  
Jenna E Haines ◽  
Michael B Eisen
Keyword(s):  
High Resolution ◽  
Three Dimensional ◽  
Physical Nature ◽  
Topological Domains ◽  
High Resolution Mapping ◽  
Insulator Proteins ◽  
Dna Elements ◽  
Resolution Mapping ◽  
Insulator Elements ◽  
Genomic Regions

High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters. Further, we show a striking correspondence between these elements and the locations of mapped polytene interband regions. We believe it is likely this relationship between insulators, topological boundaries, and polytene interbands extends across the genome, and we therefore propose a model in which decompaction of boundary-insulator-interband regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains.

scholarly journals A chromatin extension model for insulator function based on comparison of high-resolution chromatin conformation capture and polytene banding maps

2017 ◽  
Author(s):  
Michael R. Stadler ◽  
Michael B. Eisen
Keyword(s):  
High Resolution ◽  
Physical Space ◽  
Structural Features ◽  
Chromatin Conformation ◽  
Chromatin Conformation Capture ◽  
Insulator Function ◽  
Extension Model ◽  
Insulator Proteins ◽  
Topologically Associated Domains ◽  
Insulator Elements

AbstractInsulator proteins bind to specific genomic loci and have been shown to play a role in partitioning genomes into independent domains of gene expression and chromatin structure. Despite decades of study, the mechanism by which insulators establish these domains remains elusive. Here, we use genome-wide chromatin conformation capture (Hi-C) to generate a high-resolution map of spatial interactions of chromatin from Drosophila melanogaster embryos. We show that from the earliest stages of development the genome is divided into distinct topologically associated domains (TADs), that we can map the boundaries between TADs to sub-kilobase resolution, and that these boundaries correspond to 500-2000 bp insulator elements. Comparing this map with a detailed assessment of the banding pattern of a region of a polytene chromosome, we show that these insulator elements correspond to low density polytene interbands that divide compacted bands, which correspond to TADs. It has been previously shown that polytene interbands have low packing ratios allowing the conversion of small genomic distances (in base pairs) into a large physical distances. We therefore suggest a simple mechanism for insulator function whereby insulators increase the physical space between adjacent domains via the unpacking and extension of intervening chromatin. This model provides an intuitive explanation for known features of insulators, including the ability to block enhancer-promoter interactions, limit the spread of heterochromatin, and organize the structural features of interphase chromosomes.

scholarly journals Three-dimensional organization of Drosophila melanogaster interphase nuclei. II. Chromosome spatial organization and gene regulation.

1987 ◽  
Vol 104 (6) ◽  
pp. 1471-1483 ◽  
Author(s):  
M Hochstrasser ◽  
J W Sedat
Keyword(s):  
Gene Regulation ◽  
Drosophila Melanogaster ◽  
Nuclear Envelope ◽  
Spatial Organization ◽  
Polytene Chromosomes ◽  
Three Dimensional ◽  
Nucleolar Organizer ◽  
Cell Types ◽  
Functional Changes ◽  
Specific Subset

In the preceding article we compared the general organization of polytene chromosomes in four different Drosophila melanogaster cell types. Here we describe experiments aimed at testing for a potential role of three-dimensional chromosome folding and positioning in modulating gene expression and examining specific chromosome interactions with different nuclear structures. By charting the configurations of salivary gland chromosomes as the cells undergo functional changes, it is shown that loci are not repositioned within the nucleus when the pattern of transcription changes. Heterologous loci show no evidence of specific physical interactions with one another in any of the cell types. However, a specific subset of chromosomal loci is attached to the nuclear envelope, and this subset is extremely similar in at least two tissues. In contrast, no specific interactions between any locus and the nucleolus are found, but the base of the X chromosome, containing the nucleolar organizer, is closely linked to this organelle. These results are used to evaluate models of gene regulation that involve the specific intranuclear positioning of gene sequences. Finally, data are presented on an unusual class of nuclear envelope structures, filled with large, electron-dense particles, that are usually associated with chromosomes.

scholarly journals Suppression of H2-cooling in protogalaxies aided by trapped Lyα cooling radiation

2020 ◽  
Vol 500 (1) ◽  
pp. 138-144
Author(s):  
Jemma Wolcott-Green ◽  
Zoltán Haiman ◽  
Greg L Bryan
Keyword(s):  
Black Hole ◽  
High Resolution ◽  
Energy Density ◽  
Molecular Hydrogen ◽  
Thermal Evolution ◽  
Three Dimensional ◽  
Hole Formation ◽  
Massive Black Hole ◽  
Hydrodynamic Simulations ◽  
The One

ABSTRACT We study the thermal evolution of UV-irradiated atomic cooling haloes using high-resolution three-dimensional hydrodynamic simulations. We consider the effect of H− photodetachment by Lyα cooling radiation trapped in the optically-thick cores of three such haloes, a process that has not been included in previous simulations. Because H− is a precursor of molecular hydrogen, its destruction can diminish the H2 abundance and cooling. We find that the critical UV flux for suppressing H2-cooling is decreased by ∼15–50 per cent in our fiducial models. Previous one-zone modelling found a larger effect, with Jcrit reduced by a factor of a few; we show that adopting a constant halo mass to determine the trapped Lyα energy density, as is done in the one-zone models, yields a larger reduction in Jcrit, consistent with their findings. Our results nevertheless suggest that Lyα radiation may have an important effect on the thermal evolution of UV-irradiated haloes, and therefore on the potential for massive black hole formation.

scholarly journals The three-dimensional organization of polytene nuclei in male Drosophila melanogaster with compound XY or ring X chromosomes.

Genetics ◽  
1989 ◽  
Vol 121 (2) ◽  
pp. 293-311
Author(s):  
D Mathog ◽  
J W Sedat
Keyword(s):  
Drosophila Melanogaster ◽  
Salivary Glands ◽  
X Chromosome ◽  
Genetic Regulation ◽  
Polytene Chromosomes ◽  
Three Dimensional ◽  
X Chromosomes ◽  
Frequent Failure ◽  
Polytene Nucleus ◽  
Polytene Nuclei

Abstract The three-dimensional organization of polytene chromosomes within nuclei containing rearranged X chromosomes was examined in male Drosophila melanogaster. Salivary glands of third instar larvae containing either an inverted X chromosome (YSX.YL, In(1)EN/O) or a ring X chromosome (R(1) 2/BSYy+) were fixed, embedded, and serially sectioned. The nuclei in contiguous groups of cells were modeled and analyzed. We find that for both genotypes the three-dimensional behavior at each euchromatic locus is independent of the orientation of the chromosome on which it resides, independent of the behavior of loci not closely linked to it, and not similar in neighboring cells. The preference for right-handed chromosome coiling noted in previous studies is shown to be independent of homologous pairing. However, a relation between the extent of chromosome curvature and the handedness of chromosome coiling is present only in homologously paired chromosomes. The attached-XY chromosome has two previously undescribed behaviors: a nearly invariant association of the euchromatic side of the proximal heterochromatin/euchromatin junction with the nucleolus and a frequent failure of this site to attach to the chromocenter. The relative chromosome arm positions are often similar in several neighboring cells. The size of these patches of cells, assuming that they represent clones, indicates that such arrangements are at best quasi-stable: they may be maintained over at least one, but less than four, cell divisions. The observed nuclear organization in salivary glands is inconsistent with the idea that position in the polytene nucleus plays a major role in the normal genetic regulation of euchromatic loci.

High Resolution Microscopy of Multi-Layered Biological Crystals

1982 ◽  
Vol 40 ◽  
pp. 80-83
Author(s):  
H.A. Cohen ◽  
T.W. Jeng ◽  
W. Chiu
Keyword(s):  
High Resolution ◽  
Low Dose ◽  
Three Dimensional ◽  
Data Interpretation ◽  
Two Dimensional ◽  
Biological Objects ◽  
Density Maps ◽  
Density Map ◽  
Complex Crystal ◽  
High Resolution Microscopy

This tutorial will discuss the methodology of low dose electron diffraction and imaging of crystalline biological objects, the problems of data interpretation for two-dimensional projected density maps of glucose embedded protein crystals, the factors to be considered in combining tilt data from three-dimensional crystals, and finally, the prospects of achieving a high resolution three-dimensional density map of a biological crystal. This methodology will be illustrated using two proteins under investigation in our laboratory, the T4 DNA helix destabilizing protein gp32*I and the crotoxin complex crystal.

Electron crystallographic determination of the 3-D structure of staurolite at atomic resolution

1991 ◽  
Vol 49 ◽  
pp. 540-541
Author(s):  
Kenneth H. Downing ◽  
Hu Meisheng ◽  
Hans-Rudolf Went ◽  
Michael A. O'Keefe
Keyword(s):  
High Resolution ◽  
Three Dimensional ◽  
High Resolution Electron Microscopy ◽  
Atomic Resolution ◽  
Dimensional Structure ◽  
Structure Information ◽  
Resolution Electron ◽  
Scattering Effects ◽  
High Resolution Images ◽  
Effects Of Radiation

With current advances in electron microscope design, high resolution electron microscopy has become routine, and point resolutions of better than 2Å have been obtained in images of many inorganic crystals. Although this resolution is sufficient to resolve interatomic spacings, interpretation generally requires comparison of experimental images with calculations. Since the images are two-dimensional representations of projections of the full three-dimensional structure, information is invariably lost in the overlapping images of atoms at various heights. The technique of electron crystallography, in which information from several views of a crystal is combined, has been developed to obtain three-dimensional information on proteins. The resolution in images of proteins is severely limited by effects of radiation damage. In principle, atomic-resolution, 3D reconstructions should be obtainable from specimens that are resistant to damage. The most serious problem would appear to be in obtaining high-resolution images from areas that are thin enough that dynamical scattering effects can be ignored.

Three-Dimensional Immunoelectron Microscopy of Yeast Cells by a New High-Resolution Replica Method

1985 ◽  
Vol 43 ◽  
pp. 562-563
Author(s):  
Hirano T. ◽  
M. Yamaguchi ◽  
M. Hayashi ◽  
Y. Sekiguchi ◽  
A. Tanaka
Keyword(s):  
High Resolution ◽  
Plasma Polymerization ◽  
Three Dimensional ◽  
Freeze Fracture ◽  
Replica Method ◽  
Yeast Cells ◽  
Dynamic Aspect ◽  
Replica Technique ◽  
Gaseous Hydrocarbon ◽  
Transmission Electron

A plasma polymerization film replica method is a new high resolution replica technique devised by Tanaka et al. in 1978. It has been developed for investigation of the three dimensional ultrastructure in biological or nonbiological specimens with the transmission electron microscope. This method is based on direct observation of the single-stage replica film, which was obtained by directly coating on the specimen surface. A plasma polymerization film was deposited by gaseous hydrocarbon monomer in a glow discharge.The present study further developed the freeze fracture method by means of a plasma polymerization film produces a three dimensional replica of chemically untreated cells and provides a clear evidence of fine structure of the yeast plasma membrane, especially the dynamic aspect of the structure of invagination (Figure 1).

Interpretation of the Contrast of High-Resolution Electron Microscopy Images of Ni4Mo by Means of Simulated Image Maps

1990 ◽  
Vol 48 (1) ◽  
pp. 28-29
Author(s):  
A. Thust ◽  
K. Urban
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Antiphase Boundary ◽  
High Resolution Electron Microscopy ◽  
Foil Thickness ◽  
Order Structure ◽  
Simulated Image ◽  
Resolution Electron ◽  
Fcc Lattice ◽  
Direct Interpretation

The alloy of composition Ni4Mo develops, at temperatures below 860 °C, an ordered Dla-structure which is based on the fcc-lattice. This alloy has been widely investigated with respect to its physical properties and its ordering behaviour. High resolution studies are rare and concentrated mainly on its short-range order structure. The aim of the present work was to develop a detailed understanding of image contrast and to apply the results to antiphase-boundary studies in ordered Ni4Mo by means of a JEOL 4000 EX electron microscope.In high-resolution electron microscopy, depending on defocus and foil thickness, a large variety of different images is obtained. Only a few of these allow a direct interpretation concerning the location and the type of the atoms. By computing a through-focus/through-thickness map (TFTT map) before starting experimental work it is possible to determine the proper conditions at which images can be obtained which are closely related to the projected potential.

Diffraction contrast of dislocations in icosahedral quasicrystals

1990 ◽  
Vol 48 (4) ◽  
pp. 454-455
Author(s):  
K. Urban ◽  
Z. Zhang ◽  
M. Wollgarten ◽  
D. Gratias
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Complete Characterization ◽  
Extinction Condition ◽  
Burgers Vector ◽  
Diffraction Contrast ◽  
Lattice Geometry ◽  
Reference Space ◽  
Icosahedral Quasicrystals ◽  
The One

Recently dislocations have been observed by electron microscopy in the icosahedral quasicrystalline (IQ) phase of Al65Cu20Fe15. These dislocations exhibit diffraction contrast similar to that known for dislocations in conventional crystals. The contrast becomes extinct for certain diffraction vectors g. In the following the basis of electron diffraction contrast of dislocations in the IQ phase is described. Taking account of the six-dimensional nature of the Burgers vector a “strong” and a “weak” extinction condition are found.Dislocations in quasicrystals canot be described on the basis of simple shear or insertion of a lattice plane only. In order to achieve a complete characterization of these dislocations it is advantageous to make use of the one to one correspondence of the lattice geometry in our three-dimensional space (R3) and that in the six-dimensional reference space (R6) where full periodicity is recovered . Therefore the contrast extinction condition has to be written as gpbp + gobo = 0 (1). The diffraction vector g and the Burgers vector b decompose into two vectors gp, bp and go, bo in, respectively, the physical and the orthogonal three-dimensional sub-spaces of R6.

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