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 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 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.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Volcanoes geological mapping and structural geology with UAS High Resolution Digital Terrain Model : the Kuei-Shan Tao case example (Eastern Taiwan).

2021 ◽  
Author(s):  
Benoit Deffontaines ◽  
Kuo-Jen Chang ◽  
Samuel Magalhaes ◽  
Gérardo Fortunato
Keyword(s):  
High Resolution ◽  
Okinawa Trough ◽  
Volcanic Rocks ◽  
Digital Terrain Model ◽  
Structural Features ◽  
Point Of View ◽  
Geological Mapping ◽  
Lava Flows ◽  
Aerial Photographs ◽  
Structural Scheme

<p>Volcanic areas in the World are often difficult to map especially in a structural point of view as (1) fault planes are generally covered and filled by more recent lava flows and (2) volcanic rocks have very few tectonic striations. Kuei-Shan Tao (11km from Ilan Plain – NE Taiwan) is a volcanic island, located at the soutwestern tip of the South Okinawa trough (SWOT). Two incompatible geological maps had been already published both lacking faults and structural features (Hsu, 1963 and Chiu et al., 2010). We propose herein not only to up-date the Kuei-Shan Tao geological map with our high resolution dataset, but also to create the Kuei-Shan Tao structural scheme in order to better understand its geological and tectonic history.</p><p>Consequently, we first acquired aerial photographs from our UAS survey and get our new UAS high resolution DTM (HR UAS-DTM hereafter) with a ground resolution <10cm processed through classical photogrammetric methods. Taking into account common sense geomorphic and structural interpretation and reasoning deduced form our HR UAS-DTM, and the outcropping lithologies situated all along the shoreline, we have up-dated the Kuei-Shan Tao geological mapping and its major structures. To conclude, the lithologies (andesitic lava flows and pyroclastic falls) and the new structural scheme lead us to propose a scenario for both the construction as well as the dismantling of Kuei-Shan Tao which are keys for both geology and geodynamics of the SWOT.</p>

Elucidation of Polymer Microstructure by High Resolution NMR Spectroscopy

1967 ◽  
Vol 40 (2) ◽  
pp. 385-399 ◽  
Author(s):  
Raymond C. Ferguson
Keyword(s):  
Nmr Spectroscopy ◽  
High Resolution ◽  
Spectral Data ◽  
High Field ◽  
Structural Features ◽  
Polymer Microstructure ◽  
Structural Isomerism ◽  
High Resolution Nmr ◽  
Polymer Tacticity

Abstract High resolution NMR spectroscopy is proving to be a useful experimental technique for determining the microstructures of high polymers. Its major utility, aside from identifying structural features often not detectable by other methods, lies in quantitative applications. Some examples are the determination of monomer ratios in copolymers, polymer tacticity, sequence isomerism of monomer units, and other types of structural isomerism. The applicability of the method is being enhanced by continuing development of high-field spectrometers, special accessories, and new experimental techniques, and by application of computers to the analysis of spectral data.

HIGH RESOLUTION PALAEOGEOGRAPHIC MAPPING OF THE FLUVIAL-LACUSTRINE PATCHAWARRA FORMATION IN THE COOPER BASIN, SOUTH AUSTRALIA

2002 ◽  
Vol 42 (1) ◽  
pp. 65 ◽  
Author(s):  
P.C. Strong ◽  
G.R. Wood ◽  
S.C. Lang ◽  
A. Jollands ◽  
E. Karalaus ◽  
...  
Keyword(s):  
High Resolution ◽  
South Australia ◽  
River System ◽  
Structural Features ◽  
Gas Reservoirs ◽  
Predictive Tool ◽  
Sequence Stratigraphic ◽  
Channel Belt ◽  
Reservoir Connectivity ◽  
Cooper Basin

Fluvial-lacustrine reservoirs in coal-bearing strata provide a particular challenge for reservoir characterisation because of the dominance of coal on the seismic signature and the highly variable reservoir geometry, quality and stratigraphic connectivity. Geological models for the fluvial gas reservoirs in the Permian Patchawarra Formation of the Cooper Basin are critical to minimise the perceived reservoir risks of these relatively deep targets. This can be achieved by applying high-resolution sequence stratigraphic concepts and finescaled seismic mapping. The workflow begins with building a robust regional chronostratigraphic framework, focussing on widespread lacustrine flooding surfaces and unconformities, tied to seismic scale reflectors. This framework is refined by identification of local surfaces that divide the Patchawarra Formation into high-resolution genetic units. A log facies scheme is established based on wireline log character, and calibrated to cores and cuttings, supported by analogue studies, such as the modern Ob River system in Western Siberia. Stacking patterns within each genetic unit are used to determine depositional systems tracts, which can have important reservoir connectivity implications. This leads to the generation of log signature maps for each interval, from which palaeogeographic reconstructions are generated. These maps are drawn with the guiding control of syn-depositional structural features and net/ gross trends. Estimates of fluvial channel belt widths are based on modern and ancient analogues. The resultant palaeogeography maps are used with structural and production data to refine play concepts, as a predictive tool to locate exploration and development drilling opportunities, to assess volumetrics, and to improve drainage efficiency and recovery during production of hydrocarbons.

scholarly journals Analysis of the structural variability of topologically associated domains as revealed by Hi-C

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Natalie Sauerwald ◽  
Akshat Singhal ◽  
Carl Kingsford
Keyword(s):  
Structural Changes ◽  
Chromosome Structure ◽  
Three Dimensional ◽  
Replication Timing ◽  
Building Blocks ◽  
Structural Features ◽  
Genetic Sequence ◽  
Experimental Variation ◽  
Topologically Associated Domains ◽  
Integral Role

Abstract Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze 137 Hi-C samples from 9 studies under 3 measures to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and provide initial evidence that this variability does not come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of key factors influencing comparisons of chromosome structure, suggesting significant variability and the potential for cell-type-specific structural features, which has previously not been systematically explored. The lack of observed influence of heredity and genetic differences on chromosome structure suggests that factors other than the genetic sequence are driving this structure, which plays an important role in human disease and cellular functioning.

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