scholarly journals Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

2016 ◽  
Author(s):  
Nathan Harmston ◽  
Elizabeth Ing-Simmons ◽  
Ge Tan ◽  
Malcolm Perry ◽  
Matthias Merkenschlager ◽  
...  
Keyword(s):  
Long Range ◽  
Close Correspondence ◽  
Developmental Genes ◽  
Regulatory Interactions ◽  
Topologically Associating Domains ◽  
Topologically Associated Domains ◽  
The Difference ◽  
Conserved Noncoding Elements ◽  
Extreme Conservation

AbstractIn vertebrates and other Metazoa, developmental genes are found surrounded by dense clusters of highly conserved noncoding elements (CNEs). CNEs exhibit extreme levels of sequence conservation of unexplained origin, with many acting as long-range enhancers during development. Clusters of CNEs, termed genomic regulatory blocks (GRBs), define the span of regulatory interactions for many important developmental regulators. The function and genomic distribution of these elements close to important regulatory genes raises the question of how they relate to the 3D conformation of these loci. We show that GRBs, defined using clusters of CNEs, coincide strongly with the patterns of topological organisation in metazoan genomes, predicting the boundaries of topologically associating domains (TADs) at hundreds of loci. The set of TADs that are associated with high levels of non-coding conservation exhibit distinct properties compared to TADs called in chromosomal regions devoid of extreme non-coding conservation. The correspondence between GRBs and TADs suggests that TADs around developmental genes are ancient, slowly evolving genomic structures, many of which have had conserved spans for hundreds of millions of years. This relationship also explains the difference in TAD numbers and sizes between genomes. While the close correspondence between extreme conservation and the boundaries of this subset of TADs does not reveal the mechanism leading to the conservation of these elements, it provides a functional framework for studying the role of TADs in long-range transcriptional regulation.

scholarly journals OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Lin An ◽  
Tao Yang ◽  
Jiahao Yang ◽  
Johannes Nuebler ◽  
Guanjue Xiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Domain Structure ◽  
High Frequency ◽  
Spatial Organization ◽  
Structural Units ◽  
Regulatory Interactions ◽  
Link Type ◽  
Topologically Associating Domains

AbstractThe spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD.

scholarly journals CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

2020 ◽  
Author(s):  
Martin Franke ◽  
Elisa de la Calle-Mustienes ◽  
Ana Neto ◽  
Rafael Acemel ◽  
Juan Tena ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Long Range ◽  
Chromatin Structure ◽  
Ctcf Binding ◽  
Developmental Gene ◽  
Developmental Genes ◽  
Chromatin Interactions ◽  
Topologically Associating Domains ◽  
Regulatory Landscapes

Abstract CTCF is an 11-zinc-finger DNA-binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long-range chromatin looping and is enriched at the boundaries of topologically associating domains, which are sub-megabase chromatin structures that are believed to facilitate enhancer-promoter interactions within regulatory landscapes. Although CTCF is essential for cycling cells and developing embryos, its in vitro removal has only modest effects over gene expression, challenging the concept that CTCF-mediated chromatin interactions and topologically associated domains are a fundamental requirement for gene regulation. Here we link the loss of chromatin structure and gene regulation in an in vivo model and during animal development. We generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes, including many developmental genes. In addition, chromatin accessibility, both at CTCF binding sites and cis-regulatory elements, is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution, we further demonstrate that promoters fail to fully establish long-range contacts with their associated regulatory landscapes, leading to altered gene expression patterns and disruption of developmental programs. Our results demonstrate that CTCF and topologically associating domains are essential to regulate gene expression during embryonic development, providing the structural basis for the establishment of developmental gene regulatory landscapes.

scholarly journals CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

2020 ◽  
Author(s):  
Martin Franke ◽  
Elisa De la Calle-Mustienes ◽  
Ana Neto ◽  
Rafael D. Acemel ◽  
Juan J. Tena ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Long Range ◽  
Chromatin Structure ◽  
Ctcf Binding ◽  
Developmental Gene ◽  
Developmental Genes ◽  
Chromatin Interactions ◽  
Topologically Associating Domains ◽  
Regulatory Landscapes

CTCF is an 11-zinc-finger DNA-binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding1–5. CTCF mediates long-range chromatin looping and is enriched at the boundaries of topologically associating domains, which are sub-megabase chromatin structures that are believed to facilitate enhancer-promoter interactions within regulatory landscapes 6–12. Although CTCF is essential for cycling cells and developing embryos13,14, its in vitro removal has only modest effects over gene expression5,15, challenging the concept that CTCF-mediated chromatin interactions and topologically associated domains are a fundamental requirement for gene regulation16–18. Here we link the loss of chromatin structure and gene regulation in an in vivo model and during animal development. We generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes, including many developmental genes. In addition, chromatin accessibility, both at CTCF binding sites and cis-regulatory elements, is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution, we further demonstrate that promoters fail to fully establish long-range contacts with their associated regulatory landscapes, leading to altered gene expression patterns and disruption of developmental programs. Our results demonstrate that CTCF and topologically associating domains are essential to regulate gene expression during embryonic development, providing the structural basis for the establishment of developmental gene regulatory landscapes.

scholarly journals Author Correction: The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ilona E. Grabowicz ◽  
Bartek Wilczyński ◽  
Bożena Kamińska ◽  
Adria‑Jaume Roura ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Long Range ◽  
Epigenetic Modifications ◽  
Topologically Associating Domains

scholarly journals Hierarchical Domain Structure Reveals the Divergence of Activity among TADs and Boundaries

2018 ◽  
Author(s):  
Lin An ◽  
Tao Yang ◽  
Jiahao Yang ◽  
Johannes Nuebler ◽  
Guanjue Xiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Frequency ◽  
Spatial Organization ◽  
Running Speed ◽  
Structural Units ◽  
Regulatory Interactions ◽  
Topologically Associating Domains ◽  
Regulated Gene Expression ◽  
Improved Accuracy

AbstractThe spatial organization of chromatin in the nucleus has been implicated in many aspects of regulated gene expression. Maps of high frequency interactions between different segments of chromatin have revealed Topologically Associating Domains (TADs), within which most of the regulatory interactions are thought to occur. Recent studies have shown that TADs are not homogeneous structural units, but rather they appear to be organized into a hierarchy. However, precise identification of hierarchical TAD structures remains a challenge. We present OnTAD, an Optimized Nested TAD caller from Hi-C data, to identify hierarchical TADs. Compared to existing methods, OnTAD has significantly improved accuracy and running speed. Results from OnTAD reveal new biological insights on the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. The software and documentation for OnTAD are available at: https://github.com/anlin00007/OnTAD

The role of differential phase contrast in electron microscopy

1978 ◽  
Vol 36 (1) ◽  
pp. 176-177
Author(s):  
E.M. Waddell ◽  
J.N. Chapman ◽  
R.P. Ferrier
Keyword(s):  
Phase Contrast ◽  
Practical Method ◽  
Position Vector ◽  
Differential Phase ◽  
Pure Phase ◽  
Differential Phase Contrast ◽  
The Difference ◽  
Image Position ◽  
First Moment

Dekkers and de Lang (1977) have discussed a practical method of realising differential phase contrast in a STEM. The method involves taking the difference signal from two semi-circular detectors placed symmetrically about the optic axis and subtending the same angle (2α) at the specimen as that of the cone of illumination. Such a system, or an obvious generalisation of it, namely a quadrant detector, has the characteristic of responding to the gradient of the phase of the specimen transmittance. In this paper we shall compare the performance of this type of system with that of a first moment detector (Waddell et al.1977).For a first moment detector the response function R(k) is of the form R(k) = ck where c is a constant, k is a position vector in the detector plane and the vector nature of R(k)indicates that two signals are produced. This type of system would produce an image signal given bywhere the specimen transmittance is given by a (r) exp (iϕ (r), r is a position vector in object space, ro the position of the probe, ⊛ represents a convolution integral and it has been assumed that we have a coherent probe, with a complex disturbance of the form b(r-ro) exp (iζ (r-ro)). Thus the image signal for a pure phase object imaged in a STEM using a first moment detector is b2 ⊛ ▽ø. Note that this puts no restrictions on the magnitude of the variation of the phase function, but does assume an infinite detector.

On the Role of Transferrin in 67Ga Uptake by Tumor Cells

1988 ◽  
Vol 27 (04) ◽  
pp. 151-153
Author(s):  
P. Thouvenot ◽  
F. Brunotte ◽  
J. Robert ◽  
L. J. Anghileri
Keyword(s):  
Specific Binding ◽  
Subcellular Fractionation ◽  
Animal Blood ◽  
Tumor Bearing ◽  
Cell Structures ◽  
The Difference ◽  
Sarcoma Cells ◽  
In Vitro Uptake

In vitro uptake of 67Ga-citrate and 59Fe-citrate by DS sarcoma cells in the presence of tumor-bearing animal blood plasma showed a dramatic inhibition of both 67Ga and 59Fe uptakes: about ii/io of 67Ga and 1/5o of the 59Fe are taken up by the cells. Subcellular fractionation appears to indicate no specific binding to cell structures, and the difference of binding seems to be related to the transferrin chelation and transmembrane transport differences

The Role of Developmental Genes in Chordoma

Skull Base ◽  
2007 ◽  
Vol 17 (S 2) ◽  
Author(s):  
Michael Kelley ◽  
Josh Sommer ◽  
Sufeng Li ◽  
Enyu Ding ◽  
Fan Dong
Keyword(s):  
Developmental Genes

The Role of Technological Change in the Long-run Global Economy Forecasting

2013 ◽  
pp. 97-116 ◽  
Author(s):  
A. Apokin
Keyword(s):  
Technological Change ◽  
Data Quality ◽  
Long Range ◽  
Global Economy ◽  
World Economy ◽  
Qualitative Approaches ◽  
Long Run ◽  
The World ◽  
National Economies

The author compares several quantitative and qualitative approaches to forecasting to find appropriate methods to incorporate technological change in long-range forecasts of the world economy. A?number of long-run forecasts (with horizons over 10 years) for the world economy and national economies is reviewed to outline advantages and drawbacks for different ways to account for technological change. Various approaches based on their sensitivity to data quality and robustness to model misspecifications are compared and recommendations are offered on the choice of appropriate technique in long-run forecasts of the world economy in the presence of technological change.

REFLECTION COEFFICIENT OF AN ELECTROMAGNETIC WAVE IN CONDUCTIVE MEDIA

2018 ◽  
pp. 100-106
Author(s):  
M. S. Sudakova ◽  
M. L. Vladov ◽  
M. R. Sadurtdinov
Keyword(s):  
Reflection Coefficient ◽  
Ground Penetrating Radar ◽  
Electromagnetic Waves ◽  
Water Contamination ◽  
Survey Design ◽  
Direct And Inverse Problems ◽  
The Difference ◽  
Ground Penetrating ◽  
Ideal Dielectric

Within the ground penetrating radar bandwidth the medium is considered to be an ideal dielectric, which is not always true. Electromagnetic waves reflection coefficient conductivity dependence showed a significant role of the difference in conductivity in reflection strength. It was confirmed by physical modeling. Conductivity of geological media should be taken into account when solving direct and inverse problems, survey design planning, etc. Ground penetrating radar can be used to solve the problem of mapping of halocline or determine water contamination.

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