scholarly journals Extracting multi-way chromatin contacts from Hi-C data

2021 ◽  
Vol 17 (12) ◽  
pp. e1009669
Author(s):  
Lei Liu ◽  
Bokai Zhang ◽  
Changbong Hyeon
Keyword(s):  
Gene Regulation ◽  
Cell Line ◽  
Long Range ◽  
Short Range ◽  
Experimental Measurements ◽  
Body Contact ◽  
Probability Maps ◽  
Analytic Expressions ◽  
Three Body ◽  
Fundamental Units

There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.

scholarly journals Extracting multi-way chromatin contacts from Hi-C data

2021 ◽  
Author(s):  
Lei Liu ◽  
Bokai Zhang ◽  
Changbong Hyeon
Keyword(s):  
Gene Regulation ◽  
Cell Line ◽  
Long Range ◽  
Short Range ◽  
Experimental Measurements ◽  
Body Contact ◽  
Probability Maps ◽  
Analytic Expressions ◽  
Three Body ◽  
Fundamental Units

There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.

scholarly journals Generation of long range and short range potentials

2021 ◽  
Author(s):  
Shinsho Oryu
Keyword(s):  
Long Range ◽  
Short Range ◽  
Body Force ◽  
Molecular System ◽  
Mass Dependence ◽  
Particle Transfer ◽  
Three Body ◽  
Force Potential ◽  
Type Potential

Abstract The general particle transfer (GPT) potential generates not only the Yukawa-type potential but also the 1⁄r^n-type potential in the hadron system, where the mass dependence of the transferred particle is clarified. The GPT potential from the atom-molecular system to the quark-gluon system was transversally studied, where the pico-meter physics could be highlighted. It was found that the long range three-body Efimov potential is connected with the short range three-body force potential.

Contributions of Three-body Overlap Effects to the Force Fields in CaF2-type Shell-model Lattices

1972 ◽  
Vol 27 (8-9) ◽  
pp. 1196-1210
Author(s):  
Ø. Ra
Keyword(s):  
Force Field ◽  
Shell Model ◽  
Long Range ◽  
Short Range ◽  
Equations Of Motion ◽  
Exclusion Principle ◽  
Electronic Charge ◽  
Short Range Force ◽  
Model Equations ◽  
Three Body

Abstract Due to the exclusion principle the distribution of electronic charge in an ionic crystal differs from a superposition of free-ion charge densities even in the simple Heitler-London picture. This charge density deformation engenders three-body long-range forces the influence of which on lattice vibrations is not accounted for by the usual Kellermann matrix. To obtain a better separation of long-range from short-range forces in CaF2 , SrF2, and BaF2 , i. e. to avoid absorbing long-range interactions in an adjustable short-range force field, explicit formulae are derived for three-body contributions to the shell-model equations of motion. The additional dynamical matrices pertain to arbitrary wavelengths. In adding to the force field terms which are not purely volume dependent the present descirption of three-body forces is somewhat at variance with recent work on alkali halide dynamics. The deviation from pure volume dependence originates in overlap charges residing in internuclear regions.

scholarly journals Long-range chromatin interactions on the inactive X and at Hox clusters are regulated by the non-canonical SMC protein Smchd1

2018 ◽  
Author(s):  
Natasha Jansz ◽  
Andrew Keniry ◽  
Marie Trussart ◽  
Heidi Bildsoe ◽  
Tamara Beck ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Long Range ◽  
X Chromosome ◽  
Chromatin Structure ◽  
Short Range ◽  
Higher Order ◽  
Chromatin Interactions ◽  
Inactive X Chromosome ◽  
Hox Clusters

AbstractThe regulation of higher order chromatin structure is complex and dynamic; however we do not yet understand the full suite of mechanisms governing architecture. Here we reveal the non-canonical SMC protein Smchd1 as a novel regulator of long-range chromatin interactions, and add it to the canon of epigenetic proteins required for Hox gene regulation. The effect of losing Smchd1-dependent chromatin interactions has varying outcomes dependent on chromatin context. At autosomal targets transcriptionally sensitive to Smchd1 deletion, we find increased short-range interactions and ectopic enhancer activation. By contrast, the inactive X chromosome is transcriptionally refractive to Smchd1 ablation, despite chromosome-wide increases in short-range interactions. There we observe spreading of H3K27me3 domains into regions not normally decorated by this mark. Together these data suggest Smchd1 has the capacity to insulate the chromatin, thereby limiting access to other chromatin modifying proteins.

Mechanisms of human hepatobiliary transporter gene regulation in the hepatocyte-like cell line HepaRG

2008 ◽  
Vol 46 (01) ◽  
Author(s):  
IV Martin ◽  
S Voigt ◽  
S Strauch ◽  
C Trautwein ◽  
A Geier
Keyword(s):  
Gene Regulation ◽  
Cell Line ◽  
Transporter Gene

scholarly journals Structural basis of long-range to short-range synaptic transition in NHEJ

Nature ◽  
2021 ◽  
Author(s):  
Siyu Chen ◽  
Linda Lee ◽  
Tasmin Naila ◽  
Susan Fishbain ◽  
Annie Wang ◽  
...  
Keyword(s):  
Long Range ◽  
Short Range ◽  
Structural Basis

scholarly journals Comparison of short-range order in irradiated dysprosium titanates

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Roman Sherrod ◽  
Eric C. O’Quinn ◽  
Igor M. Gussev ◽  
Cale Overstreet ◽  
Joerg Neuefeind ◽  
...  
Keyword(s):  
Long Range ◽  
Short Range ◽  
Structural Model ◽  
Ion Irradiation ◽  
Function Analysis ◽  
Ion Beam ◽  
Structural Response ◽  
Heavy Ion ◽  
Range Order ◽  
Radiation Resistant

AbstractThe structural response of Dy2TiO5 oxide under swift heavy ion irradiation (2.2 GeV Au ions) was studied over a range of structural length scales utilizing neutron total scattering experiments. Refinement of diffraction data confirms that the long-range orthorhombic structure is susceptible to ion beam-induced amorphization with limited crystalline fraction remaining after irradiation to 8 × 1012 ions/cm2. In contrast, the local atomic arrangement, examined through pair distribution function analysis, shows only subtle changes after irradiation and is still described best by the original orthorhombic structural model. A comparison to Dy2Ti2O7 pyrochlore oxide under the same irradiation conditions reveals a different behavior: while the dysprosium titanate pyrochlore is more radiation resistant over the long-range with smaller degree of amorphization as compared to Dy2TiO5, the former involves more local atomic rearrangements, best described by a pyrochlore-to-weberite-type transformation. These results highlight the importance of short-range and medium-range order analysis for a comprehensive description of radiation behavior.

SHORT-RANGE AND LONG-RANGE ORDER OF TITANIUM IN Ti1+xS2

1977 ◽  
Vol 38 (C7) ◽  
pp. C7-202-C7-206 ◽  
Author(s):  
R. MORET ◽  
M. HUBER ◽  
R. COMÈS
Keyword(s):  
Long Range ◽  
Short Range ◽  
Range Order ◽  
Long Range Order
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