Additive scaling law for structural organization of chromatin in chicken erythrocyte nuclei

Abstract

Additive scaling law for structural organization of chromatin in chicken erythrocyte nuclei Iashina Important noteTo cite this publication, please use the final published version (if applicable). Please check the document version above. CopyrightOther than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons. Takedown policyPlease contact us and provide details if you believe this document breaches copyrights. We will remove access to the work immediately and investigate your claim. Small-angle neutron scattering (SANS) on nuclei of chicken erythrocytes demonstrates the cubic dependence of the scattering intensity Q −3 in the range of momentum transfer Q ∈ 10 −3 -10 −2 nm −1 . Independent spin-echo SANS measurements give the spin-echo function, which is well described by the exponential law in a range of sizes (3 × 10 2 )-(3 × 10 4 ) nm. Both experimental dependences reflect the nature of the structural organization of chromatin in the nucleus of a living cell, which corresponds to the correlation function γ (r) = ln(ξ/r) for r < ξ, where ξ = (3.69 ± 0.07) × 10 3 nm, the size of the nucleus. It has the specific scaling property of the logarithmic fractal γ (r/a) = γ (r) + ln(a), i.e., the scaling down by a gives an additive constant to the correlation function, which distinguishes it from the mass fractal, which is characterized by multiplicative constant.

Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment

“…However, it needs to be noted that the fractal globule is a metastable state, unlike the equilibrium globule, and that its lifetime depends on topological constraints, which, in real cells, can be affected by enzymes and DNA-binding proteins. Fractal globules have been observed experimentally in Hi-C experiments (Lieberman-Aiden et al, 2009;Rao et al, 2014;Ghosh and Jost, 2018) and Small Angle Neutron Scattering (SANS) experiments (Ilatovskiy et al, 2012;Iashina et al, 2017). The relationship between the physical environment of a fractal chromatin fiber and transcription has been studied in several works, such as Almassalha et al (2017), in which the analytical correspondence between changes in the fractal dimension of the chromatin fiber and increment of chromatin accessibility and compaction heterogeneity was studied.…”

“…Experimental validation has been attempted also for some among the most exotic theoretical models proposed for chromatin, namely those hypothesizing fractal globules. Fractal globules have been observed experimentally in Hi-C experiments (Lieberman-Aiden et al, 2009) and Small-Angle Neutron Scattering (SANS) experiments (Ilatovskiy et al, 2012;Iashina et al, 2017). The important question tackled by works on this topic is the way in which fractal states with stable longlived properties are formed.…”

“…Two more tails extend from the C-terminals of H2A histones, amounting to a total of ten unstructured dynamic domains (McGinty and Tan, 2014). Nucleosomes are connected to each other by varying lengths of linker DNA strands, but it has been calculated that the spooling of DNA around nucleosomes alone makes DNA shorter by seven times (Iashina et al, 2017). Chromatin is a molecule that demands multiscale analysis since changes as small as the absence of one DNA bp in nucleosomal or linker DNA can cause non-local changes in the topology of the fiber.…”

Anisotropic fractal magnetic domain pattern in bulk Mn$_{1.4}$PtSn

“…I(q) obeys a power-function trend I ∝ q −D with two different exponents below and above the crossover momentum q 0 = 0.013 Å−1 , where the slope changes. The fitting yields D = 2.65 for momenta below q 0 down to the lowest accessible momentum of ∼0.002 Å−1 , which is a signature of the scattering from fractal objects [44][45][46][47] . This implies a complex intertwined arrangement of the domain walls of the rectangular domain pattern.…”

Electrostatics and Solvation: Essential Determinants of Chromatin Compaction

“…Experimental validation has been attempted also for some among the most exotic theoretical models proposed for chromatin, namely those hypothesising fractal globules. Fractal globules have been observed experimentally in Hi-C experiments (56) and Small-Angle Neutron Scattering (SANS) experiments (57,58). SANS has been considered a good technique for experiments looking for fractal structures in the nucleus because of its extended spatial range, from approximately 15 nm to 10 µm (59).…”