title: Single cell correlation fractal dimension of chromatin: a framework to interpret 3D single molecule super-resolution.
abstract: Chromatin is a major nuclear component, and it is an active matter of debate to understand its different levels of spatial organization, as well as its implication in gene regulation. Measurements of nuclear chromatin compaction were recently used to understand how DNA is folded inside the nucleus and to detect cellular dysfunctions such as cancer. Super-resolution imaging opens new possibilities to measure chromatin organization in situ. Here, we performed a direct measure of chromatin compaction at the single cell level. We used histone H2B, one of the 4 core histone proteins forming the nucleosome, as a chromatin density marker. Using photoactivation localization microscopy (PALM) and adaptive optics, we measured the three-dimensional distribution of H2B with nanometric resolution. We computed the distribution of distances between every two points of the chromatin structure, namely the Ripley K(r) distribution. We found that the K(r) distribution of H2B followed a power law, leading to a precise measurement of the correlation fractal dimension of chromatin of 2.7. Moreover, using photoactivable GFP fused to H2B, we observed dynamic evolution of chromatin sub-regions compaction. As a result, the correlation fractal dimension of chromatin reported here can be interpreted as a dynamically maintained non-equilibrium state.
authors.affiliation: Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France; Paris Descartes University; Paris, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Récamier
authors.affiliation: Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France.
authors.forename: Ignacio
authors.initials: I
authors.lastname: Izeddin
authors.affiliation: Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France; Molecular and Cellular Biology Department; University of California; Berkeley, CA USA.
authors.forename: Lana
authors.initials: L
authors.lastname: Bosanac
authors.affiliation: Laboratoire Physico-Chimie Curie; Institut Curie; CNRS UMR168; Université Pierre et Marie Curie-Paris; Paris, France.
authors.forename: Maxime
authors.initials: M
authors.lastname: Dahan
authors.affiliation: Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Proux
authors.affiliation: Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Darzacq
mesh_terms: D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000648:ultrastructure; D002843:Chromatin / Q000648:ultrastructure*; D042002:Chromatin Assembly and Disassembly / Q000502:physiology*; D004247:DNA / Q000648:ultrastructure; D017709:Fractals; D049452:Green Fluorescent Proteins; D006657:Histones / Q000737:chemistry; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods
chemical_list: D002843:Chromatin; D006657:Histones; D049452:Green Fluorescent Proteins; D004247:DNA
keywords: PALM; adaptive optics; chromatin organization; fractals; super-resolution microscopy