1
|
Chiariello AM, Bianco S, Esposito A, Fiorillo L, Conte M, Irani E, Musella F, Abraham A, Prisco A, Nicodemi M. Physical mechanisms of chromatin spatial organization. FEBS J 2021; 289:1180-1190. [DOI: 10.1111/febs.15762] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/22/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Andrea M. Chiariello
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant’Angelo Naples Italy
| | - Simona Bianco
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant’Angelo Naples Italy
| | - Andrea Esposito
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant’Angelo Naples Italy
| | - Luca Fiorillo
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant’Angelo Naples Italy
| | - Mattia Conte
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant’Angelo Naples Italy
| | - Ehsan Irani
- Berlin Institute for Medical Systems BiologyMax‐Delbrück Centre (MDC) for Molecular Medicine Berlin Germany
| | - Francesco Musella
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant’Angelo Naples Italy
| | - Alex Abraham
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant’Angelo Naples Italy
| | | | - Mario Nicodemi
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant’Angelo Naples Italy
- Berlin Institute for Medical Systems BiologyMax‐Delbrück Centre (MDC) for Molecular Medicine Berlin Germany
- Berlin Institute of Health (BIH)MDC‐Berlin Germany
| |
Collapse
|
2
|
Chromatin as an active polymeric material. Emerg Top Life Sci 2020; 4:111-118. [PMID: 32830859 DOI: 10.1042/etls20200010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023]
Abstract
The patterns of the large-scale spatial organization of chromatin in interphase human somatic cells are not random. Such patterns include the radial separation of euchromatin and heterochromatin, the territorial organization of individual chromosomes, the non-random locations of chromosome territories and the differential positioning of the two X chromosomes in female cells. These features of large-scale nuclear architecture follow naturally from the hypothesis that ATP-consuming non-equilibrium processes associated with highly transcribed regions of chromosomes are a source of 'active' forces. These forces are in excess of those that arise from Brownian motion. Simulations of model chromosomes that incorporate such activity recapitulate these features. In addition, they reproduce many other aspects of the spatial organization of chromatin at large scales that are known from experiments. Our results, reviewed here, suggest that the distribution of transcriptional activity across chromosomes underlies many aspects of large-scale nuclear architecture that were hitherto believed to be unrelated.
Collapse
|
3
|
Agrawal A, Ganai N, Sengupta S, Menon GI. Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus. Biophys J 2019; 118:2229-2244. [PMID: 31818465 DOI: 10.1016/j.bpj.2019.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 10/25/2022] Open
Abstract
Model approaches to nuclear architecture have traditionally ignored the biophysical consequences of ATP-fueled active processes acting on chromatin. However, transcription-coupled activity is a source of stochastic forces that are substantially larger than the Brownian forces present at physiological temperatures. Here, we describe an approach to large-scale nuclear architecture in metazoans that incorporates cell-type-specific active processes. The model predicts the statistics of positional distributions, shapes, and overlaps of each chromosome. Simulations of the model reproduce common organizing principles underlying large-scale nuclear architecture across human cell nuclei in interphase. These include the differential positioning of euchromatin and heterochromatin, the territorial organization of chromosomes (including both gene-density-based and size-based chromosome radial positioning schemes), the nonrandom locations of chromosome territories, and the shape statistics of individual chromosomes. We propose that the biophysical consequences of the distribution of transcriptional activity across chromosomes should be central to any chromosome positioning code.
Collapse
Affiliation(s)
- Ankit Agrawal
- Computational Biology Group, The Institute of Mathematical Sciences, Taramani, Chennai, India; Homi Bhabha National Institute, Mumbai, India
| | - Nirmalendu Ganai
- Department of Physics, Nabadwip Vidyasagar College, Nabadwip, Nadia, India
| | - Surajit Sengupta
- TIFR Centre for Interdisciplinary Sciences, Serilingampally Mandal, Ranga Reddy District, Hyderabad, India
| | - Gautam I Menon
- Computational Biology Group, The Institute of Mathematical Sciences, Taramani, Chennai, India; Homi Bhabha National Institute, Mumbai, India; Department of Physics, Ashoka University, Rajiv Gandhi Education City, National Capital Region P.O.Rai, Sonepat, India.
| |
Collapse
|
4
|
Bohn M, Diesinger P, Kaufmann R, Weiland Y, Müller P, Gunkel M, von Ketteler A, Lemmer P, Hausmann M, Heermann DW, Cremer C. Localization microscopy reveals expression-dependent parameters of chromatin nanostructure. Biophys J 2010; 99:1358-67. [PMID: 20816047 DOI: 10.1016/j.bpj.2010.05.043] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 03/29/2010] [Accepted: 05/04/2010] [Indexed: 12/12/2022] Open
Abstract
A combined approach of 2D high-resolution localization light microscopy and statistical methods is presented to infer structural features and density fluctuations at the nuclear nanoscale. Hallmarks of nuclear nanostructure are found on the scale below 100 nm for both human fibroblast and HeLa cells. Mechanical measures were extracted as a quantitative tool from the histone density fluctuations inside the cell to obtain structural fluctuations on the scale of several micrometers. Results show that different mechanisms of expression of the same nuclear protein type lead to significantly different patterns on the nanoscale and to pronounced differences in the detected compressibility of chromatin. The observed fluctuations, including the experimental evidence for dynamic looping, are consistent with a recently proposed chromatin model.
Collapse
Affiliation(s)
- Manfred Bohn
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Baddeley D, Weiland Y, Batram C, Birk U, Cremer C. Model based precision structural measurements on barely resolved objects. J Microsc 2010; 237:70-8. [PMID: 20055920 DOI: 10.1111/j.1365-2818.2009.03304.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A model based method for the accurate quantification of the 3D structure of fluorescently labelled cellular objects similar in size to the optical resolution limit is presented. This method is applied to both simulated confocal images of chromatin structures and to real confocal data obtained on a Fluorescence in situ Hybridization (FISH) labelled gene domain. The model assumes that the object is composed of a small number of discrete points which are convolved with the microscope point spread function to give the image. Fitting this model to image data results in a method to assess object structure which is accurate, shows a low bias, and does not require user intervention or the potentially subjective setting of a threshold.
Collapse
Affiliation(s)
- D Baddeley
- Kirchhoff Institut für Physik, Universität Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany.
| | | | | | | | | |
Collapse
|
6
|
Abstract
Chromosomes are not distributed randomly in nuclei. Appropriate positioning can activate (or repress) genes by bringing them closer to active (or inactive) compartments like euchromatin (or heterochromatin), and this is usually assumed to be driven by specific local forces (e.g., involving H bonds between nucleosomes or between nucleosomes and the lamina). Using Monte Carlo simulations, we demonstrate that nonspecific (entropic) forces acting alone are sufficient to position and shape self-avoiding polymers within a confining sphere in the ways seen in nuclei. We suggest that they can drive long flexible polymers (representing gene-rich chromosomes) to the interior, compact/thick ones (and heterochromatin) to the periphery, looped (but not linear) ones into appropriately shaped (ellipsoidal) territories, and polymers with large terminal beads (representing centromeric heterochromatin) into peripheral chromocenters. Flexible polymers tend to intermingle less than others, which is in accord with observations that gene-dense (and so flexible) chromosomes make poor translocation partners. Thus, entropic forces probably participate in the self-organization of chromosomes within nuclei.
Collapse
Affiliation(s)
- Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, England, UK.
| | | |
Collapse
|
7
|
Odenheimer J, Heermann DW, Kreth G. Brownian dynamics simulations reveal regulatory properties of higher-order chromatin structures. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:749-56. [DOI: 10.1007/s00249-009-0486-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Revised: 05/06/2009] [Accepted: 05/13/2009] [Indexed: 01/04/2023]
|
8
|
Diesinger PM, Heermann DW. The influence of the cylindrical shape of the nucleosomes and H1 defects on properties of chromatin. Biophys J 2008; 94:4165-72. [PMID: 18234821 PMCID: PMC2480696 DOI: 10.1529/biophysj.107.113902] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 10/22/2007] [Indexed: 11/18/2022] Open
Abstract
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes, and the distance d between the in and outgoing DNA strands orthogonal to the axis of the corresponding nucleosome cylinder. Factoring these chromatin features in, one gets essential changes in the chromatin phase diagram: Not only the shape of the excluded-volume borderline changes but also the orthogonal distance d has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus, we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded-volume, borderline, or missing H1 histones can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values.
Collapse
Affiliation(s)
- Philipp M Diesinger
- Department of Physics, Institut für Theoretische Physik, and Interdisziplinäres Zentrum für Wissenschaftliches Rechnen, Heidelberg University, Heidelberg, Germany
| | | |
Collapse
|
9
|
|
10
|
Rauch J, Knoch TA, Solovei I, Teller K, Stein S, Buiting K, Horsthemke B, Langowski J, Cremer T, Hausmann M, Cremer C. Light optical precision measurements of the active and inactive Prader-Willi syndrome imprinted regions in human cell nuclei. Differentiation 2007; 76:66-82. [PMID: 18039333 DOI: 10.1111/j.1432-0436.2007.00237.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Despite the major advancements during the last decade with respect to both knowledge of higher order chromatin organization in the cell nucleus and the elucidation of epigenetic mechanisms of gene control, the true three-dimensional (3D) chromatin structure of endogenous active and inactive gene loci is not known. The present study was initiated as an attempt to close this gap. As a model case, we compared the chromatin architecture between the genetically active and inactive domains of the imprinted Prader-Willi syndrome (PWS) locus in human fibroblast and lymphoblastoid cell nuclei by 3D fluorescence in situ hybridization and quantitative confocal laser scanning microscopy. The volumes and 3D compactions of identified maternal and paternal PWS domains were determined in stacks of light optical serial sections using a novel threshold-independent approach. Our failure to detect volume and compaction differences indicates that possible differences are below the limits of light optical resolution. To overcome this limitation, spectral precision distance microscopy, a method of localization microscopy at the nanometer scale, was used to measure 3D distances between differentially labeled probes located both within the PWS region and in its neighborhood. This approach allows the detection of intranuclear differences between 3D distances down to about 70-90 nm, but again did not reveal clearly detectable differences between active and inactive PWS domains. Despite this failure, a comparison of the experimental 3D distance measurements with computer simulations of chromatin folding strongly supports a non-random higher order chromatin configuration of the PWS locus and argues against 3D configurations based on giant chromatin loops. Our results indicate that the search for differences between endogenous active and inactive PWS domains must be continued at still smaller scales than hitherto possible with conventional light microscopic procedures. The possibilities to achieve this goal are discussed.
Collapse
Affiliation(s)
- Joachim Rauch
- Kirchhoff Institute of Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|