Diffusion-driven looping provides a consistent framework for chromatin organization.

Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection betwee...

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Autores principales:	Manfred Bohn, Dieter W Heermann
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/804639bbe6004c3cbfcbf5da0bb9b955
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spelling	oai:doaj.org-article:804639bbe6004c3cbfcbf5da0bb9b9552021-11-18T06:35:45ZDiffusion-driven looping provides a consistent framework for chromatin organization.1932-620310.1371/journal.pone.0012218https://doaj.org/article/804639bbe6004c3cbfcbf5da0bb9b9552010-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20811620/?tool=EBIhttps://doaj.org/toc/1932-6203Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection between genome folding and function. Chromosomes fold into a confined subspace of the nucleus and form distinct territories. Chromatin looping seems to play a dominant role both in transcriptional regulation as well as in chromatin organization and has been assumed to be mediated by long-range interactions in many polymer models. However, it remains a crucial question which mechanisms are necessary to make two chromatin regions become co-located, i.e. have them in spatial proximity. We demonstrate that the formation of loops can be accomplished solely on the basis of diffusional motion. The probabilistic nature of temporary contacts mimics the effects of proteins, e.g. transcription factors, in the solvent. We establish testable quantitative predictions by deriving scale-independent measures for comparison to experimental data. In this Dynamic Loop (DL) model, the co-localization probability of distant elements is strongly increased compared to linear non-looping chains. The model correctly describes folding into a confined space as well as the experimentally observed cell-to-cell variation. Most importantly, at biological densities, model chromosomes occupy distinct territories showing less inter-chromosomal contacts than linear chains. Thus, dynamic diffusion-based looping, i.e. gene co-localization, provides a consistent framework for chromatin organization in eukaryotic interphase nuclei.Manfred BohnDieter W HeermannPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 8, p e12218 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Manfred Bohn Dieter W Heermann Diffusion-driven looping provides a consistent framework for chromatin organization.
description	Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection between genome folding and function. Chromosomes fold into a confined subspace of the nucleus and form distinct territories. Chromatin looping seems to play a dominant role both in transcriptional regulation as well as in chromatin organization and has been assumed to be mediated by long-range interactions in many polymer models. However, it remains a crucial question which mechanisms are necessary to make two chromatin regions become co-located, i.e. have them in spatial proximity. We demonstrate that the formation of loops can be accomplished solely on the basis of diffusional motion. The probabilistic nature of temporary contacts mimics the effects of proteins, e.g. transcription factors, in the solvent. We establish testable quantitative predictions by deriving scale-independent measures for comparison to experimental data. In this Dynamic Loop (DL) model, the co-localization probability of distant elements is strongly increased compared to linear non-looping chains. The model correctly describes folding into a confined space as well as the experimentally observed cell-to-cell variation. Most importantly, at biological densities, model chromosomes occupy distinct territories showing less inter-chromosomal contacts than linear chains. Thus, dynamic diffusion-based looping, i.e. gene co-localization, provides a consistent framework for chromatin organization in eukaryotic interphase nuclei.
format	article
author	Manfred Bohn Dieter W Heermann
author_facet	Manfred Bohn Dieter W Heermann
author_sort	Manfred Bohn
title	Diffusion-driven looping provides a consistent framework for chromatin organization.
title_short	Diffusion-driven looping provides a consistent framework for chromatin organization.
title_full	Diffusion-driven looping provides a consistent framework for chromatin organization.
title_fullStr	Diffusion-driven looping provides a consistent framework for chromatin organization.
title_full_unstemmed	Diffusion-driven looping provides a consistent framework for chromatin organization.
title_sort	diffusion-driven looping provides a consistent framework for chromatin organization.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/804639bbe6004c3cbfcbf5da0bb9b955
work_keys_str_mv	AT manfredbohn diffusiondrivenloopingprovidesaconsistentframeworkforchromatinorganization AT dieterwheermann diffusiondrivenloopingprovidesaconsistentframeworkforchromatinorganization
_version_	1718424424873459712

Diffusion-driven looping provides a consistent framework for chromatin organization.

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