Chromatin Folding in Relation to Human Genome Function

Mateos‐Langerak, Julio; Giromus, Osdilly; Leeuw, Wim de; Bohn, Manfred A.; Verschure, Pernette J.; Kreth, Gregor; Heermann, Dieter W.; Driel, Roel van; Goetze, Sandra

doi:10.48550/arxiv.0705.1656

Cited by 2 publications

(14 citation statements)

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“…The model can quite well explain the levelling-off at genomic distances above a few mega-base pairs as well as the rise at small genomic distances. As we have shown that on small genomic distances we have a globular-state-like behaviour [6], this random-walk-based model does not yield perfect results here.…”

Section: A Comparison To Experimental Datamentioning

confidence: 70%

“…In this paper we present a polymer model for the folding of the chromatin fibre in the interphase nucleus, based on recent experimental results [6]. These show that the chromatin fibre inside the human cell nucleus is ruled by two different folding regimes: At small genomic distances, i.e.…”

Section: Discussionmentioning

confidence: 95%

“…Assuming that eq. ( 2) also holds for intra-chain distances in the limit of large N , one can compare the experimental data to these models [6]. Relation ( 2) is no longer valid as soon as we introduce longrange interactions along the chain, such as chromatin looping.…”

Section: Theory a Polymer Modelsmentioning

confidence: 99%

“…In a recent publication [6] we already mentioned that plotting R 2 n versus n is not a very sensitive method to check for the correctness of a model. Looking at the n ¸∼ n with a changed effective contour length compared to the free random walk.…”

Section: A Comparison To Experimental Datamentioning

confidence: 99%

“…One method that has been applied by several groups is fluorescence in situ hybridization (FISH ). By labelling chromatin in the intact cell with pairs of * Electronic address: bohn@tphys.uni-heidelberg.de FISH -markers one can measure the mean squared physical distance R 2 between these markers as a function of the genomic distance d. A recent study has shed light on the folding at larger length scales [6]. It was shown that there is a levelling-off in the physical vs. genomic distance plot at genomic distances longer than a few mega base pairs (Mb), so that approximately R 2 ∼ O(1) for large d. At shorter length scales, i.e.…”

Section: Introductionmentioning

confidence: 99%

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Random loop model for long polymers

2007

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Remarkably little is known about the higher-order folding motifs of the chromatin fibre inside the cell nucleus. Folding depends among others on local gene density and transcriptional activity and plays an important role in gene regulation. Strikingly, at fibre lengths above 5 to 10 Mb the measured mean square distance˙R 2¸b etween any two points on the chromatin fibre is independent of polymer length. We propose a polymer model that can explain this levelling-off by means of random looping. We derive an analytical expression for the mean square displacement between two arbitrary beads. Here the average is taken over the thermal ensemble with a fixed but random loop configuration, while quenched averaging over the ensemble of different loop configurationswhich turns out to be equivalent to averaging over an ensemble of random matrices -is performed numerically. A detailed investigation of this model shows that loops on all scales are necessary to fit experimental data.

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Section: A Comparison To Experimental Datamentioning

confidence: 70%

Section: Discussionmentioning

confidence: 95%

Section: Theory a Polymer Modelsmentioning

confidence: 99%

Section: A Comparison To Experimental Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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