Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus.

Abstract

Abstract. We determined the folding of chromosomes in interphase nuclei by measuring the distance between points on the same chromosome. Over 25,000 measurements were made in G0/G1 nuclei between DNA sequences separated by 0.15-190 megabase pairs (Mbp) on three human chromosomes. The DNA sequences were specifically labeled by fluorescence in situ hybridization. The relationship between mean-square interphase distance and genomic separation has two linear phases, with a transition at N2 Mbp. This biphasic relationship indicates the existence of two organizational levels at scales >100 kbp. On one level, chromatin appears to be arranged in large loops several Mbp in size. Within each loop, chromatin is randomly folded. On the second level, specific loop-attachment sites are arranged to form a supple, backbonelike structure, which also shows characteristic random walk behavior. This random walk/giant loop model is the simplest model that fully describes the observed large-scale spatial relationships. Additional evidence for large loops comes from measurements among probes in Xq28, where interphase distance increases and then locally decreases with increasing genomic separation. SIaORXLY after cell division, the mitotic chromosomes decondense and diffuse into the interphase nucleus. While individual chromosomes cannot be discerned, important processes related to chromosome function take place. Regulatory factors interact with chromatin, DNA is made accessible for transcription, RNA is produced and processed, DNA is replicated, and repairs are made of DNA strand breaks. When the chromosomes reappear for the next mitosis, they have been duplicated and prepared for rapid partitioning over the daughter cells. The complexity of these processes raises many questions about the large-scale organization of chromosomes and how this organization relates to cell function (e.g., Blobel, 1985;Manuelidis and Chen, 1990;Cook, 1991;Lawrence and Singer, 1991;De Boni, 1994).Diverse models, ranging from highly random to highly organized, have been proposed for the higher-order organization of interphase chromatin. These models variously involve irregularly folded fibers (DuPraw, 1965), radial loop structures (Manuelidis and Chen, 1990), giant loops (Ostashevsky and Lange, 1994), semirigid orientation ("Rabl" configuration) (Rabl, 1885;Comings, 1968), or random polymers confined by tethering or external forces (Hahnfeldt et al., 1993). Some models assign to chromo-

Complexity of chromatin folding is captured by the strings and binders switch model

“…The experimental observations (9,34,35) Measurements of K from previous models produce a constant value of K. The randomly folded polymer (SAW) model produces K ¼ 1.5 (22). Previous polymer models that consider the effects of both specified chromatin loops at fixed lengths of 120 kb and 3 Mb (12,36), and the possibility of chromatin loops of all sizes (37), also produce constant K values.…”

“…In principle, K carries information about genomic locus-to-locus and cell-to-cell variations. Interestingly, K has been measured experimentally by FISH (9,34,35) and found to vary between 1.5 and 4.4, depending on the locus and cell type studied (Fig. 4A).…”

Spatial Organization of Chromatin Domains and Compartments in Single Chromosomes

“…19,20,[22][23][24]. In one effort, a three-color barcoding approach has been used to simultaneously label multiple chromatin loci to trace the conformation of a chromosome arm in Drosophila blastoderm embryos (24).…”

Dynamic Simulation of Active/Inactive Chromatin Domains

“…Therefore, the number of attractive sites suggested by the evaluation of the diameter, namely about 11 per 1 Mbp domain, is consistent with the number proposed by the exponent. The exponent of 0.32±0.02 was obtained by Münkel [15] based on the experiments by Yokota et al [38] for genomic distances of several Mbps. The parameter range yielded by our simulation results is therefore in good agreement with experiment.…”