Nucleosome Assembly on Telomeric Sequences

Abstract

The organization of telomeric chromatin differs from that of bulk chromatin in some peculiar features, such as the unusually short nucleosomal spacing found in vertebrates. Telomeric DNAs are straight, since they consist mostly of 6-8-bp repeated sequences, therefore out of phase with the B DNA period. This feature should be of relevance in nucleosome formation, suggesting the usefulness of studying simple model systems of nucleosome assembly. We reconstituted nucleosomes in vitro, by using purified histone octamers and/or by octamer transfer from chicken erythrocyte nucleosomes, onto telomeric sequences from human, Arabidopsis thaliana, and Saccharomyces cerevisiae. All of these telomeres contain GGG and GGT triplets but are characterized by different repeat lengths (6, 7, and 8 bp). The free energies involved in the association process are the highest among the biological sequences so far assayed, suggesting a main role of DNA flexibility in the assembly of telomeric chromatin. Digestion studies with DNase I, hydroxyl radicals, exonuclease III, and lambda exonuclease indicate that telomeric nucleosomes are characterized by multiple translational positioning without rotational phasing, whereas the telomeric DNA folding around the histone octamer shows the canonical periodicity of about 10.2 bp. The experimental results and a theoretical simulation of DNase I digestion indicate a multiple nucleosome positioning with the periodicity of telomeric DNA. This suggests a main role of local chemical recognition between telomeric sequences and the histone octamer in nucleosome assembly.

Nucleosome organization and chromatin dynamics in telomeres

“…Nucleosome assembly on the telomeric sequences from various organisms has been extensively analyzed, by competitive reconstitution assays in vitro (4,(9)(10)(11). These studies revealed that all telomeric sequences tested show comparative positive free energies in nucleosome formation, relative to average nucleosomal DNA.…”

Predicting nucleosome positioning in genomes: Physical and bioinformatic approaches

“…Differential free energy data were collected by different authors for synthetic and natural DNA tracts with different length and intrinsic curvatures [32][33][34][35][36][37][38][40][41][42][43][44][45][46][47][48][49] as well as sequences with virtually highest affinity as obtained by SELEX procedures [39]. Despite the DNA tracts investigated are characterized by a variety of sequences, lengths and curvatures, the free energy range is limited to a few kilocalories per nucleosome.…”

“…Despite the DNA tracts investigated are characterized by a variety of sequences, lengths and curvatures, the free energy range is limited to a few kilocalories per nucleosome. It is interesting to note that the free energies involved in nucleosome formation on the telomeres are the highest among the synthetic and biological sequences investigated so far [38,40,41,[45][46][47].…”

“…Furthermore, free energy data of competitive nucleosome reconstitution experiments obtained with a large pool of different DNA tracts strongly suggested a significant relation with the DNA intrinsic curvature [32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49].…”

Tiptoeing to chromosome tips: facts, promises and perils of today's human telomere biology

“…Most of the double-stranded telomeric DNA is packed with histone octamers in nucleosomes (Tommerup et al 1994), whereas a nonnucleosomal structure termed the telosome (Wright et al 1992) may be present only at telomere ends (Lingner & Cech 1998). Studies of telomeric chromatin have shown its speci c features: on the one hand a lack of nucleosome positioning, and on the other hand a speci c and very short nucleosome spacing as revealed by micrococcal nuclease digestion (Fajkus et al 1995;Makarov et al 1993;Rossetti et al 1998). On the basis of these properties and on accumulated experimental data, we proposed a model for a columnar packing of nucleosomes in telomeric chromatin in which the DNA is continuously wound in a parallel manner around the stacked histone cores (Fajkus & Trifonov 2001).…”