Telomeric nucleosomes: forgotten players at chromosome ends.

Telomeres are the special nucleoprotein structures that protect chromosome ends from both recombination and degradation. In most organisms, telomeric DNA consists of short sequences repeated in tandem ending in single-stranded G-rich overhangs. In higher eukaryotes, about 80% of telomeric DNA is organized in tightly packed nucleosomes separated by 10-20 bp of linker DNA. Several specific proteins contribute to telomeric structure. At the moment, a satisfactory description of telomere organization is still lacking. Whereas the role played by telomeric proteins in telomere function and regulation has been widely investigated, little is known about the contribution of nucleosomes to the protection of chromosome ends. In this review we present an overview on the chromatin organization in lower and higher eukaryotes, and discuss the recent results on the peculiar features of telomeric nucleosomes and on the epigenetic status of mammalian telomeres.

Specific interactions of the telomeric protein Rap1p with nucleosomal binding sites.

The telomeres of Saccharomyces cerevisiae are structurally and functionally well characterized. Their telomeric DNA is packaged by the protein Rap1p (repressor activator protein 1). Rap1p is a multifunctional, sequence-specific, DNA-binding protein which, besides participating in the regulation of telomeres structure and length, is also involved in transcriptional regulation of genes essential for cell growth and in silencing. Whereas the long tracts of telomeric DNA repeats of higher eukaryotes are mostly organized in closely spaced canonical nucleosomal arrays, it has been proposed that the 300 base-pairs of S. cerevisiae telomeric DNA are organized in a large non-nucleosomal structure that has been called the telosome. Recently, nucleosomes have been found also in Tetrahymena thermophila telomeres, suggesting that, in general, telomere structural differences between lower and higher eukaryotes could be quantitative, rather than qualitative. Using an in vitro model system, we have addressed the question of whether Rap1p can form a stable ternary complex with nucleosomes containing telomeric binding sites, or competes with nucleosome core formation. The approach we have taken is to place a single Rap1p-binding site at different positions within a nucleosome core and then test the binding of Rap1p and its DNA-binding domain (Rap1p-DBD). We show here that both proteins are able to specifically recognize their nucleosomal binding site, but that binding is dependent on the location of the site within the nucleosome core structure. These results show that a ternary complex between a nucleosome and Rap1p is stable and could be a possible intermediate between telomeric nucleosomes and telosomes in the dynamics of S. cerevisiae telomere organization.

The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs.

Using a competitive reconstitution assay, we measured the free energy spent in nucleosome formation of eight telomeric DNAs, differing in sequence and/or in length. The obtained values are in satisfactorily good agreement with those derived from a theoretical model that allows the calculation of the free energy of nucleosome formation on the basis of sequence-dependent DNA elasticity, using a statistical thermodynamic approach. Both theoretical and experimental evaluations show that telomeres are characterized by the highest free energies of nucleosome formation among all the DNA sequences so far studied. The free energy of nucleosome formation varies according to the different telomeric sequences and the length of the fragments. Theoretical analysis and experimental mapping by lambda exonuclease show that telomeric nucleosomes occupy multiple positions spaced every telomeric repeat. Sequence-dependent DNA elasticity appears as the main determinant of the stability of telomeric nucleosomes and their multiple translational positioning.

Nucleosome assembly on telomeric sequences.

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.

Multiple nucleosome positioning with unique rotational phasing on multimers of the light-responsive elements of pea rbcS-3A and rbcS-3.6 genes: comparison between experimental and theoretical mapping.

Nucleosome positioning along two DNA tracts, corresponding to tetramers of the light-responsive elements of pea rbcS-3A and rbcS-3.6 genes, were studied by experimental (exonuclease III mapping and band shift electrophoresis) as well as theoretical methods. Multiple nucleosome positioning with unique rotational phase was derived from both methods in satisfactorily good agreement, if nucleosome dyad axis positions are considered. Theoretical and experimental distributions of nucleosome frequencies appear different, probably on account of DNA sequence dependent digestion kinetics of exonuclease III.

In vitro low propensity to form nucleosomes of four telomeric sequences.

The structural aspects of nucleosome assembly on telomeres are largely unknown. We analyzed by competitive reconstitution the affinities for the histone octamer of telomeric sequences from four different eukaryotic groups, Arabidopsis thaliana, mammals, Tetrahymena, and Saccharomyces cerevisiae. All telomeres reconstitute in nucleosomes with lower association constants than average nucleosomal DNA. DNase I digestion analysis suggests a multiple translational positioning and the lack of rotational positioning, probably due to telomeric repeats length (in most cases 6-8 bp), out of phase with the DNA helical repeat on the nucleosome (10.2 bp). These results could partly explain the lack of nucleosomes on lower eukaryote telomeres, and suggest a high in vivo mobility of telomeric nucleosomes.

Superstructural features of the upstream regulatory regions of two pea rbcS genes and nucleosomes positioning: theoretical prediction and experimental evaluation.

Nucleosome positioning on two 384 bp DNA fragments, obtained from the upstream regulatory region of two pea rbcS genes, relevant in photoregulated transcription, was predicted using our theoretical method, based on the evaluation of the sequence dependent DNA bending energy. The theoretical prediction was checked by experimental evaluation of nucleosome positions after in vitro reconstitution, by mapping Exonuclease III-resistant borders and by digesting monomeric sequences with various restriction enzymes. Both approaches satisfactorily confirmed the theoretical predictions, showing that the nucleotide sequence intrinsic bendability has a dominant role in nucleosome positioning.

Different flexibility of the upstream regulatory regions of two differently expressed pea rbcS genes studied by theoretical evaluation of DNA distortion energy and cyclization kinetics.

Different superstructural features of the upstream regulatory regions of the two pea genes rbcS-3A and rbcS-E9 have been derived using a theoretical method, developed in our laboratory a few years ago, which evaluates the DNA distortion energy from a matrix of the deviations of the 16 possible dinucleotides from the standard B conformation. The theoretical analysis, which predicts different flexibilities of the regulatory regions of the two genes, is in satisfactorily good agreement with experimental evaluations from gel electrophoretic mobility and cyclization kinetics, suggesting a possible model to explain the largely different transcription efficiencies of the two genes.

Different superstructural features of the complexes between spermine and the light responsive elements of the two pea genes rbcS-3A and rbcS-3.6. Gel electrophoresis and circular dichroism studies.

Two light responsive elements (LREs), DNA sequences, 62 base pairs long, relevant to the light control during transcription of the pea genes rbcS-3A and rbcS-3.6, were synthesized and ligated to obtain multimers with defined superstructural features. Their gel electrophoretic mobilities were studied in the presence of the tetracation, spermine, since it was previously suggested, on the basis of theoretical analysis, that spermine can increase DNA bending and thus could be useful in revealing DNA superstructural features. In fact, the difference between the curvatures of the two LREs, derived from gel electrophoresis retardation ratios, increases in the presence of spermine. Circular dichroism spectra of the complexes between spermine and the two LREs, at different neutralization ratios, show that the polyamine is able to induce the formation of asymmetric arrangements of complexes of molecules. The chirality of these complexes appears dramatically different for the two LREs, suggesting that their different superstructural features give rise to different interactions with the polyamine.

Different interactions of spermine with a "curved" and a "normal" DNA duplex: (CA4T4G)n and (CT4A4G)n. Gel electrophoresis and circular dichroism studies.

Two nucleotide sequences, (CA4T4G)n and (CT4A4G)n, are generally considered as prototypes of a "curved" and a "normal" DNA duplex on the basis of their different behaviour with respect to physico-chemical and/or biochemical properties. We have studied their gel electrophoretic mobilities in the presence of the biologically significant tetracation spermine and have found that spermine causes a decrease of the gel electrophoretic mobility of "curved" DNA, but does not influence that of "normal" DNA. Circular dichroism spectra of the complexes between spermine and the two examined DNAs show dramatically different features. These findings suggest that different DNA superstructures are relevant in interactions not only with proteins, but also with polycations, such as spermine.

Different superstructural features of the light responsive elements of the pea genes rbcS-3A and rbcS-3.6.

Analyses of the DNA sequences, named Light Responsive Elements (LREs), relevant in the photoactivation of the two pea genes rbcS-3A and rbcS-3.6, encoding the same protein but differently expressed, have been carried out, taking advantage of two complementary methods; a theoretical analysis, based on conformational energy calculations, and an experimental evaluation of LREs curvature, derived from gel electrophoretic mobilities of multimers of the LREs and of oligonucleotides corresponding to the three boxes in which they can be dissected. Theoretical and experimental analyses show that the curvature of the rbcS-3A LRE is larger than that of rbcS-3.6 LRE, and seems to be correlated with rbcS-3A higher transcription efficiency.

Synthetic oligonucleotides as models of the superstructural features of the upstream regulative regions of the five pea rbcs genes.

Superstructural features of the upstream regulative regions of the five pea rbcS genes have been studied, using theoretical curvature profiles and electrophoretic properties of synthetic oligonucleotides as models of the DNA curved regions. The curvatures derived from both methods are in good agreement and seem correlated with the different transcription efficiency of the five genes.

Periodical polydeoxynucleotides and DNA curvature.

A theoretical method to predict DNA curvature was developed, and a strikingly good correlation between the experimental retardations and theoretical curvature of all the periodical biosynthetic DNAs so far reported in the literature was found. The analysis has been extended to G- and C-rich synthetic polynucleotides, which show a behavior in agreement with the theoretical prediction. A possible application of the method to biologically significant DNA tracts is shown in the case of the regulative region of one of the genes which code for the small subunit of ribulose-1,5-bisphosphate carboxylase in Pisum sativum. While curvature measurements have not so far been reported for this system, biochemical analysis has indicated short nucleotide sequences (boxes I-III) as recognition sites for regulative proteins. On the basis of the theoretical curvature profile of the region and of the electrophoretic retardation measurements of synthetic polynucleotides, obtained by ligating monomers mimicking the boxes, we suggest that the proteins could use DNA local curvature as structural motif in the recognition process.

Curvature of the light-responsive element of the plant gene rbcS-3A encoding the small subunit of ribulose-1,5-bisphosphate carboxylase.

The possible curvature in the light-responsive element (LRE) of the plant gene which codes for the small subunit of ribulose-1,5-bisphosphate carboxylase has been derived from the nucleotide sequence of the LRE on the basis of a theoretical method previously developed in our research group. The oligonucleotides corresponding to regions of higher curvature in the profile, taking also into account biochemical data, have been synthesized and their electrophoretic mobilities have been measured after ligation. Retardation effects have been found, increasing with length of the multimers, in good agreement with theoretical prediction. These results suggest that the curvature of LRE could be the structural determinant in the control of rbcS-3A gene photoactivation.

Selective binding of actinomycin D induces a reversible conformational transition of nucleosomes.

Equilibrium and hydrodynamic studies on the complex of actinomycin D with H1-H5 depleted, 175 basepair nucleosomes are reported. By spectral titration the intrinsic affinities of actinomycin D for nucleosomes and for DNA are found strictly comparable. Sedimentation analysis shows that actinomycin can apparently unfold the nucleosome, like ethidium bromide and daunomycin, but it does so at a much lower bound drug to DNA molar ratio (about 1 drug molecule to 45 basepairs). Since about four bound actinomycin molecules are able to induce the reversible conformational transition of a nucleosome, it is suggested that the sites of interaction may correspond to the kinked DNA sites evidenced by Klug and collaborators (Richmond, T.J., Finch, J.T., Rushton, B., Rhodes, D. and Klug, A. (1984) Nature 311, 532-537) in the structure of the nucleosome. A relevance of these findings to the interaction of actinomycin with "active chromatin" is also suggested.