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At least 19 recordsLinked to original sources
PubMed1990

Affinity chromatography of mammalian and yeast nucleosomes. Two modes of binding of transcriptionally active mammalian nucleosomes to organomercurial-agarose columns, and contrasting behavior of the active nucleosomes of yeast.

The reasons for the selective binding of nucleosomes from transcriptionally active genes to the organomercurial-agarose columns have been investigated. At least two modes of binding are identified by a new two-stage elution procedure that discriminates between nucleosomes which are retained by the Hg-column because of their salt-labile associations with SH-reactive non-histone proteins, and nucleosomes in which a conformational change has made the thiol groups of histone H3 accessible to SH-reagents. The first class is released from the column in 0.5 M NaCl; the second class is eluted in 10 mM dithiothreitol which displaces the bound H3-thiols. In mammalian cells, both classes of Hg-bound nucleosomes are enriched in the DNA sequences being transcribed at the time, and their histones H3 and H4 are hyperacetylated. In yeast cells, in which histone H3 lacks cysteinyl residues, only a small fraction of nucleosomes binds to the mercury column, and it has no enrichment of DNA sequences derived from the actively transcribed GAL, HIS4, and ACT1 genes. Since few nucleosomes remain on the column after elution in 0.5 M NaCl, the bound nucleosomes of yeast are retained primarily because of salt-labile associations with thiol-reactive nonhistone proteins. Thus, the presence of histone H3-thiol groups appears to be essential for the mercury binding of the second class of nucleosomes which, in mammalian cells, is derived from the transcriptionally active genes. The results support models of reversible nucleosome unfolding during transcription in mammalian cells to reveal previously inaccessible H3-SH groups, and they also indicate that other thiol-containing proteins, including high mobility group 1 and 2, become closely but transiently associated with the chromatin subunits during their transcription.

Acetylation↗
PubMed2001

Plasma levels of nucleosomes and nucleosome-autoantibody complexes in murine lupus: effects of disease progression and lipopolyssacharide administration.

OBJECTIVE: To evaluate the effect of disease progression and lipopolysaccharide (LPS) administration on the presence of nucleosomes, antinucleosome reactivity, and nucleosome-Ig complexes in the circulation of MRL and control mice. METHODS: Plasma samples from lupus-prone (MRL/lpr and MRL/+) and control (CBA, Swiss, and BALB/c) mice were tested in enzyme-linked immunosorbent assays for the presence of nucleosomes, antinucleosome antibodies, and nucleosome-Ig complexes. Nucleosome kinetics, apoptosis induction, and phagocytosis of apoptotic cells were also analyzed in MRL/lpr, MRL/+, and CBA control mice after a single injection of LPS or phosphate buffered saline. RESULTS: Nucleosomes were found in the circulation of MRL/lpr and MRL/+ mice from week 4 onward. Nucleosomes were also detected in young control mice, but with increasing age, the nucleosomes disappeared. Antinucleosome antibodies, nucleosome-Ig complexes, and albuminuria were found only in the MRL/lpr mice. LPS administration led to a significant increase in circulating nucleosomes (3-8-fold) in all strains tested. In only the MRL/lpr mice was this increase followed by a significant decrease in antinucleosome titers and an increase in nucleosome-Ig complexes. The number of apoptotic cells in the thymus after LPS was significantly higher in the MRL/lpr mice than in the MRL/+ and CBA control mice. LPS caused a profound reduction (50-70%) of the phagocytosis of apoptotic cells by peritoneal macrophages, which was comparable for all strains. CONCLUSION: In MRL lupus-prone mice, nucleosomes are persistently present in the circulation, whereas in control mice, nucleosomes are present only at a young age. The formation of antinucleosome antibodies and nucleosome-Ig complexes is a characteristic feature of MRL/lpr mice. LPS administration increases systemic nucleosome release due to an enhancement of apoptosis and a decrease in the clearance of apoptotic cells.

Age Factors↗
PubMed2002

Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation.

Intrinsic nucleosome dynamics termed "site exposure" provides spontaneous and cooperative access to buried regions of nucleosomal DNA in vitro. Two different mechanisms for site exposure have been proposed, one based on nucleosome translocation, the other on dynamic nucleosome conformational changes in which a stretch of the nucleosomal DNA is transiently released off the histone surface. Here we report on three experiments that distinguish between these mechanisms. One experiment investigates the effects on the accessibilities of restriction enzyme target sites inside nucleosomes when extra DNA (onto which the nucleosome may move at low energetic cost) is appended onto one end. The other two experiments test directly for nucleosome mobility under the conditions used to probe accessibility to restriction enzymes: one on a selected nonnatural nucleosome positioning sequence, the other on the well-studied 5S rRNA gene nucleosome positioning sequence. We find from all three assays that restriction enzymes gain access to sites throughout the entire length of the nucleosomal DNA without contribution from nucleosome translocation. We conclude that site exposure in nucleosomes in vitro occurs via a nucleosome conformational change that leads to transient release of a stretch of DNA from the histone surface, most likely involving progressive uncoiling from an end. Recapture at a distal site along DNA that has partially uncoiled would result in looped structures which are believed to contribute to RNA polymerase elongation and may contribute to spontaneous or ATP-driven nucleosome mobility. Transient open states may facilitate the initial entry of transcription factors and enzymes in vivo.

Animals↗
PubMed1996

The effect of nucleosome phasing sequences and DNA topology on nucleosome spacing.

The distances between the nucleosomes in eukaryotic chromatin that define the nucleosome repeat length are not universally constant, but vary between different cell types and activity states. We have previously established in a cell-free system that nucleosome spacing is essentially governed by electrostatic principles, most likely through charge neutralisation of linker DNA by cations either free in solution or on flexible histone domains. On the basis of the tight correlation between the parameters that affect nucleosome spacing and those that influence the folding of the nucleosomal fiber into higher order structures, we suggested that there is an intimate relationship between nucleosome spacing and chromatin folding. Here we describe DNA topology as a new parameter that influences nucleosome spacing in a predictable way. The effects of topology and cation concentrations integrate to define the final repeat length. The phenomenon of "nucleosome phasing" describes nucleosomal arrays that are generated through positioning of nucleosomes by the underlying DNA sequence. To determine the relative contribution of DNA sequence and the parameters intrinsic to physiological chromatin for nucleosomal positions, we created situations where these two principles were in conflict. We found that nucleosome repeats directed by a strong positioning sequence are dominated by the cation-induced spacing as well as by the effects of topology. We conclude that the DNA sequence effects nucleosome spacing only by "fine tuning" of nucleosome positions within the framework of a repeat pattern that is established by other principles.

Animals↗
PubMed1991

Nucleosome fractionation by mercury affinity chromatography. Contrasting distribution of transcriptionally active DNA sequences and acetylated histones in nucleosome fractions of wild-type yeast cells and cells expressing a histone H3 gene altered to encode a cysteine 110 residue.

A technique for the separation of transcriptionally active and inactive nucleosomes by mercury affinity chromatography has been applied to study the nucleosomal distribution of DNA sequences from the GAL1, ACT1, HIS4, MAT alpha, and HMRa genes of yeast. In mammalian cells, the method has been shown to separate active from inactive nucleosomes and to fractionate the active nucleosomes into two classes, one retained on the mercury column because of salt-labile associations with certain thiol-reactive non-histone proteins, and the other bound by covalent linkage of the cysteine 110 thiol groups of histone H3 molecules to the mercurated support. The first class of nucleosomes is elutable in 0.5 M NaCl; the second is displaced by 10 mM dithiothreitol (DTT) (Walker, J., Chen, T. A., Sterner, R., Berger, M., Winston, F., and Allfrey, V.G. (1990) J. Biol. Chem. 265, 5736-5746). We show that, in wild-type yeast cells, in which histone H3 lacks cysteinyl residues, very little DNA and a negligible complement of nucleosomes appear in the DTT-eluate, confirming the requirement for the H3-thiols in the mercury-binding reaction. Moreover, the DTT-eluted fraction is seriously deficient in the actively transcribed GAL1, ACT1, HIS4, and MAT alpha DNA sequences. Site-directed mutagenesis was employed to create an H3 gene containing a cysteine codon in place of the alanine codon at position 110 of the yeast H3 amino acid sequence. A strain was constructed containing the mutant histone H3 gene instead of the normal H3 gene. Subsequent fractionations of the mutant nucleosomes by mercury-affinity chromatography revealed a characteristic nucleosome peak in the DTT-eluted fraction. Its content of transcribed GAL1, ACT1, and HIS4 DNA sequences was 20- to 500-fold higher than that of the corresponding DTT-eluted fraction of wild-type yeast. Although this result is in accord with the finding that, in mammalian cells, the thiol groups of histone H3 become accessible when nucleosomes "unfold" during transcription, we find that nucleosomes containing the GAL1 DNA sequences of the yeast H3-mutant also bind to the mercury column when that gene is not being expressed. We conclude that many yeast nucleosomes are maintained in a "primed," potentially active state, possibly due to the very high constitutive levels of acetylation of the core histones. However, the nucleosomes of the HMRa gene, which is not expressed in a MAT alpha yeast strain, are virtually absent from the DTT-eluted nucleosome fractions of the H3-mutant cells, indicating that prolonged silencing of the gene is accompanied by compaction and loss of H3-thiol reactivity of its nucleosomes.

Acetylation↗
PubMed2004

Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning.

DNA sequence is an important determinant of the positioning, stability, and activity of nucleosomes, yet the molecular basis of these effects remains elusive. A "consensus DNA sequence" for nucleosome positioning has not been reported and, while certain DNA sequence preferences or motifs for nucleosome positioning have been discovered, how they function is not known. Here, we report that an unexpected observation concerning the reassembly of nucleosomes during salt gradient dialysis has allowed a breakthrough in our efforts to identify the nucleosomal locations of the DNA sequence motifs that dominate histone-DNA interactions and nucleosome positioning. We conclude that a previous selection experiment for high-affinity, nucleosome-forming DNA sequences exerted selective pressure chiefly on the central stretch of the nucleosomal DNA. This observation implies that algorithms for aligning the selected DNA sequences should seek to optimize the alignment over much less than the full 147 bp of nucleosomal DNA. A new alignment calculation implemented these ideas and successfully aligned 19 of the 41 sequences in a non-redundant database of selected high-affinity, nucleosome-positioning sequences. The resulting alignment reveals strong conservation of several stretches within a central 71 bp of the nucleosomal DNA. The alignment further reveals an inherent palindromic symmetry in the selected DNAs; it makes testable predictions of nucleosome positioning on the aligned sequences and for the creation of new positioning sequences, both of which are upheld experimentally; and it suggests new signals that may be important in translational nucleosome positioning.

Algorithms↗
PubMed2001

Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF.

Nucleosome Remodeling Factor (NURF) is an ATP-dependent nucleosome remodeling complex that alters chromatin structure by catalyzing nucleosome sliding, thereby exposing DNA sequences previously associated with nucleosomes. We systematically studied how the unstructured N-terminal residues of core histones (the N-terminal histone tails) influence nucleosome sliding. We used bacterially expressed Drosophila histones to reconstitute hybrid nucleosomes lacking one or more histone N-terminal tails. Unexpectedly, we found that removal of the N-terminal tail of histone H2B promoted uncatalyzed nucleosome sliding during native gel electrophoresis. Uncatalyzed nucleosome mobility was enhanced by additional removal of other histone tails but was not affected by hyperacetylation of core histones by p300. In addition, we found that the N-terminal tail of the histone H4 is specifically required for ATP-dependent catalysis of nucleosome sliding by NURF. Alanine scanning mutagenesis demonstrated that H4 residues 16-KRHR-19 are critical for the induction of nucleosome mobility, revealing a histone tail motif that regulates NURF activity. An exchange of histone tails between H4 and H3 impaired NURF-induced sliding of the mutant nucleosome, indicating that the location of the KRHR motif in relation to global nucleosome structure is functionally important. Our results provide functions for the N-terminal histone tails in regulating the mobility of nucleosomes.

Adenosine Triphosphate↗
PubMed2005

Structural dynamics of nucleosome core particle: comparison with nucleosomes containing histone variants.

The present study provides insights on the dominant mechanisms of motions of the nucleosome core particle and the changes in its functional dynamics in response to histone variants. Comparative analysis of the global dynamics of nucleosomes with native and variant H2A histones, using normal mode analysis revealed that the dynamics of the nucleosome is highly symmetric, and its interaction with the nucleosomal DNA plays a vital role in its regulation. The collective dynamics of nucleosomes are predicted to be dominated by two types of large-scale motions: (1) a global stretching-compression of nucleosome along the dyad axis by which the nucleosome undergoes a breathing motion with a massive distortion of nucleosomal DNA, modulated by histone-DNA interactions; and (2) the flipping (or bending) of both the sides of the nucleosome in an out-of-plane fashion with respect to the dyad axis, originated by the highly dynamic N-termini of H3 and (H2A.Z-H2B) dimer in agreement with the experimentally observed perturbed dynamics of the particular N-terminus under physiological conditions. In general, the nucleosomes with variant histones exhibit higher mobilities and weaker correlations between internal motions compared to the nucleosome containing ordinary histones. The differences are more pronounced at the L1 and L2 loops of the respective monomers H2B and H2A, and at the N-termini of the monomers H3 and H4, all of which closely interact with the wrapping DNA.

Amino Acid Motifs↗
PubMed1998

Gcn5p, a transcription-related histone acetyltransferase, acetylates nucleosomes and folded nucleosomal arrays in the absence of other protein subunits.

Gcn5p is the catalytic subunit of several type A histone acetyltransferases (HATs). Previous studies performed under a limited range of solution conditions have found that nucleosome core particles and nucleosomal arrays can be acetylated by Gcn5p only when it is complexed with other proteins, e.g. Gcn5-Ada, HAT-A2, and SAGA. Here we demonstrate that when assayed in buffer containing optimum concentrations of either NaCl or MgCl2, purified yeast recombinant Gcn5p (rGcn5p) efficiently acetylates both nucleosome core particles and nucleosomal arrays. Furthermore, under conditions where nucleosomal arrays are extensively folded, rGcn5p acetylates folded arrays approximately 40% faster than nucleosome core particles. Finally, rGcn5p polyacetylates the N termini of free histone H3 but only monoacetylates H3 in nucleosomes and nucleosomal arrays. These results demonstrate both that rGcn5p in and of itself is catalytically active when assayed under optimal solution conditions and that this enzyme prefers folded nucleosomal arrays as a substrate. They further suggest that the structure of the histone H3 N terminus, and concomitantly the accessibility of the H3 acetylation sites, changes upon assembly into nucleosomes and nucleosomal arrays.

Acetylation↗
PubMed2003

Nucleosome positioning on yeast plasmids is determined only by the internal signal of DNA sequence occupied by the nucleosome.

The possible role of border factors in determining the nucleosome positioning on a DNA sequence was investigated. To this end a family of recombinant plasmids based on Gal10Cyc1 promoter and neomycin phosphotransferase gene NPTII were created. A DNA sequence adjoining the GalCyc promoter was varied in these plasmids. Three nearly equally represented nucleosome positions on the GalCyc promoter were found. In the basal plasmid an FRT sequence adjoins the GalCyc promoter at the right. It contains an internal signal of multiple positioning. Its replacement with different DNA sequences does not affect nucleosome positioning on the GalCyc promoter. The nucleosome positioning on the GalCyc promoter does not depend on nucleosome positioning (or its absence) on adjoining sequences. The same is true for nucleosome positioning on FRT sequence. It was found also that nucleosomes' positioning on the NPTII gene and their mutual disposition, namely the spacing between neighboring nucleosomes (linker length) are determined by the location of positioning signals only. Generally the nucleosome positioning in our experimental model is determined solely by internal DNA sequence occupied by nucleosome. On the other hand, the action of this internal positioning signal does not extend to neighboring DNA sequences.

Base Sequence↗
PubMed1994

DNA damage induced by bleomycin, neocarzinostatin, and melphalan in a precisely positioned nucleosome. Asymmetry in protection at the periphery of nucleosome-bound DNA.

The antitumor drugs bleomycin, neocarzinostatin, and melphalan all damage DNA by mechanisms which involve binding in the minor groove. In order to examine at high resolution the modulating effects of chromatin structure on the action of these drugs, an end-labeled DNA fragment from the Xenopus laevis 5 S rRNA gene was reconstituted with histone octamers to form a precisely positioned nucleosome. For each drug, DNA damage at specific sequence positions in the fragment was then compared for nucleosome-bound versus naked DNA. Reconstitution into nucleosomes resulted in a marked inhibition of the DNA cleavage induced by bleomycin (5-fold) and neocarzinostatin (2.4-fold) in the central region of nucleosomal DNA. However, at the periphery of nucleosome-bound DNA, a distinct asymmetry was apparent, with marked inhibition of cleavage toward the upstream side, but little if any inhibition toward the downstream side, which overlaps the binding site of the transcription factor TFIIIA. In the case of melphalan, alkylation at adenine N-3 was inhibited by nearly 2-fold throughout the nucleosome, whereas alkylation at guanine N-7 was either slightly inhibited or slightly enhanced, depending on sequence position. None of the drugs showed the 10-base pair periodicity characteristic of hydroxyl radical-induced cleavage of nucleosomal DNA. The results are consistent with a model in which minor groove sites in nucleosome-bound DNA remain relatively accessible to small molecules, even where the minor groove faces the histone core, and in which drug-induced DNA damage is inhibited by conformational constraints imposed on DNA by nucleosome structure. Furthermore, the degree of such constraints appears to be sequence-dependent, at least near the periphery of nucleosome-bound DNA.

Animals↗
PubMed2004

N-terminal tail domains of core histones in nucleosome block the access of anticancer drugs, mithramycin and daunomycin, to the nucleosomal DNA.

Mithramycin (MTR) and daunomycin are two anticancer drugs that bind reversibly to double stranded DNA with (G.C) base specificity leading to inhibition of transcription. MTR is a groove binder of DNA in the presence of a divalent cation such as Mg(2+), while daunomycin intercalates in the double stranded DNA structure. In order to understand the mechanism of action of the two types of transcription inhibitor, namely, groove binder and intercalator, we have studied the effect of N-terminal tail domains in histone proteins of the nucleosome upon the association of both MTR and daunomycin with the nucleosome core particle, because the tails modulate the accessibility to nucleosome during gene expression. Using a combination of spectroscopic, thermodynamic and biochemical studies, we have shown that N-terminal intact and chopped core particles interact differently with the same ligand and the N-terminal tail domains of core histones in the nucleosome stand in the way of free access of these ligands to the nucleosomal DNA. Tryptic removal of N-terminal tail domains of core histones enhances the binding potential and accessibility of both MTR and daunomycin to nucleosomal DNA. They disassemble the nucleosome structure leading to a release of DNA, N-terminal chopped nucleosomes being more susceptible for disruption compared to N-terminal intact nucleosomes. The extent of these effects is more pronounced in case of the intercalator daunomycin. Thus, N-terminal tail domains protect the eukaryotic genome from external agents, such as anticancer drugs, and the degree of protection is dependent upon the mode of binding to DNA.

Animals↗
PubMed1992

Artificial nucleosome positioning sequences tested in yeast minichromosomes: a strong rotational setting is not sufficient to position nucleosomes in vivo.

DNA sequences that support bending around the histone octamer ('rotational setting') are considered to be a major determinant of nucleosome positions. TG5 is an artificial positioning sequence containing 100 bp of an (A/T)3NN(G/C)3NN motif repeated with a 10 bp period. It provides a strong rotational setting and is superior to natural sequences in nucleosome formation in vitro [Shrader, T.E. and Crothers, D.M. (1989) Proc. Natl. Acad. Sci. USA, 86, 7418-7422]. To investigate the contribution of the rotational setting to nucleosome positioning in vivo, TG sequences were inserted in a nucleosome, at the edge of a nucleosome and in a nuclease sensitive region of yeast minichromosomes and the chromatin structures were analysed. In none of the constructs were TG sequences folded in a positioned nucleosome, demonstrating that the rotational setting played a subordinate role in the rough positioning in vivo. The rotational setting might fine tune the positions. Positioned nucleosomes were found overlapping the ends of TG, indicating that a discontinuity of the 10 bp periodicity of (A/T)3 and (G/C)3 near the centre of a nucleosome might be favourable for positioning and serve as a translational signal.

Base Sequence↗
PubMed2006

The human telomeric protein TRF1 specifically recognizes nucleosomal binding sites and alters nucleosome structure.

Telomeres are dynamic nucleoprotein structures that cap the ends of eukaryotic chromosomes. In humans, the long (TTAGGG)(n) double-stranded telomeric DNA repeats are bound specifically by the two related proteins TRF1 and TRF2, and are organized in nucleosomes. Whereas the role of TRF1 and TRF2 in telomeric function has been studied extensively, little is known about the involvement of telomeric nucleosomes in telomere structures or how chromatin formation may affect binding of the TRFs. Here, we address the question of whether TRF1 is able to bind to telomeric binding sites in a nucleosomal context. We show that TRF1 is able to specifically recognize telomeric binding sites located within nucleosomes, forming a ternary complex. The formation of this complex is strongly dependent on the orientation of binding sites on the nucleosome surface, rather than on the location of the binding sites with respect to the nucleosome dyad. Strikingly, TRF1 binding causes alterations in nucleosome structure without dissociation of histone subunits. These results indicate that nucleosomes contribute to the establishment of a telomeric capping complex, whose structure and dynamics can be modulated by the binding of telomeric factors.

Base Sequence↗
PubMed1997

Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes.

The characteristic AA(TT) sequence pattern of the nucleosome DNA derived earlier is used for prediction of nucleosome positions around splice junctions of eukaryotic genes. Two large datasets (2000 sequences each) were collected consisting of DNA segments with the exon/intron and intron/exon splice junctions, from various eukaryotic species. Positions of predicted nucleosomes near the junction sites were calculated. Those junctions which are found to belong to the nucleosomes, are located preferentially within a few base pairs from the midpoint of the nucleosome DNA. That is, obligatory GT- and AG-ends of the introns are more frequently located near the nucleosome dyad axis, within the best protected middle 10-15 base pairs of the nucleosome DNA. In addition, a tendency is observed for the strongest nucleosomes to form more often in the introns, in accordance with the hypothesis on the chromatin-organizing role of introns.

DNA↗
PubMed1985

Nucleosome rearrangement in vitro. 2. Formation of nucleosomes in newly repaired regions of DNA.

We have reported previously that immediately following nucleotide excision repair in human cells the newly repaired DNA lacks a nucleosome conformation [Smerdon, M. J., & Lieberman, M. W. (1980) Biochemistry 19, 2992-3000]. In this study, we have examined the ability of these nascent DNA regions to acquire a nucleosome structure in vitro by incubating intact or H1-depleted nuclei in buffers containing different salt concentrations (0.025-0.625 M KCl) at 0 or 37 degrees C. Nucleosomes were detected in these regions by an increase in the level of repair-incorporated nucleotides associated with isolated nucleosome core particle DNA. Our results indicate that the nascent DNA is resistant to nucleosome formation during the low-salt transition where the limiting repeat length decreases from approximately 190 to 168 base pairs (bp) [Watkins, J. F., & Smerdon, M. J. (1985) Biochemistry (preceding paper in this issue)]. This result provides further evidence that the nascent DNA is indeed in a nonnucleosomal state. At higher salt concentrations (greater than 0.4 M), where the nucleosome repeat length decreases to a limiting value of approximately 146 bp, there was an increase in nucleosome formation in nascent DNA that correlated with the decrease in limiting repeat length. However, we did not observe a complete randomization of the repair-incorporated nucleotides. Indeed, even at the highest salt concentration used (0.625 M), we never observed more than 50% of the nascent DNA associated with the isolated core particles. This was the case even though a major portion of the nucleosomes had a limiting value repeat length following the high-salt incubation.(ABSTRACT TRUNCATED AT 250 WORDS)

Carbon Radioisotopes↗
PubMed1987

Competition for formation of nucleosomes on fragmented SV40 DNA: a hyperstable nucleosome forms on the termination region.

We have studied the relative abilities of different simian virus 40 (SV40) DNA segments to reconstitute into nucleosomes in vitro. The SV40 genome was separated into 15 discrete fragments by restriction endonuclease digestion and reconstituted with calf thymus core histones under conditions of varying histone-to-DNA ratios. Three fragments show very different abilities to form nucleosomes when low histone-to-DNA ratios require all fragments to compete for available histones. Two of these fragments, both from within protein-coding regions, are significantly underreconstituted. The third fragment, covering the SV40 termination region, competes much more effectively for histones than the other 14 fragments. The fragment containing the SV40 origin region formed nucleosomes with about average probability. Overall, the SV40 fragments differed by approximately an order of magnitude in their abilities to support nucleosome formation in vitro. The stability of the nucleosomes was measured by challenge with high concentrations of the destabilizing reagent heparin. The fragment that reconstituted most effectively also formed nucleosomes that were unusually stable to heparin challenge. These observations are intriguing since this fragment contains the sequences where replication of SV40 DNA commonly terminates and where early messenger RNA synthesis may terminate as well. The existence of unique hyperstable nucleosomes in this region suggests the interesting possibility that such nucleosomes may assist in termination events by assisting in the pausing of replication or transcription complexes.

Animals↗
PubMed2004

Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling.

Linker DNA was found to be critical for the specific docking of ISW2 with nucleosomes as shown by mapping the physical contacts of ISW2 with nucleosomes at base-pair resolution. Hydroxyl radical footprinting revealed that ISW2 not only extensively interacts with the linker DNA, but also approaches the nucleosome from the side perpendicular to the axis of the DNA superhelix and contacts two disparate sites on the nucleosomal DNA from opposite sides of the superhelix. The topography of the ISW2-nucleosome was further delineated by finding which of the ISW2 subunits are proximal to specific sites within the linker and nucleosomal DNA regions by site-directed DNA photoaffinity labeling. Although ISW2 was shown to contact approximately 63 bp of linker DNA, a minimum of 20 bp of linker DNA was required for stable binding of ISW2 to nucleosomes. The remaining approximately 43 bp of flanking linker DNA promoted more efficient binding under competitive binding conditions and was functionally important for enhanced sliding of nucleosomes when ISW2 was significantly limiting.

Adenosine Triphosphatases↗