U.S. flag

An official website of the United States government

NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-2013.

Cover of Madame Curie Bioscience Database

Madame Curie Bioscience Database [Internet].

Show details

The Role of Unusual DNA Structures in Chromatin Organization for Transcription


The structural and mechanical properties of DNA influence nucleosome positioning and the manner in which DNA is organized in chromatin. Curved DNA structures, poly(dA•dT) sequences, and Z-DNA-forming sequences frequently occur near transcription start sites. Many reports have indicated that curved DNA structures play an important role in the formation, stability and positioning of nucleosomes, and consequently in DNA packaging in nuclei. Curved DNA structures and poly(dA•dT) sequences can increase the accessibility of target DNA elements of activators in chromatin to facilitate initiation of transcription. Z-DNA seems to be implicated in gene activation coupled with chromatin remodeling, and eukaryotes may use triplex DNA and cruciform structures to manipulate nucleosome organization in a site-specific manner.


DNA is highly compacted in a nucleus. In humans, the genomic DNA measures about a meter if unraveled. Thus, it follows that in the nucleus of a somatic cell, about 1x10-5 m in diameter, our chromosomal DNA must be compacted in length by as much as 200,000-fold. Biologically important DNA regions, such as the origins of replication, regulatory regions of transcription, and recombination loci must also be compacted. A narrow fiber of DNA is first folded into nucleosomes, the most fundamental unit of chromatin. It is generally thought that if nucleosomes assemble over a promoter region, they block initiation of transcription, because they inhibit access and/or assembly of transcription factors.

Histone modifications and ATP-dependent chromatin remodeling play a central role to suppress or amplify the inherently repressive effects of chromatin.1-14 There are several mechanisms to explain how these phenomena participate in gene regulation. One model of transcription initiation is as follows: (i) a transcription factor (activator) binds to its target sequence in chromatin; (ii) the activator recruits a remodeling complex by direct protein-protein interaction; (iii) the complex alters the structure of the surrounding nucleosomes; (iv) the altered chromatin structure allows general transcription factors and RNA polymerase to bind to the promoter; (v) transcription starts.4 Activators can bind to their target DNA elements, even when the target is adjacent to nucleosomes, or actually within a nucleosome.15-19

What chromatin structure is it that activators can bind? At present, we cannot clearly answer this question. This problem is still a “missing link” in the transcription cascade. The structural and mechanical properties of DNA have been often argued in relation to their effects on the nucleosome positioning and their effects on the way DNA is organized in chromatin. In this chapter, I focus on whether unusual DNA structures affect the packaging of genomic DNA into chromatin, and on how transcription is initiated.

Curved DNA and DNA Packaging in Chromatin

Both intrinsic DNA curvature and anisotropic DNA bendability (flexibility) influence the formation, stability and positioning of nucleosomes.20-42 Thus, they may play an important role in the packaging of transcriptional control regions into chromatin.43,44 This section focuses on the role of intrinsic DNA curvature, and considers how the packaged DNA keeps cis elements accessible to transcription factors. The role of DNA bendability is described in the next chapter.

DNA curvature seems to have general significance for DNA packaging. Because DNA has to be bent to fit closely around a histone core, it seems thermodynamically favorable to form nucleosomes on DNA sequences that are already appropriately curved. In fact, it has been experimentally shown that nucleosomes often preferentially associate with curved DNA fragments.26,28-30,35,37,38,41 For example, Widlund et al constructed a library of nucleosome core DNA from the mouse genome, and screened those sequences that form the most stable nucleosomes.37 The identified fragments contained phased runs of three or more consecutive adenines (or thymines), and showed retarded migration in non-denaturing polyacrylamide gel electrophoresis. Thus, curved DNA structure was found to be the most common feature among the screened fragments.

Curved DNA structures may also stabilize chromatin through their interaction with histone N-terminal tail domains that are the major sites of histone modifications such as acetylation, methylation and phosphorylation.1,5,8,10,12,13 These modifications are implicated in transcription activation and gene silencing. Interactions between N-terminal domains and intrinsic DNA curvature could influence nucleosome positioning and stability.45,46 On rigid, intrinsically curved DNA sequences, interactions between DNA and the histone tails stabilizes the formation of nucleosomes by ca. 250 cal/mol.46

The next question is whether curved DNA structures occur frequently in eukaryotic genomes. There are some clear answers to this. For example, repetitive DNA sequences, including satellite DNAs, very often contain one or more curved DNA structures (Table 1).47-52 Curved DNA structures may be a common feature shared by all satellites, which are universally associated with regions of constitutive heterochromatin and comprise anywhere from a few percent to > 50% of mammalian genomes.53,54 If the hypothesis is correct, then curved DNA structures must contribute significantly to genome packaging. Some satellites, however, do not show the electrophoretic retardation characteristic of curved DNA structures. A fragment from bovine satellite I DNA is one such example. It behaves normally in non-denaturing polyacrylamide gels. Interestingly, an “unseen DNA curvature” was found in the fragment, in which another structural property that causes rapid migration had suppressed the effect of the curved DNA.55 Interestingly, repeatedly occurring curved DNA sites are not restricted to satellite DNA, but are also reported for human ε-, Gγ-Aγ-ψβ-, δ-, and β-globin, c-myc, and immunoglobulin heavy chain μ loci, and in mouse βmajor-globin locus.56-59 Considering that most findings of naturally occurring curved DNA structures have been based on detection of retarded migration, the finding of “unseen curved DNA” strongly suggests that there are many more curved DNA loci on eukaryotic genomes than expected.

Table 1. Repetitive sequences that contain a curved DNA structure in the repeating unit.

Table 1

Repetitive sequences that contain a curved DNA structure in the repeating unit.

Now, let's consider promoter packaging into chromatin. Positioning of nucleosomes on a DNA sequence plays an important role in controlling the access of specific DNA-binding proteins to regulatory DNA elements.60-65 Curved DNA often occurs in transcriptional control regions irrespective of the promoter type (Chapter 5). Thus, curved DNA may regulate positioning of nucleosomes in these regions, so as to allow the binding of activators.44 Logically, the target DNA elements could become accessible by one of two mechanisms: either by positioning the target on a nucleosome and exposing it toward the environment; or by making it free of nucleosomes (fig. 1).

Figure 1. Target DNA elements of transcription activators could become accessible in chromatin, either by making the region free of nucleosomes, or by exposing it toward environment on the nucleosome.

Figure 1

Target DNA elements of transcription activators could become accessible in chromatin, either by making the region free of nucleosomes, or by exposing it toward environment on the nucleosome. In the figure, the rope represents the DNA, and wooden cylinders (more...)

An example of the first mechanism is the nucleosome structure formed on the long terminal repeat of the mouse mammary tumor virus (MMTV-LTR). In this case, four glucocorticoid receptor recognition elements (GREs) are located on the surface of a positioned nucleosome, and the major grooves of two GREs are exposed towards the environment.60 These sites can be recognized by the receptor (a zinc finger protein), which initiates transcription. By what mechanism are these two GREs exposed on the surface of the nucleosome? An early study implicated curved DNA.66 It was subsequently suggested that this curved DNA has a left-handed curved trajectory of its helical axis.44

If the helical axis adopts a left-handed curved trajectory, it will resemble the negatively supercoiled DNA seen on a nucleosome, and thus it may recruit core histones easily. Furthermore, if a cis-DNA element is involved in, or is located near, the curved DNA structure, rotational setting of the element on the histone core (or even in linker DNA region in some cases) would be restricted by the DNA curvature. When its recognition site is displayed toward the environment by the curvature, the recognition step would be facilitated. Recently, this hypothesis was substantiated by using synthetic DNA segments with different conformations.65 When left-handed curved DNA was linked to the herpes simplex virus thymidine kinase (HSV tk) promoter at a specific rotational phase and distance, in COS-7 cells, it activated the promoter approximately 10-fold. Mechanistically, the curved DNA attracted a histone core and the TATA box was thereby left in the linker DNA with its minor groove facing outwards (fig. 2). Neither planar DNA curvature, nor right-handedly curved DNA, nor straight DNA, had this effect.

Figure 2. Synthetic curved DNA with a close resemblance to part of a negative supercoil can activate transcription by modulating local chromatin structure.

Figure 2

Synthetic curved DNA with a close resemblance to part of a negative supercoil can activate transcription by modulating local chromatin structure. The figure shows an example using the HSV tk promoter as a test system. This curved DNA can attract histone (more...)

On the other hand, when a given DNA is dissimilar to the negative supercoil, it would make the region free of nucleosomes (the second mechanism). The adenylate kinase gene promoter of Saccharomyces cerevisiae, which has a curved DNA of this type, seems to be an example of this. This promoter was shown to be free of nucleosomes.67 In the yeast GAL1 promoter and GAL80 promoter, curved DNA may make the UAS (upstream activation sequence) escape from being incorporated into nucleosomes. The underlying mechanisms are, however, different. Under inactivated (non-inducing) conditions, the GAL1 promoter, which has two strong DNA curvatures in the upstream of the TATA box,68 is incorporated into a nucleosome, referred to as nucleosome B. The bend centers lie within the terminal 20 bp or so on each end of the 147 bp sequence bound to the nucleosome B.68 The UASG is located in the non-nucleosomal region just upstream of the nucleosome B. In this case, high nucleosome-forming ability of the two curved DNA structures seems to be used to make the UAS free of nucleosomes. In contrast, in the GAL80 promoter, a single intrinsic DNA curvature which is located close to UASGAL80 seems to exclude nucleosome formation on the UAS.68 It can be imagined that similarity or dissimilarity between a given DNA curvature and the negatively supercoiled DNA seen on a nucleosome determines how easily the curved DNA can be incorporated into nucleosomes.

Besides the mechanism described above, curved DNA may also alter nucleosome structures to make target DNA elements accessible on the surface of nucleosomes. An interesting result was obtained in an experiment using DNA fragments composed of a synthetic DNA bending sequence (the repeated (A/T)3NN(G/C)3NN motifs; TG-motifs) and the binding site for the nuclear factor 1 (NF-1) with an A5 tract on both sides.69 The TG-motifs are anisotropically flexible and have a high nucleosome-forming ability.27 When nucleosomes were reconstituted on the fragments, the NF-1 binding affinity was higher when the flanking A-tracts were out-of-phase with the TG-motifs, than when they were in-phase. An altered nucleosome structure was also formed on a poly(dA•dT) sequence,17 which is described in the next section.

Poly(dA•dT) Sequences and Nucleosome Positioning

DNA sequences of (dA•dT)n also frequently occur in eukaryotic genomes. They are rigid and adopt a unique DNA conformation that has a narrow minor groove.70-72 In Homo sapiens, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae, there are more poly(dA•dT) sequences present than would be expected if the DNA sequence were random, while in Escherichia coli and Mycobacterium tuberculosis, no difference is observed between actual and expected occurrences.73 In promoter regions, (dA•dT)n-rich sequences, where several (dA•dT)n sequences are connected by other short sequences, have frequently been found. For example, in yeast, promoters of the genes HIS3, PET56, DED1, CBS2, ARG4, URA3 and ADH2 contain or are flanked by them.74-78 The (dA•dT)n-rich sequences act as upstream promoter elements in HIS3, PET56, DED1, ARG4, and URA3.74,75,77 In the rest of this section, the relationships between poly(dA•dT) sequences, nucleosome formation, and transcription are considered further.

In Vitro Reconstitution of Nucleosomes on Poly(dA•dT) Sequences

It is not yet clear whether poly(dA•dT) sequences always impede nucleosome formation. Earlier studies showed that long poly(dA•dT) sequences resisted nucleosome formation.79-81 It was also shown that nucleosome formation over one member of a young Alu subfamily, which had recently transposed immediately downstream of a T14A11 stretch in the human neurofibromatosis type 1 gene locus, was impeded by the stretch.82 On the other hand, human genomic DNA fragments containing long (dA•dT)n tracts (e.g., n=32, 34, or 41) were successfully incorporated into nucleosome cores.83,84 Furthermore, nucleosomes were reconstituted successfully on the yeast DED1 promoter, containing a T6 tract, two T5 tracts and a T9 tract.85,86 In this case, the characteristic T-tract conformation was lost upon folding into nucleosomes, indicating that the structural constraints in a nucleosome dominate over the intrinsic conformation of the T-tract. Higher temperatures apparently favor reconstitution.87 The length of poly(dA•dT), the number of the poly(dA•dT) sequences, the DNA sequences surrounding poly(dA•dT), and conditions used for reconstitution, all seem to determine whether poly(dA•dT) sequences can form nucleosomes.

Influence of Poly(dA•dT) Sequences on Nucleosome Formation in Vivo

Some promoters carrying one or more poly(dA•dT) sequences are not packaged into stable nucleosomes in vivo,88-90 while others are packaged.78,91 Shimizu et al, found that in the yeast minichromosome, A15TATA16 and A34 tracts disrupt nucleosome formation, whereas a shorter A5TATA4 tract is incorporated into the positioned nucleosome.92 They also reported that the longer A-tracts retained their unique DNA conformation in vivo. Using in vivo UV photofootprinting and DNA repair by photolyase, Suter et al demonstrated that in yeast, poly(dA•dT) sequences in promoters such as HIS3, URA3 and ILV1 were not folded in nucleosomes.89 Like the report by Shimizu et al, this group also suggested that poly(dA•dT) sequences maintain their characteristic DNA structure in vivo. Interestingly, in the Candida glabrata AMT1 gene (encoding copper-metalloregulatory transcription factor), nucleosome formation was allowed but the poly(dA•dT) sequence influenced the resulting nucleosome structure. The promoter harbors a (dA•dT)16 sequence slightly upstream of a metal response element (MRE). These two sequences are packaged into a positioned nucleosome that exhibits the (dA•dT)16—dependent localized distortion (fig. 3). This nucleosome makes the MRE accessible.17,93

Figure 3. A putative nucleosome structure formed on the poly(dA•dT)-containing wild-type AMT1 promoter (left).

Figure 3

A putative nucleosome structure formed on the poly(dA•dT)-containing wild-type AMT1 promoter (left). Also shown is a putative nucleosome structure formed on a mutant promoter (right), which carried “normal” DNA instead of the poly(dA•dT) (more...)

Functional Significance of Poly(dA•dT) Sequences in Transcription

Poly(dA•dT) sequences seem to make target DNA elements in chromatin more accessible, which is essentially the same as the proposed effect of curved DNA. To do this, they either prevent nucleosome formation, or change nucleosome structures. As described above, in some cases, the poly(dA•dT) sequences are incorporated into nucleosomes, with either the original conformation, or with an altered conformation,17,86,92,93 while in other cases they are not incorporated.89,92 Although it is not clear what determines this difference, the lengths of poly(dA•dT) sequences and a slight difference in the conformational and/or mechanical properties of the poly(dA•dT)-containing sequences may be key parameters. In addition, to establish non-nucleosomal regions, or to form distorted nucleosomes, assistance of some factors [e.g., poly(dA•dT)-binding proteins or histone modifying enzymes] may be required. In this sense, the HMG-I(Y) family of “high mobility group” proteins may be important. HMG proteins organize the structure of DNA-protein complexes in the context of chromatin (Chapter 11). HMG-I(Y) can preferentially bind to certain types of poly(dA•dT) sequences on the surface of nucleosomes and alter the local setting of DNA on the nucleosomes.94 Thus, poly(dA•dT) sequences may also function as a signal to introduce structural changes into nucleosomes.

Chromatin and Z-DNA, Triple-Stranded DNA, and Cruciform DNA

The bulk of the eukaryotic genome is believed not to be torsionally stressed, even though it is negatively supercoiled, because such supercoilings are largely accommodated by the DNA writhing in nucleosomes. Unconstrained negative supercoils, however, can be still generated. For example, they are generated behind an RNA polymerase transcribing a DNA template (Chapter 10).95 The negative supercoils stabilize non-B DNA structures such as Z-DNA, triplex DNA and cruciform DNA. DNA elements with sequences suitable for the formation of Z-DNA are found at various positions in genomes. An early study estimated that the human genome contains approximately 100,000 copies of potential Z-DNA-forming sequences.96 Interestingly, similar to curved DNA and poly(dA•dT) sequences, Z-DNA-forming sequences occur more frequently near transcription start sites.97 Do they function to position nucleosomes or to inhibit nucleosome formation? It is thought that the actual Z-DNA structure lies in non-nucleosomal regions in chromatin.98 However, we do not yet know whether Z-DNA can regulate nucleosome position.

An interesting study has been reported recently. Z-DNA seems to be implicated in gene activation coupled with chromatin remodeling (fig. 4). The promoter of the human colony-stimulating factor 1 (CSF1) gene is flanked by TG repeats (Z-DNA forming sequence), which were converted to Z-DNA upon activation by the SWI/SNF-like BRG1-associated factor (BAF) complex in vivo. Furthermore, the in vitro data showed that the BAF complex facilitates Z-DNA formation in a nucleosomal template.99 These data suggest that at the CSF1 promoter, BAF-induced Z-DNA formation stabilizes an open chromatin structure. This illustrates why promoters sometimes contain, or are flanked by, Z-DNA forming sequences.

Figure 4. A model depicting NFI- and Z-DNA-facilitated chromatin remodeling by the BAF complex, at the CSF1 promoter.

Figure 4

A model depicting NFI- and Z-DNA-facilitated chromatin remodeling by the BAF complex, at the CSF1 promoter. Prior binding of NFI/CTF to its target site in the CSF1 promoter is required for the recruitment of the BAF complex. Activation of the promoter (more...)

Triple-stranded DNA seems unable to be accommodated within nucleosomes.100 This conclusion is strengthened by the report by Espinas et al, who performed in vitro assembly of mono-nucleosomes onto 180 bp DNA fragments containing (GA•TC)22, or onto 190 bp fragments with (GA•TC)10.101 Although the repeated sequences themselves had no influence on nucleosome positioning, nucleosome assembly was strongly inhibited when the triple-stranded DNA was formed at the (GA•TC)n site. On the other hand, triplex formation was difficult when the (GA•TC)n site was incorporated into a nucleosome. Thus, nucleosome assembly and triplex formation are presumably competing processes. In conclusion, triplexes seem unable to determine the position of nucleosomes by recruiting histone cores.

Cruciform structures are located mainly on internucleosomal DNA,102 perhaps because they cannot associate with histone cores103 and as a result, they could induce an alternative positioning of nucleosomes. The cruciform structures could also act over a distance to destabilize adjacent nucleosomes.104 Thus, cruciforms are probably not used to recruit histone octamers to form positioned nucleosomes. However, eukaryotes may use triplex structures and cruciforms to form open chromatin structures.

Linker histones are probably implicated in transcriptional regulation.105,106 However, the interaction between unusual DNA structures and linker histones has not been studied adequately. Interestingly, H1 seems to bind preferentially to curved DNA structures that are flanked with specific sequences.107 It is evident that more information is needed, on the interaction between linker histones and DNA of various conformations.


Curved DNA and poly(dA•dT) structures can enhance the accessibility of cis-DNA elements in chromatin by exposing them to the milieu while on the nucleosome (curved DNA), or by preventing nucleosome formation [both curved DNA and poly(dA•dT)], or in some cases by forming altered nucleosomal structures [poly(dA•dT)]. Z-DNA seems to be implicated in gene activation coupled with chromatin remodeling, and triplex DNA and cruciform structures may be used to form open chromatin structures.


The author would like to acknowledge the contributions of Jun-ichi Nishikawa, Yoshiro Fukue, and Junko Ohyama. The studies reported from my laboratory were supported in part by Grants-in-Aid for Scientific Research from the Ministry of Education, Science, Sports and Culture of Japan.


Imhof A, Wolffe AP. Transcription: gene control by targeted histone acetylation. Curr Biol. 1998;8:R422–424. [PubMed: 9637914]
Workman JL, Kingston RE. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem. 1998;67:545–579. [PubMed: 9759497]
Kornberg RD, Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell. 1999;98:285–294. [PubMed: 10458604]
Aalfs JD, Kingston RE. What does ‘chromatin remodeling’ mean? Trends Biochem Sci. 2000;25:548–555. [PubMed: 11084367]
Turner BM. Histone acetylation and an epigenetic code. Bioessays. 2000;22:836–845. [PubMed: 10944586]
Vignali M, Hassan AH, Neely KE. et al. ATP-dependent chromatin-remodeling complexes. Mol Cell Biol. 2000;20:1899–1910. [PMC free article: PMC110808] [PubMed: 10688638]
Wu J, Grunstein M. 25 years after the nucleosome model: chromatin modifications. Trends Biochem Sci. 2000;25:619–623. [PubMed: 11116189]
Jenuwein T. Re-SET-ting heterochromatin by histone methyltransferases. Trends Cell Biol. 2001;11:266–273. [PubMed: 11356363]
Becker PB, Hörz W. ATP-dependent nucleosome remodeling. Annu Rev Biochem. 2002;271:247–273. [PubMed: 12045097]
Geiman TM, Robertson KD. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together? J Cell Biochem. 2002;87:117–125. [PubMed: 12244565]
Narlikar GJ, Fan HY, Kingston RE. Cooperation between complexes that regulate chromatin structure and transcription. Cell. 2002;108:475–487. [PubMed: 11909519]
Turner BM. Cellular memory and the histone code. Cell. 2002;111:285–291. [PubMed: 12419240]
Carrozza MJ, Utley RT, Workman JL. et al. The diverse functions of histone acetyltransferase complexes. Trends Genet. 2003;19:321–329. [PubMed: 12801725]
Lusser A, Kadonaga JT. Chromatin remodeling by ATP-dependent molecular machines. Bioessays. 2003;25:1192–1200. [PubMed: 14635254]
Almer A, Rudolph H, Hinnen A. et al. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 1986;5:2689–2696. [PMC free article: PMC1167170] [PubMed: 3536481]
Archer TK, Cordingley MG, Wolford RG. et al. Transcription factor access is mediated by accurately positioned nucleosomes on the mouse mammary tumor virus promoter. Mol Cell Biol. 1991;11:688–698. [PMC free article: PMC359719] [PubMed: 1846670]
Zhu Z, Thiele DJ. A specialized nucleosome modulates transcription factor access to a C. glabrata metal responsive promoter. Cell. 1996;87:459–470. [PubMed: 8898199]
Wolffe AP. Chromatin: Structure and function3rd ed. London: Academic press,1998 .
Onishi Y, Kiyama R. Interaction of NF-E2 in the human β-globin locus control region before chromatin remodeling. J Biol Chem. 2003;278:8163–8171. [PubMed: 12509425]
Zhurkin VB, Lysov YP, Ivanov VI. Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res. 1979;6:1081–1096. [PMC free article: PMC327755] [PubMed: 440969]
Trifonov EN, Sussman JL. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci USA. 1980;77:3816–3820. [PMC free article: PMC349717] [PubMed: 6933438]
Dickerson RE, Kopka ML, Pjura P. A random-walk model for helix bending in B-DNA. Proc Natl Acad Sci USA. 1983;80:7099–7103. [PMC free article: PMC390000] [PubMed: 6580629]
Drew HR, Travers AA. DNA bending and its relation to nucleosome positioning. J Mol Biol. 1985;186:773–790. [PubMed: 3912515]
Zhurkin VB. Sequence-dependent bending of DNA and phasing of nucleosomes. J Biomol Struct Dyn. 1985;2:785–804. [PubMed: 3917119]
Satchwell SC, Drew HR, Travers AA. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986;191:659–675. [PubMed: 3806678]
Pennings S, Muyldermans S, Meersseman G. et al. Formation, stability and core histone positioning of nucleosomes reassembled on bent and other nucleosome-derived DNA. J Mol Biol. 1989;207:183–192. [PubMed: 2738923]
Shrader TE, Crothers DM. Artificial nucleosome positioning sequences. Proc Natl Acad Sci USA. 1989;86:7418–7422. [PMC free article: PMC298075] [PubMed: 2798415]
Wolffe AP, Drew HR. Initiation of transcription on nucleosomal templates. Proc Natl Acad Sci USA. 1989;86:9817–9821. [PMC free article: PMC298593] [PubMed: 2690074]
Costanzo G, di MauroE, Salina G. et al. Attraction, phasing and neighbour effects of histone octamers on curved DNA. J Mol Biol. 1990;216:363–374. [PubMed: 2174975]
Shrader TE, Crothers DM. Effects of DNA sequence and histone-histone interactions on nucleosome placement. J Mol Biol. 1990;216:69–84. [PubMed: 2172553]
Ioshikhes I, Bolshoy A, Trifonov EN. Preferred positions of AA and TT dinucleotides in aligned nucleosomal DNA sequences. J Biomol Struct Dyn. 1992;9:1111–1117. [PubMed: 1637505]
Patterton H-G, Simpson RT. Modified curved DNA that could allow local DNA underwinding at the nucleosomal pseudodyad fails to position a nucleosome in vivo. Nucleic Acids Res. 1995;23:4170–4179. [PMC free article: PMC307359] [PubMed: 7479081]
Sivolob AV, Khrapunov SN. Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending stiffness. J Mol Biol. 1995;247:918–931. [PubMed: 7723041]
Baldi P, Brunak S, Chauvin Y. et al. Naturally occurring nucleosome positioning signals in human exons and introns. J Mol Biol. 1996;263:503–510. [PubMed: 8918932]
De SantisP, Kropp B, Leoni L. et al. Influence of DNA superstructural features and histones aminoterminal domains on mononucleosome and dinucleosome positioning. Biophys Chem. 1996;62:47–61. [PubMed: 8962471]
Ioshikhes I, Bolshoy A, Derenshteyn K. et al. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J Mol Biol. 1996;262:129–139. [PubMed: 8831784]
Widlund HR, Cao H, Simonsson S. et al. Identification and characterization of genomic nucleosome-positioning sequences. J Mol Biol. 1997;267:807–817. [PubMed: 9135113]
Fitzgerald DJ, Anderson JN. Unique translational positioning of nucleosomes on synthetic DNAs. Nucleic Acids Res. 1998;26:2526–2535. [PMC free article: PMC147625] [PubMed: 9592133]
Olson WK, Gorin AA, Lu XJ. et al. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA. 1998;95:11163–11168. [PMC free article: PMC21613] [PubMed: 9736707]
Anselmi C, Bocchinfuso G, De Santis P. et al. Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J Mol Biol. 1999;286:1293–1301. [PubMed: 10064697]
Widlund HR, Kuduvalli PN, Bengtsson M. et al. Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence. J Biol Chem. 1999;274:31847–31852. [PubMed: 10542209]
Roychoudhury M, Sitlani A, Lapham J. et al. Global structure and mechanical properties of a 10-bp nucleosome positioning motif. Proc Natl Acad Sci USA. 2000;97:13608–13613. [PMC free article: PMC17623] [PubMed: 11095739]
Pedersen AG, Baldi P, Chauvin Y. et al. DNA structure in human RNA polymerase II promoters. J Mol Biol. 1998;281:663–673. [PubMed: 9710538]
Ohyama T. Intrinsic DNA bends: an organizer of local chromatin structure for transcription. Bioessays. 2001;23:708–715. [PubMed: 11494319]
Kropp B, Leoni L, Sampaolese B. et al. Influence of DNA superstructural features and histone amino-terminal domains on nucleosome positioning. FEBS Lett. 1995;364:17–22. [PubMed: 7750535]
Widlund HR, Vitolo JM, Thiriet C. et al. DNA sequence-dependent contributions of core histone tails to nucleosome stability: differential effects of acetylation and proteolytic tail removal. Biochemistry. 2000;39:3835–3841. [PubMed: 10736184]
Radic MZ, Lundgren K, Hamkalo BA. Curvature of mouse satellite DNA and condensation of heterochromatin. Cell. 1987;50:1101–1108. [PubMed: 2441880]
Benfante R, Landsberger N, Tubiello G. et al. Sequence-directed curvature of repetitive AluI DNA in constitutive heterochromatin of Artemia franciscana. Nucleic Acids Res. 1989;17:8273–8282. [PMC free article: PMC334963] [PubMed: 2813062]
Martínez-Balbás A, Rodríguez-Campos A, García-Ramírez M. et al. Satellite DNAs contain sequences that induce curvature. Biochemistry. 1990;29:2342–2348. [PubMed: 2110830]
Pasero P, Sjakste N, Blettry C. et al. Long-range organization and sequence-directed curvature of Xenopus laevis satellite 1 DNA. Nucleic Acids Res. 1993;21:4703–4710. [PMC free article: PMC331494] [PubMed: 7901836]
Fitzgerald DJ, Dryden GL, Bronson EC. et al. Conserved patterns of bending in satellite and nucleosome positioning DNA. J Biol Chem. 1994;269:21303–21314. [PubMed: 8063755]
Kralovics R, Fajkus J, Kovarík A. et al. DNA curvature of the tobacco GRS repetitive sequence family and its relation to nucleosome positioning. J Biomol Struct Dyn. 1995;12:1103–1119. [PubMed: 7626243]
John B, Miklos GLG. Functional aspects of satellite DNA and heterochromatin. Int Rev Cytol. 1979;58:1–114. [PubMed: 391760]
Singer MF. Highly repeated sequences in mammalian genomes. Int Rev Cytol. 1982;76:67–112. [PubMed: 6749748]
Ohyama T, Tsujibayashi H, Tagashira H. et al. Suppression of electrophoretic anomaly of bent DNA segments by the structural property that causes rapid migration. Nucleic Acids Res. 1998;26:4811–4817. [PMC free article: PMC147913] [PubMed: 9776739]
Wada-Kiyama Y, Kiyama R. Periodicity of DNA bend sites in human ε-globin gene region. Possibility of sequence-directed nucleosome phasing. J Biol Chem. 1994;269: 22238–22244. [PubMed: 8071350]
Wada-Kiyama Y, Kiyama R. Conservation and periodicity of DNA bend sites in the human β -globin gene locus. J Biol Chem. 1995;270:12439–12445. [PubMed: 7759485]
Wada-Kiyama Y, Kiyama R. An intrachromosomal repeating unit based on DNA bending. Mol Cell Biol. 1996;16:5664–5673. [PMC free article: PMC231566] [PubMed: 8816479]
Ohki R, Hirota M, Oishi M. et al. Conservation and continuity of periodic bent DNA in genomic rearrangements between the c-myc and immunoglobulin heavy chain μ loci. Nucleic Acids Res. 1998;26:3026–3033. [PMC free article: PMC147631] [PubMed: 9611251]
Piña B, Brüggemeier U, Beato M. Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell. 1990;60: 719–731. [PubMed: 2155706]
Schild C, Claret F-X, Wahli W. et al. A nucleosome-dependent static loop potentiates estrogen-regulated transcription from the Xenopus vitellogenin B1 promoter in vitro. EMBO J. 1993;12:423–433. [PMC free article: PMC413225] [PubMed: 8440235]
Imbalzano AN, Kwon H, Green MR. et al. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature. 1994;370:481–485. [PubMed: 8047170]
Godde JS, Nakatani Y, Wolffe AP. The amino-terminal tails of the core histones and the translational position of the TATA box determine TBP/TFIIA association with nucleosomal DNA. Nucleic Acids Res. 1995;23:4557–4564. [PMC free article: PMC307425] [PubMed: 8524642]
Wong J, Li Q, Levi B-Z. et al. Structural and functional features of a specific nucleosome containing a recognition element for the thyroid hormone receptor. EMBO J. 1997;16:7130–7145. [PMC free article: PMC1170314] [PubMed: 9384590]
Nishikawa J, Amano M, Fukue Y. et al. Left-handedly curved DNA regulates accessibility to cis-DNA elements in chromatin. Nucleic Acids Res. 2003;31: 6651–6662. [PMC free article: PMC275550] [PubMed: 14602926]
Piña B, Barettino D, Truss M. et al. Structural features of a regulatory nucleosome. J Mol Biol. 1990;216:975–990. [PubMed: 2176242]
Angermayr M, Oechsner U, Gregor K. et al. Transcription initiation in vivo without classical transactivators: DNA kinks flanking the core promoter of the housekeeping yeast adenylate kinase gene, AKY2, position nucleosomes and constitutively activate transcription. Nucleic Acids Res. 2002;30:4199–4207. [PMC free article: PMC140550] [PubMed: 12364598]
Bash RC, Vargason JM, Cornejo S. et al. Intrinsically bent DNA in the promoter regions of the yeast GAL1-10 and GAL80 genes. J Biol Chem. 2001;276:861–866. [PubMed: 11013248]
Blomquist P, Belikov S, Wrange Ö. Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure. Nucleic Acids Res. 1999;27:517–525. [PMC free article: PMC148209] [PubMed: 9862974]
Alexeev DG, Lipanov AA, Skuratovskii IY. Poly(dA)•poly(dT) is a B-type double helix with a distinctively narrow minor groove. Nature. 1987;325:821–823. [PubMed: 3821870]
Nelson HC, Finch JT, Luisi BF. et al. The structure of an oligo(dA)•oligo(dT) tract and its biological implications. Nature. 1987;330:221–226. [PubMed: 3670410]
Park HS, Arnott S, Chandrasekaran R. et al. Structure of the α-form of poly[d(A)] •poly[d(T)] and related polynucleotide duplexes. J Mol Biol. 1987;197:513–523. [PubMed: 3441009]
Dechering KJ, Cuelenaere K, Konings RN. et al. Distinct frequency-distributions of homopolymeric DNA tracts in different genomes. Nucleic Acids Res. 1998;26:4056–4062. [PMC free article: PMC147789] [PubMed: 9705519]
Struhl K. Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci USA. 1985;82:8419–8423. [PMC free article: PMC390927] [PubMed: 3909145]
Roy A, Exinger F, Losson R. cis- and trans-acting regulatory elements of the yeast URA3 promoter. Mol Cell Biol. 1990;10:5257–5270. [PMC free article: PMC361211] [PubMed: 2204810]
Schlapp T, Rödel G. Transcription of two divergently transcribed yeast genes initiates at a common oligo(dA-dT) tract. Mol Gen Genet. 1990;223:438–442. [PubMed: 2270084]
Thiry-Blaise LM, Loppes R. Deletion analysis of the ARG4 promoter of Saccharomyces cerevisiae: a poly(dAdT) stretch involved in gene transcription. Mol Gen Genet. 1990;223:474–480. [PubMed: 2270087]
Verdone L, Camilloni G, Di Mauro E. et al. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol Cell Biol. 1996;16:1978–1988. [PMC free article: PMC231185] [PubMed: 8628264]
Simpson RT, Künzler P. Chromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. Nucleic Acids Res. 1979;6:1387–1415. [PMC free article: PMC327779] [PubMed: 450700]
Rhodes D. Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. Nucleic Acids Res. 1979;6:1805–1816. [PMC free article: PMC327812] [PubMed: 450714]
Kunkel GR, Martinson HG. Nucleosomes will not form on double-stranded RNA or over poly(dA)•poly(dT) tracts in recombinant DNA. Nucleic Acids Res. 1981;9:6869–6888. [PMC free article: PMC327648] [PubMed: 7335494]
Englander EW, Howard BH. A naturally occurring T14A11 tract blocks nucleosome formation over the human neurofibromatosis type 1 (NF1)-Alu element. J Biol Chem. 1996;271:5819–5823. [PubMed: 8621451]
Fox KR. Wrapping of genomic polydA•polydT tracts around nucleosome core particles. Nucleic Acids Res. 1992;20:1235–1242. [PMC free article: PMC312164] [PubMed: 1561079]
Brown PM, Fox KR. DNA triple-helix formation on nucleosome-bound poly(dA)•poly(dT) tracts. Biochem J. 1998;333:259–267. [PMC free article: PMC1219581] [PubMed: 9657964]
Losa R, Omari S, Thoma F. Poly(dA)•poly(dT) rich sequences are not sufficient to exclude nucleosome formation in a constitutive yeast promoter. Nucleic Acids Res. 1990;18:3495–3502. [PMC free article: PMC331002] [PubMed: 2194162]
Schieferstein U, Thoma F. Modulation of cyclobutane pyrimidine dimer formation in a positioned nucleosome containing poly(dA•dT) tracts. Biochemistry. 1996;35:7705–7714. [PubMed: 8672471]
Puhl HL, Behe MJ. Poly(dA)•poly(dT) forms very stable nucleosomes at higher temperatures. J Mol Biol. 1995;245:559–567. [PubMed: 7844826]
Lascaris RF, de GrootE, Hoen PB. et al. Different roles for Abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res. 2000;28:1390–1396. [PMC free article: PMC111049] [PubMed: 10684934]
Suter B, Schnappauf G, Thoma F. Poly(dA•dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res. 2000;28:4083–4089. [PMC free article: PMC113125] [PubMed: 11058103]
Iyer V, Struhl K. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 1995;14:2570–2579. [PMC free article: PMC398371] [PubMed: 7781610]
Rubbi L, Camilloni G, Caserta M. et al. Chromatin structure of the Saccharomyces cerevisiae DNA topoisomerase I promoter in different growth phases. Biochem J. 1997;328:401–407. [PMC free article: PMC1218934] [PubMed: 9371694]
Shimizu M, Mori T, Sakurai T. et al. Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA)•poly(dT) tracts in vivo. EMBO J. 2000;19:3358–3365. [PMC free article: PMC313933] [PubMed: 10880448]
Koch KA, Thiele DJ. Functional analysis of a homopolymeric (dA-dT) element that provides nucleosomal access to yeast and mammalian transcription factors. J Biol Chem. 1999;274:23752–23760. [PubMed: 10446135]
Reeves R, Wolffe AP. Substrate structure influences binding of the non-histone protein HMG-I(Y) to free nucleosomal DNA. Biochemistry. 1996;35:5063–5074. [PubMed: 8664299]
Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA. 1987;84:7024–7027. [PMC free article: PMC299221] [PubMed: 2823250]
Hamada H, Kakunaga T. Potential Z-DNA forming sequences are highly dispersed in the human genome. Nature. 1982;298:396–398. [PubMed: 6283389]
Schroth GP, Chou PJ, Ho PS. Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. J Biol Chem. 1992;267:11846–11855. [PubMed: 1601856]
van HoldeK, Zlatanova J. Unusual DNA structures, chromatin and transcription. Bioessays. 1994;16:59–68. [PubMed: 8141807]
Liu R, Liu H, Chen X. et al. Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell. 2001;106:309–318. [PubMed: 11509180]
Westin L, Blomquist P, Milligan JF. et al. Triple helix DNA alters nucleosomal histone-DNA interactions and acts as a nucleosome barrier. Nucleic Acids Res. 1995;23:2184–2191. [PMC free article: PMC307006] [PubMed: 7610046]
Espinás ML, Jiménez-García E, Martínez-Balbás Á. et al. Formation of triple-stranded DNA at d(GA•TC)n sequences prevents nucleosome assembly and is hindered by nucleosomes. J Biol Chem. 1996;271:31807–31812. [PubMed: 8943221]
Battistoni A, Leoni L, Sampaolese B. et al. Kinetic persistence of cruciform structures in reconstituted minichromosomes. Biochim Biophys Acta. 1988;950:161–171. [PubMed: 2838086]
Nobile C, Nickol J, Martin RG. Nucleosome phasing on a DNA fragment from the replication origin of simian virus 40 and rephasing upon cruciform formation of the DNA. Mol Cell Biol. 1986;6:2916–2922. [PMC free article: PMC367860] [PubMed: 3023953]
Kotani H, Kmiec EB. DNA cruciforms facilitate in vitro strand transfer on nucleosomal templates. Mol Gen Genet. 1994;243:681–690. [PubMed: 8028585]
Zlatanova J. Histone H1 and the regulation of transcription of eukaryotic genes. Trends Biochem Sci. 1990;15: 273–276. [PubMed: 2098005]
Alami R, Fan Y, Pack S. et al. Mammalian linker-histone subtypes differentially affect gene expression in vivo. Proc Natl Acad Sci USA. 2003;100:5920–5925. [PMC free article: PMC156302] [PubMed: 12719535]
Yaneva J, Schroth GP, van Holde KE. et al. High-affinity binding sites for histone H1 in plasmid DNA. Proc Natl Acad Sci USA. 1995;92:7060–7064. [PMC free article: PMC41471] [PubMed: 7624369]
Copyright © 2000-2013, Landes Bioscience.
Bookshelf ID: NBK6060


  • PubReader
  • Print View
  • Cite this Page

Related information

  • PMC
    PubMed Central citations
  • PubMed
    Links to PubMed

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...