Palindromic Symmetry Research Articles

Super-resolution imaging of linearized chromatin in tunable nanochannels.

Nanofluidic linearization and optical mapping of naked DNA have been reported in the research literature, and implemented in commercial instruments. However, the resolution with which DNA features can be resolved is still inherently limited by both Brownian motion and diffraction-limited optics. Direct analysis of native chromatin is further hampered by difficulty in electrophoretic manipulation, which is routinely used for DNA analysis. This paper describes the development of a three-layer, tunable, nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Furthermore, through careful selection of self-blinking fluorescent dyes and the design of the nanochannel system, we achieve direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging of the linearized chromatin. As an initial demonstration, rDNA chromatin extracted from Tetrahymena is analyzed by multi-color imaging of total DNA, newly synthesized DNA, and newly synthesized histone H3. Our analysis reveals a relatively even distribution of newly synthesized H3 across two halves of the rDNA chromatin with palindromic symmetry, supporting dispersive nucleosome segregation. As a proof-of-concept study, our work achieves super-resolution imaging of native chromatin fibers linearized and immobilized in tunable nanochannels. It opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.

Proper cyclic symmetries of multidimensional continued fractions

We show that palindromic continued fractions exist in an arbitrary dimension. For dimension $n=4$ we also prove a criterion for an algebraic continued fraction to have a proper cyclic palindromic symmetry. Klein polyhedra are considered as multidimensional generalizations of continued fractions. Bibliography: 11 titles.

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets.

In some dimeric cases of transcription factor (TF) binding, the specificity of dimeric motifs has been observed to differ notably from what would be expected were the two factors to bind to DNA independently of each other. Current motif discovery methods are unable to learn monomeric and dimeric motifs in modular fashion such that deviations from the expected motif would become explicit and the noise from dimeric occurrences would not corrupt monomeric models. We propose a novel modeling technique and an expectation maximization algorithm, implemented as software tool MODER, for discovering monomeric TF binding motifs and their dimeric combinations. Given training data and seeds for monomeric motifs, the algorithm learns in the same probabilistic framework a mixture model which represents monomeric motifs as standard position-specific probability matrices (PPMs), and dimeric motifs as pairs of monomeric PPMs, with associated orientation and spacing preferences. For dimers the model represents deviations from pure modular model of two independent monomers, thus making co-operative binding effects explicit. MODER can analyze in reasonable time tens of Mbps of training data. We validated the tool on HT-SELEX and ChIP-seq data. Our findings include some TFs whose expected model has palindromic symmetry but the observed model is directional.

A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea.

Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B1 biosynthesis and its transcriptional regulation in Archaea are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in Archaea and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with Metallosphaera spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of Archaea.

A generalized asymmetry model for square contingency tables with ordered categories

For square contingency tables with ordered categories, the present paper proposes an asymmetry model with m-additional parameters, which indicates (1) the generalized marginal homogeneity and (2) the structure of quasi-symmetry for cumulative probabilities. The proposed model includes a modified palindromic symmetry model by Iki, Oda and Tomizawa [7]. Also the present paper gives the decomposition of the symmetry model using the proposed model. Examples are given.

Decompositions of symmetry using extended palindromic symmetry models for square contingency tables

For square contingency tables with ordered categories, this paper gives the theorem that the symmetry model holds if and only if the following three models hold: (1) extended palindromic symmetry, (2) equality of marginal moments, and (3) subsymmetry of cumulative probabilities from the upper right and lower left corners of the table.

A Modified Palindromic Symmetry Model for Square Contingency Tables with Ordered Categories

For the analysis of square contingency tables with the same row and column ordinal classifications, McCullagh (1978) considered the palindromic symmetry (PS) model, which has a multiplicative form for cumulative probabilities that an observation will fall in row (column) category i or below and column (row) category j (> i) or above. The present paper proposes a modified PS model which indicates that (1) the symmetric odds for cumulative probabilities with distance 1 from main diagonal of the table are constant and (2) there is the structure of quasi-symmetry for them with distance k (≥ 2). Also the present paper gives the decomposition of the symmetry model using the proposed model. Examples are given.

Decomposition of Symmetry Using Palindromic Symmetry Model in a Two-Way Classification

For square contingency tables with ordered categories, we decompose the symmetry model into three models; i.e., the palindromic symmetry, the marginal means equality, and the cumulative subsymmetry models. The palindromic symmetry model is also decomposed into the generalized palindromic symmetry and the extended marginal homogeneity models. The decompositions are applied to the unaided vision data.

Protein assemblies with palindromic structure motifs.

Symmetric DNA sequence motifs allow the formation of palindromic protein/DNA complexes. Although symmetric protein sequence motifs are less common, recent structural discoveries have unraveled a few protein/protein complexes with palindromic symmetry. Remarkably, symmetric protein/protein complexes can be generated either by adjacent or remote sequence motifs, which may be repeated or inverted. This contribution reflects and comments on recent findings of palindromic protein/protein complexes.

Isospectral families of high‐order systems

AbstractEarlier work of the authors concerning the generation of isospectral families of second order (vibrating) systems is generalized to higher‐order systems (with no spectrum at infinity). Results and techniques are developed first for systems without symmetries, then with Hermitian symmetry and, finally, with palindromic symmetry. The construction of linearizations which retain such symmetries is discussed. In both cases, the notion of strictly isospectral families of systems is introduced – implying that properties of both the spectrum and the sign‐characteristic are preserved. Open questions remain in the case of strictly isospectral families of palindromic systems. Intimate connections between Hermitian and unitary systems are discussed in an Appendix.

Nothing: A User's Manual

In introducing this enigmatic topic, I often begin with a riddle that points to its elusive, mobile character: What is greater than God, more powerful than evil, the rich have it, the poor need it, and if you eat it, you die? -Nothing. In the multiple contexts in which I've navigated the topic of nothing (course, conference, collection of essays, special issue), it has proved a subject that provokes mirth, irony, and skepticism. When I have told colleagues that I'm teaching A Course About the responses I get range from Oh...it must have a short reading list, to Well, I'm going to teach my class now-at least it's about something, to Uhhuh or just Huh. (I have a slight preference for huh because it is linked to nothing through its palindromic symmetry (h-u-h), plus it is resolutely noncommittal; it says nothing.) And when I sent out a Call for Papers for this special several people thought it was a hoax; I received many responses that said, Dear Dr. Harris, please find below my submission for your journal issue, with the rest left blank. Still others wondered whether the topic of Nothing could lead to anything but more postmodern nihilism or empty intellectual solipsisms. Finally, on a pragmatic, pedagogical level, in setting out to investigate Nothing, one faces fundamental questions regarding both the utility and the futility of the topic. On the one hand, of what use could it be to pursue Nothing? And on the other, how can any search for it, any attempt to define or capture it, end up in anything but futility? While I have obviously not found definitive answers to these queries, I would maintain that a preliminary way of responding to them has emerged from teaching a class on Nothing. The use of Nothing lies in the simple fact that reading and thinking and talking about it leads down paths one would otherwise never traverse, and in following these lines of thought, one begins to develop a different way of thinking. This mode of reflection strives to avoid approaching Nothing from a standpoint grounded in the world of Being, where Presence and Something are presupposed to exist, and Nothing is seen as nothing but nonbeing. It is

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.

Interarm Interaction of DNA Cruciform Forming at a Short Inverted Repeat Sequence

A novel interarm interaction of DNA cruciform forming at inverted repeat sequence was characterized using an S1 nuclease digestion, permanganate oxidation, and microscopic imaging. An inverted repeat consisting of 17 bp complementary sequences was isolated from the bluegill sunfish Lepomis macrochirus (Perciformes) and subcloned into the pUC19 plasmid, after which the supercoiled recombinant plasmid was subjected to enzymatic and chemical modification. In high salt conditions (200 mM NaCl, or 100–200 mM KCl), S1 nuclease cut supercoiled DNA at the center of palindromic symmetry, suggesting the formation of DNA cruciform. On the other hand, S1 nuclease in the presence of 150 mM NaCl or less cleaved mainly the 3′-half of the repeat, thereby forming an unusual structure in which the 3′-half of the inverted repeat, but not the 5′-half, was retained as an unpaired strand. Permanganate oxidation profiles also supported the presence of single-stranded part in the 3′-half of the inverted repeat in addition to the center of the symmetry. Both electron microscopy and atomic force microscopy have detected a thick protrusion on the supercoiled DNA harboring the inverted repeat. We hypothesize that the cruciform hairpins at conditions favoring triplex formation adopt a parallel side-by-side orientation of the arms allowing the interaction between them supposedly stabilized by hydrogen bonding of base triads.

Sequence-Dependent DNA Curvature and Flexibility from Scanning Force Microscopy Images

This paper reports a study of the sequence-dependent DNA curvature and flexibility based on scanning force microscopy (SFM) images. We used a palindromic dimer of a 1878-bp pBR322 fragment and collected a large pool of SFM images. The curvature of each imaged chain was measured in modulus and direction. It was found that the ensemble curvature modulus does not allow the separation of static and dynamic contributions to the curvature, whereas the curvature, when its direction in the two dimensions is taken into account, permits the direct separation of the intrinsic curvature contributions static and dynamic contributions. The palindromic symmetry also acted as an internal gauge of the validity of the SFM images statistical analysis. DNA static curvature resulted in good agreement with the predicted sequence-dependent intrinsic curvature. Furthermore, DNA sequence-dependent flexibility was found to correlate with the occurrence of A·T-rich dinucleotide steps along the chain and, in general, with the normalized basepair stacking energy distribution.

Magnesium concentration effects on cruciform extrusion in supercoiled DNA examined by atomic force microscopy

Cruciform structures can form in DNA sequences with inverted repeats or palindromic symmetry under unwinding torsional stress. DNA repeats are widespread in the genomes of eukaryotes and prokaryotes, and their extrusion into cruciform structures may be involved in various genetic processes, including transcription and replication. Intracellular Mg 2+ may change the free energy of supercoiling to provide the driving force for cruciform extrusion. We have used atomic force microscopy (AFM) to image the effects of magnesium concentrations on cruciform extrusions in supercoiled DNA. Mg 2+ concentration dependent cruciform extrusions were observed in the supercoiled topoisomer of the pPR-PARP plasmid (〈 σ〉=−0.065). These data show an application of AFM imaging to demonstrate that the presence of Mg 2+ results in increased extrusions and promotes compact cruciform conformation.

Mapping the intrinsic curvature and flexibility along the DNA chain.

The energy of DNA deformation plays a crucial and active role in its packaging and its function in the cell. Considerable effort has gone into developing methodologies capable of evaluating the local sequence-directed curvature and flexibility of a DNA chain. These studies thus far have focused on DNA constructs expressly tailored either with anomalous flexibility or curvature tracts. Here we demonstrate that these two structural properties can be mapped also along the chain of a "natural" DNA with any sequence on the basis of its scanning force microscope (SFM) images. To know the orientation of the sequence of the investigated DNA molecules in their SFM images, we prepared a palindromic dimer of the long DNA molecule under study. The palindromic symmetry also acted as an internal gauge of the statistical significance of the analysis carried out on the SFM images of the dimer molecules. It was found that although the curvature modulus is not efficient in separating static and dynamic contributions to the curvature of the population of molecules, the curvature taken with its direction (its sign in two dimensions) permits the direct separation of the intrinsic curvature from the flexibility contributions. The sequence-dependent flexibility seems to vary monotonically with the chain's intrinsic curvature; the chain rigidity was found to modulate as its local thermodynamic stability and does not correlate with the dinucleotide chain rigidities evaluation made from x-ray data by other authors.

Loss of palindromic symmetry in Tg.AC mice with a nonresponder phenotype

The Tg.AC transgenic mouse carries the v-Ha-ras oncogene under the control of the ζ-globin promoter and is currently being used in a short-term carcinogenesis assay for safety testing of pharmaceuticals. A subset of hemizygous Tg.AC mice was found to be nonresponsive to the tumor promoter 12-O-tetradecanoylphorbol-13-acetate, which characteristically induces skin papillomas in these mice with repeated dermal applications. We previously showed that responder and nonresponder hemizygous Tg.AC mice carry about 40 copies of transgene but that the nonresponders had lost a 2-kb BamHI fragment containing the ζ-globin promoter sequence. The present restriction enzyme and S1 nuclease digestion experiments strongly suggested that the 2-kb BamHI fragment resulted from the orientation of two transgenes in an inverted repeat formation. Two subsets of nonresponder Tg.AC mice were identified. Restriction enzyme and S1 nuclease digestion experiments suggested that one nonresponder genotype was produced by a large deletion of one or more near complete copies of transgene sequence and the other genotype was produced by a small deletion near the apex of the “head-to-head” juncture of the inverted repeat. Polymerase chain reaction amplification, cloning, and sequencing results confirmed the palindromic orientation of transgene in Tg.AC mice. Our results indicated that, despite the presence of multiple copies of transgene in a direct repeat orientation, loss of symmetry in the palindromic array of transgene sequence results in the loss of the responder phenotype in Tg.AC mice. Mol. Carcinog. 30:99–110, 2001. Published 2001 Wiley-Liss, Inc.

Loss of palindromic symmetry in Tg.AC mice with a nonresponder phenotype

The Tg.AC transgenic mouse carries the v-Ha-ras oncogene under the control of the zeta-globin promoter and is currently being used in a short-term carcinogenesis assay for safety testing of pharmaceuticals. A subset of hemizygous Tg.AC mice was found to be nonresponsive to the tumor promoter 12-O-tetradecanoylphorbol-13-acetate, which characteristically induces skin papillomas in these mice with repeated dermal applications. We previously showed that responder and nonresponder hemizygous Tg.AC mice carry about 40 copies of transgene but that the nonresponders had lost a 2-kb BamHI fragment containing the zeta-globin promoter sequence. The present restriction enzyme and S1 nuclease digestion experiments strongly suggested that the 2-kb BamHI fragment resulted from the orientation of two transgenes in an inverted repeat formation. Two subsets of nonresponder Tg.AC mice were identified. Restriction enzyme and S1 nuclease digestion experiments suggested that one nonresponder genotype was produced by a large deletion of one or more near complete copies of transgene sequence and the other genotype was produced by a small deletion near the apex of the "head-to-head" juncture of the inverted repeat. Polymerase chain reaction amplification, cloning, and sequencing results confirmed the palindromic orientation of transgene in Tg.AC mice. Our results indicated that, despite the presence of multiple copies of transgene in a direct repeat orientation, loss of symmetry in the palindromic array of transgene sequence results in the loss of the responder phenotype in Tg.AC mice. Mol. Carcinog. 30:99-110, 2001. Published 2001 Wiley-Liss, Inc.

A novel palindromic triple-stranded structure formed by homopyrimidine dodecamer d-CTTCTCCTCTTC and homopurine hexamer d-GAAGAG.

We have carried out NMR and molecular mechanics studies on a complex formed when a palindromic homopyrimidine dodecamer (d-CTTCTCCTCTTC) and a homopurine hexamer (d-GAAGAG) are mixed in 1:1 molar ratio in aqueous solutions. Such studies unequivocally establish that two strands of each oligomer combine to form a triple-stranded DNA structure with a palindromic symmetry and with six T.A:T and six C+. G:C hydrogen-bonded base triads. The two purine strands are placed head to head, with their 3' ends facing each other in the center of the structure. One-half of each pyrimidine strand contains protonated and the other half contains non-protonated cytosines. The two half segments containing protonated cytosines are hydrogen bonded to each of the two purine hexamers through Hoogsteen T.A and C+.G base pairing. The segments containing non-protonated cytosines are involved in Watson-Crick (A:T and G:C) base pairing. This leads to a palindromic triplex with a C2-dyad symmetry with respect to the center of the structure. The complex is less stable at neutral pH, but the cytosines involved in Hoogsteen base pairing remain protonated even under these conditions. Molecular mechanics calculations using NMR constraints have provided a detailed three-dimensional structure of the complex. The entire stretches of purine, and the pyrimidine nucleotides have a conformation close to B-DNA.

Site-specific insertion of IS1301 and distribution in Neisseria meningitidis strains

The insertion element IS1301 has been shown to mediate capsule phase variation in Neisseria meningitidis found in N. serogroup B by reversible insertional inactivation of the siaA gene. We have determined the target site specificity of this element by cloning and sequencing the insertion sites of 12 identical IS1301 copies found in N. meningitidis B1940. A target consensus core of 5'-AYTAG-3' was identified, with the central TA being duplicated following insertion. Additional features around the target sites, including extended palindromic symmetry, stem-loop formation, and the high incidence of AT tracts, indicate that other factors, such as DNA secondary structure, are involved in target recognition. The left inverted repeat of an IS1016-like element acts as a hot spot for insertion, with one insertion element combination located upstream of their gene. According to further sequence analysis, we were able to place IS1301 in the IS5 subgroup within the IS4 family of elements. A survey of 135 Neisseria strains indicated the presence of IS1301 in 27.9 to 33.3% of N. meningitides serogroup B, C, and W135 strains and in 86.7% of serogroup Y strains. IS1301 did not occur in serogroup A strains, in Neisseria gonorrhoeae, or in apathogenic Neisseria spp.