On the symmetries of multi-palindromic DNA sequences

There are several instances of multiple, overlapping palindromes in DNA sequences which have recently been reported. To ascertain the likelihood of specific biological function for these interdigitating symmetries it is necessary to calculate their probabilities of occurrence. While the probability of occurrence of a single palindrome in a random sequence is calculated in a straightforward fashion, the occurrence of overlapping palindromes is not so simply analyzed. In this paper a general method for handling multiple symmetries is presented. Several theorems concerning the constraints which overlapping symmetries place on each other are presented. A general result is that the probability of occurrence of a symmetry can be significantly enhanced by already existing symmetries. As examples of the theorems and methods developed, the lac operator, the lac CAP-binding site and a region of the λ left operator are examined. The occurrence of several overlapping symmetries appears to be fairly common in such sequences.     

Compositional Bias is a Major Determinant of the Distribution Pattern and Abundance of Palindromes in Drosophila melanogaster

Palindromic sequences are important DNA motifs related to gene regulation, DNA replication and recombination, and thus, investigating the evolutionary forces shaping the distribution pattern and abundance of palindromes in the genome is substantially important. In this article, we analyzed the abundance of palindromes in the genome, and then explored the possible effects of several genomic factors on the palindrome distribution and abundance in Drosophila melanogaster. Our results show that the palindrome abundance in D. melanogaster deviates from random expectation and the uneven distribution of palindromes across the genome is associated with local GC content, recombination rate, and coding exon density. Our data suggest that base composition is the major determinant of the distribution pattern and abundance of palindromes and the correlation between palindrome density and recombination is a side-product of the effect of compositional bias on the palindrome abundance.     

Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis

MOTIVATION: The importance of the various kinds of repetitive nucleotide sequences for the workings of bacterial DNA has been widely recognized. This work is concerned with the distribution of a particular group of repetitive sequences, the short-sequenced interrupted extragenic palindromes, on the genetic maps of Escherichia coli K-12, Haemophilus influenzae Rd and Neisseria meningitidis Z2491 and MC58. A tool has been developed based upon a statistical hypothesis test taking into account the markovian structure of random sequences in order to determine the non-random character of extragenic palindromes. RESULTS: Totals of 7631, 12904, 4722 and 5477 non-random short interrupted palindromes have been found on the E.coli, H.influenzae, and N.meningitidis serogroup A and serogroup B genomes, respectively. Their distribution patterns on the respective genomes vary according to the bacterial species considered. Based on their position on the genome, palindromes could be distinguished as those which integrate longer, repetitive sequences; those which stand in isolation, and still others are associated to specific genome sites. AVAILABILITY: The complete list of the observed palindromes is available at the site http://www/lncc.br/~atrv. CONTACT: atrv@lncc.br     

Species-specific Typing of DNA Based on Palindrome Frequency Patterns

DNA in its natural, double-stranded form may contain palindromes, sequences which read the same from either side because they are identical to their reverse complement on the sister strand. Short palindromes are underrepresented in all kinds of genomes. The frequency distribution of short palindromes exhibits more than twice the inter-species variance of non-palindromic sequences, which renders palindromes optimally suited for the typing of DNA. Here, we show that based on palindrome frequency, DNA sequences can be discriminated to the level of species of origin. By plotting the ratios of actual occurrence to expectancy, we generate palindrome frequency patterns that allow to cluster different sequences of the same genome and to assign plasmids, and in some cases even viruses to their respective host genomes. This finding will be of use in the growing field of metagenomics.     

Detection of periodic patterns in RNA sequences: the first encapsidated region of the TMV RNA

A method is developed to study the periodic properties of nucleotide sequences allowing the favoured pattern of the repeating unit, as well as the length and localization of this periodic segment to be determined simultaneously. The degree of periodicity is evaluated calculating the probabilities for random occurrence of the maximal deviations of the nucleotide composition in each phase, making use of the binomial formula.The nucleotide sequence of the tobacco mosaic virus (TMV) RNA responsible for recognition of the homologous protein (“assembly origin”, AO) (Zimmern & Butler, 1977) was investigated in order to find periodic regions of primary structure which might be essential in the recognition process. As a result the most periodic segments of the AO consisting of 31 and 17 nucleotides corresponding to the schemes GAU or GA1 have been found. However, the periodicities in these regions do not exceed that expected for random sequences. It can be considered as an evidence that in addition to peculiarities of primary structure, some other features such as RNA secondary or tertiary structure are essential in this interaction.For comparison the nucleotide sequences of the other fragments of TMV RNA as well as MS2 RNA, TYMV RNA, 16S rRNA and phage fd DNA were investigated by the same method.     

Letter: Filamentous bacterial viruses. X. X-ray diffraction studies of the R4-protein mutant

Eukaryotic DNA fragments that are totally denatured by alkali swiftly re-form duplex regions that are several hundred up to several thousand nucleotide pairs in length. A combination of sedimentation and electron microscopic studies demonstrate that they arise by the folding-back of a single linear chain, and not from cross-linking between the two complementary chains. Thus these “hairpin”-like structures must come from inverted repetitions of the type A B C t C′B′A′ that are located at intervals along the chromatid. Electron microscopic studies, reveal no unpaired single-chain regions in the “turn-around” t. The resistance of these hairpins to single-chain specific nucleases indicates that t must only consist of a few nucleotides. Therefore we call these regions in double-chain DNA palindromes, because, given the antiparallel arrangement of the polynucleotide chains, these sequences read the same both backwards and forwards. The thermal stability profile of these hairpins is nearly identical to that of sonicated duplex fragments of comparable length. Since these hairpins have the same average base composition as bulk DNA, the palindromes are nearly perfect. By studying the fraction of DNA retained on hydroxyapatite as a function of chain length, one may determine the distribution of palindromes along the DNA. These experiments are best explained by clusters of palindromes located at intervals of 10 to 80 /gm depending on the species. The presence of such long, well-matched palindromes suggests that the linear double helix may sometimes adopt an alternative configuration, the cruciform, in which mismatches that may occur are eliminated by excision and repair.     

Formation of large palindromic DNA by homologous recombination of short inverted repeat sequences in Saccharomyces cerevisiae

Large DNA palindromes form sporadically in many eukaryotic and prokaryotic genomes and are often associated with amplified genes. The presence of a short inverted repeat sequence near a DNA double-strand break has been implicated in the formation of large palindromes in a variety of organisms. Previously we have established that in Saccharomyces cerevisiae a linear DNA palindrome is efficiently formed from a single-copy circular plasmid when a DNA double-strand break is introduced next to a short inverted repeat sequence. In this study we address whether the linear palindromes form by an intermolecular reaction (that is, a reaction between two identical fragments in a head-to-head arrangement) or by an unusual intramolecular reaction, as it apparently does in other examples of palindrome formation. Our evidence supports a model in which palindromes are primarily formed by an intermolecular reaction involving homologous recombination of short inverted repeat sequences. We have also extended our investigation into the requirement for DNA double-strand break repair genes in palindrome formation. We have found that a deletion of the RAD52 gene significantly reduces palindrome formation by intermolecular recombination and that deletions of two other genes in the RAD52-epistasis group (RAD51 and MRE11) have little or no effect on palindrome formation. In addition, palindrome formation is dramatically reduced by a deletion of the nucleotide excision repair gene RAD1.     

The properties of sequences involved in insertion and deletion mutagenesis in rodents

We analyzed nucleotide sequences that were inserted to or deleted from genomic DNA during the divergence from common ancestor. The median length of these sequences is 3 nucleotides; they are enriched with palindromes and often repeat in adjacent DNA.     

A family of repetitive palindromic sequences found in Neurospora mitochondrial DNA is also found in a mitochondrial plasmid DNA

Neurospora mtDNA contains a repetitive, 18 nucleotide palindromic sequence (5'-CCCTGCAGTACTGCAGGG-3') that contains two closely spaced PstI sites (CTGCAG) in the arms of the palindrome (Yin, S., Heckman, J., and RajBhandary, U. L. (1981) Cell 26, 325-332). In the present study, DNA sequence analysis was carried out to determine whether PstI palindromes are present in an apparently distinct genetic element, the 3.6-kilobase mitochondrial plasmid from Neurospora crassa strain Mauriceville-1c (FGSC 2225). The plasmid contains a cluster of closely spaced PstI sites extending over a 0.4-kilobase region (Collins, R. A., Stohl, L. L., Cole, M. D., and Lambowitz, A. M. (1981) Cell 24, 443-452). The DNA sequence shows that the cluster consists of eight PstI sites organized in five palindromic elements. Two of the elements are identical with the canonical sequence found in mtDNA, whereas the remaining three elements differ from the canonical sequence by a few nucleotides. The occurrence of the PstI palindromes in two otherwise unrelated DNA species is consistent with the hypothesis that they are related to mobile DNA sequences that either propagate or were once capable of propagating within mitochondria.     

Assessing Diversity of DNA Structure-Related Sequence Features in Prokaryotic Genomes

Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the DNA molecule. We present a survey of local sequence patterns which have a potential to promote non-canonical DNA conformations (i.e. different from standard B-DNA double helix) and interpret the results in terms of relationships with organisms'' habitats, phylogenetic classifications, and other characteristics. Our present work differs from earlier similar surveys not only by investigating a wider range of sequence patterns in a large number of genomes but also by using a more realistic null model to assess significant deviations. Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented. Representation of patterns that promote Z-DNA and intrinsic DNA curvature increases with increasing optimal growth temperature (OGT), and decreases with increasing oxygen requirement. Additionally, representations of close direct repeats, palindromes and inverted repeats exhibit clear negative trends with increasing OGT. The observed relationships with environmental characteristics, particularly OGT, suggest possible evolutionary scenarios of structural adaptation of DNA to particular environmental niches.     

Singular over-representation of an octameric palindrome, HIP1, in DNA from many cyanobacteria.

An octameric palindrome (5'-GCGATCGC-3') is abundant in cyanobacterial sequences within databases (GenBank/EMBL) and was designated HIP1 (highly iterated palindrome). The frequency of occurrence of all 256 octameric palindromes has now been determined in sub-databases revealing large and unique over-representation of HIP1 in cyanobacterial entries. DNA sequences from other bacteria were searched for any over-represented octameric palindromes analogous to HIP1. Only two sequences were identified, in the genomes of a thermophile and halophilic archaebacteria, although these were less abundant than HIP1 in cyanobacteria and relate to codon usage. To test the proposed widespread distribution of HIP1 in DNA from the cyanobacterium Synechococcus PCC 6301, randomly selected genomic clones were partly sequenced. HIP1 constituted 2.5% of the novel sequences, equivalent to a site on average once every 320 nucleotides. An oligonucleotide including HIP1 was also tested in PCR. Multiple products were obtained using template DNA from cyanobacterial strains in which HIP1 is abundant in known sequences, and some strains generated characteristic HIP-PCR banding patterns. However, analysis of DNA from one strain (not previously represented in databases) by random sequencing, HIP-PCR and Pvul digestion, confirms that not all cyanobacterial genomes are rich in HIP1.     

Wavelet Analysis of DNA Walks on the Human and Chimpanzee MAGE/CSAG-palindromes

The palindrome is one class of symmetrical duplications with reverse complementary characters,which is widely distributed in many organisms.Graphical representation of DNA sequence provides a simple way of viewing and comparing various genomic structures.Through 3-D DNA walk analysis,the similarity and differences in nucleotide composition,as well as the evolutionary relationship between human and chimpanzee MAGE/CSAG-palindromes,can be clearly revealed.Further wavelet analysis indicated that duplicated segments have irregular patterns compared to their surrounding sequences.However,sequence similarity analysis suggests that there is possible common ancestor between human and chimpanzee MAGE/CSAG-palindromes.Based on the specific distribution and orientation of the repeated sequences,a simple possible evolutionary model of the palindromes is suggested,which may help us to better understand the evolutionary course of the genes and the symmetrical sequences.     

Ecological correlates of the spatial co‐occurrence of sympatric mammalian carnivores worldwide

The composition of local mammalian carnivore communities has far‐reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108 087 trap days across 12 countries spanning five continents. We estimate local probabilities of co‐occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co‐occurrence. Within individual study areas, species pairs co‐occurred more frequently than expected at random. Co‐occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co‐occurrence decreased as compared to other species pairs when the pair included a large‐bodied carnivore. Our results suggest that a combination of shared traits and top‐down regulation by large carnivores shape local carnivore communities globally.     

Junctions between repetitive DNAs on the PSR chromosome of Nasonia vitripennis: Association of palindromes with recombination

The Paternal-Sex-Ratio (PSR) chromosome of Nasonia vitripennis contains several families of repetitive DNAs that show significant sequence divergence but share two palindromic regions. This study reports on the analysis of junctions between two of these repetitive DNA families (psr2 and psr18). Three lambda clones that hybridized to both repeat families were isolated from PSR-genomic DNA libraries through multiple screenings and analyzed by Southern blots. Analysis of clones showed a region in which the two repeat types are interspersed, flanked by uniform blocks of each repeat type. PCR amplification of genomic DNA confirmed the contiguous arrangement of psr2 and psr18 on PSR and identified an additional junction region between these repeats that was not present in the lambda inserts. We isolated and sequenced 41 clones from the lambda inserts and genomic PCR products containing junction sequences. Sequence analysis showed that all transitions between psr2 and psr18 repeats occurred near one of the two palindromes. Based on the inheritance pattern of PSR, recombination between repeats on this chromosome must be mitotic (rather than meiotic) in origin. The occurrence of exchanges near the palindromes suggests that these sequences enhance recombination between repeat units. Rapid amplification of repetitive DNA may have been an important factor in the evolution of the PSR chromosome. Correspondence to: John H. Werren     

Large DNA palindromes as a common form of structural chromosome aberrations in human cancers

Breakage-fusion-bridge cycles contribute to chromosome aberrations and generate large DNA palindromes that facilitate oncogene amplification in cancer cells. At the molecular level, large DNA palindrome formation is initiated by chromosome breaks, and genomic architecture such as short inverted repeat sequences facilitates this process in mammalian cells. However, the prevalence of DNA palindromes in cancer cells is currently unknown. To determine the prevalence of DNA palindromes in human cancer cells, we have developed a new microarray-based approach called Genome-wide Analysis of Palindrome Formation (GAPF, Tanaka et al., Nat Genet 2005; 37: 320-7). This approach is based on a relatively simple and efficient method to purify "snap-back DNA" from large DNA palindromes by intramolecular base-pairing, followed by elimination of single-stranded DNA by nuclease S1. Comparison of Genome-wide Analysis of Palindrome Formation profiles between cancer and normal cells using microarray can identify genome-wide distributions of somatic palindromes. Using a human cDNA microarray, we have shown that DNA palindromes occur frequently in human cancer cell lines and primary medulloblastomas. Significant overlap of the loci containing DNA palindromes between Colo320DM and MCF7 cancer cell lines suggests regions in the genome susceptible to chromosome breaks and palindrome formation. A subset of loci containing palindromes is associated with gene amplification in Colo320DM, indicating that the location of palindromes in the cancer genome serves as a structural platform that supports subsequent gene amplification.     

The distribution of the frequency of occurrence of nucleotide subsequences, based on their overlap capability

DNA's genetic code can be represented as an alphabetic sequence composed of the four letters A, C, G, and T, which represent the four types of nucleotides--adenylic, cytidylic, guanylic, and thymidylic acid--of which DNA is composed. Now that these sequences have been identified for many genes and are available in computer-readable form, scientists can analyze these data and search for patterns in an attempt to learn more about the regulatory functions of the gene. One area of study is that of the frequency of occurrence of specific nucleotide subsequences (e.g., ACAC) within part or all of a nucleotide sequence. This paper derives the probability distribution of the frequency of occurrence of a subsequence within a nucleotide sequence, under the hypothesis that the four nucleotides occur at random and with equal probability. This distribution is nontrivial because different subsequences have different "overlap capability." For example, the subsequence AAAA can occur up to 17 times in a sequence of length 20 (which would happen if the sequence were composed solely of A's), but the subsequence ACGT cannot occur more than 5 times in a sequence of length 20. Thus, the frequency distributions are different for each type of overlap capability. It is of interest to assess and compare the degree of nonrandomness for different subsequences or among different portions of a sequence; the existence and degree of nonrandomness may be related to the type and degree of functionality of a nucleotide (sub)sequence. The frequency distributions provided here can be used to perform exact significance tests of the hypothesis of randomness. An approximate test is also described for use with long sequences; this can be used to test a more general null hypothesis of nucleotides occurring with unequal probabilities.     

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes,comparing genes and pseudogenes

Based on searches for disabled homologs to known proteins, we have identified a large population of pseudogenes in four sequenced eukaryotic genomes—the worm, yeast, fly and human (chromosomes 21 and 22 only). Each of our nearly 2500 pseudogenes is characterized by one or more disablements mid-domain, such as premature stops and frameshifts. Here, we perform a comprehensive survey of the amino acid and nucleotide composition of these pseudogenes in comparison to that of functional genes and intergenic DNA. We show that pseudogenes invariably have an amino acid composition intermediate between genes and translated intergenic DNA. Although the degree of intermediacy varies among the four organisms, in all cases, it is most evident for amino acid types that differ most in occurrence between genes and intergenic regions. The same intermediacy also applies to codon frequencies, especially in the worm and human. Moreover, the intermediate composition of pseudogenes applies even though the composition of the genes in the four organisms is markedly different, showing a strong correlation with the overall A/T content of the genomic sequence. Pseudogenes can be divided into ‘ancient’ and ‘modern’ subsets, based on the level of sequence identity with their closest matching homolog (within the same genome). Modern pseudogenes usually have a much closer sequence composition to genes than ancient pseudogenes. Collectively, our results indicate that the composition of pseudogenes that are under no selective constraints progressively drifts from that of coding DNA towards non-coding DNA. Therefore, we propose that the degree to which pseudogenes approach a random sequence composition may be useful in dating different sets of pseudogenes, as well as to assess the rate at which intergenic DNA accumulates mutations. Our compositional analyses with the interactive viewer are available over the web at http://genecensus.org/pseudogene.     

Structure and distribution of inverted repeats (palindromes)

The size and distribution of renatured inverted repeats (palindromes) in D. melanogaster DNA were studied by electron microscopy (EM). The results of these studies differ from the previously published observations regarding the number, distribution and the size of inverted repeats (ir) present in DNA. -1. In contrast to the previous published observation almost all (96%) of the ir were found in crowded clusters. The DNA strands with clustered palindromes contained 2-21 palindromes (4-42 ir), with an average of 7.25 palindromes (14.5 ir) per strand. No correlation could be found between the length of the DNA strands and the number of ir per strand. -2, Also contrary to some previously published results, most (80%) of the ir formed on renaturation unlooped palindromes and these were always clustered. Looped palindromes (hairpins, formed by renaturation of ir separated by a non-homologous sequence long enough to be seen in EM as single-stranded loop) were found 1-2 per DNA strand, as part of clusters or as solitary palindromes in a DNA strand. The average spacing length (inside clusters) between centers of all palindromes was 2.349 kb, and between centers of looped palindromes 7.6 kb. - 3. The length of the ir was found to be smaller than documented in most of the previously published results. The majority, 80-90%, of the ir found in the unlooped and looped palindromes, respectively, belonged to one main-size class with a range of 30-210 bp and an average length of 100 bp, but longer ir were also observed. The average length of the ir in unlooped palindromes was 124 bp, in looped 244 bp, and the total average was 148 bp - 4. It was calculated that there are about 30,000 palindromes (60,000 ir) in the D, melanogaster genome, of which about 24,000 are unlooped and 6,000 looped, with the spacing between centers of all palindromes averaging about 4.4 kb in length.