Matej Lexa

Contrasting patterns of transposable element and satellite distribution on sex chromosomes (XY1Y2) in the dioecious plant Rumex acetosa.

Rumex acetosa is a dioecious plant with the XY1Y2 sex chromosome system. Both Y chromosomes are heterochromatic and are thought to be degenerated. We performed low-pass 454 sequencing and similarity-based clustering of male and female genomic 454 reads to identify and characterize major groups of R. acetosa repetitive DNA. We found that Copia and Gypsy retrotransposons dominated, followed by DNA transposons and nonlong terminal repeat retrotransposons. CRM and Tat/Ogre retrotransposons dominated the Gypsy superfamily, whereas Maximus/Sireviruses were most abundant among Copia retrotransposons. Only one Gypsy subfamily had accumulated on Y1 and Y2 chromosomes, whereas many retrotransposons were ubiquitous on autosomes and the X chromosome, but absent on Y1 and Y2 chromosomes, and others were depleted from the X chromosome. One group of CRM Gypsy was specifically localized to centromeres. We also found that majority of previously described satellites (RAYSI, RAYSII, RAYSIII, and RAE180) are accumulated on the Y chromosomes where we identified Y chromosome-specific variant of RAE180. We discovered two novel satellites—RA160 satellite dominating on the X chromosome and RA690 localized mostly on the Y1 chromosome. The expression pattern obtained from Illumina RNA sequencing showed that the expression of transposable elements is similar in leaves of both sexes and that satellites are also expressed. Contrasting patterns of transposable elements (TEs) and satellite localization on sex chromosomes in R. acetosa, where not only accumulation but also depletion of repetitive DNA was observed, suggest that a plethora of evolutionary processes can shape sex chromosomes.

RAP: a new computer program for de novo identification of repeated sequences in whole genomes

MOTIVATION DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design. Several efficient algorithms based on word counting are available, but too short words decrease specificity while long words decrease sensitivity, particularly in degenerated repeats. RESULTS The Repeat Analysis Program (RAP) is based on a new word-counting algorithm optimized for high resolution repeat identification using gapped words. Many different overlapping gapped words can be counted at the same genomic position, thus producing a better signal than the single ungapped word. This results in better specificity both in terms of low-frequency detection, being able to identify sequences repeated only once, and highly divergent detection, producing a generally high score in most intron sequences. AVAILABILITY The program is freely available for non-profit organizations, upon request to the authors. CONTACT giorgio.valle@unipd.it SUPPLEMENTARY INFORMATION The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analysis has been implemented in the UCSC Genome Browser and is accessible at http://genome.cribi.unipd.it.

PRIMEX: rapid identification of oligonucleotide matches in whole genomes

SUMMARY PRIMEX (PRImer Match EXtractor) can detect oligonucleotide sequences in whole genomes, allowing for mismatches. Using a word lookup table and server functionality, PRIMEX accepts queries from client software and returns matches rapidly. We find it faster and more sensitive than currently available tools. AVAILABILITY Running applications and source code have been made available at http://bioinformatics.cribi.unipd.it/primex

Preferential Binding of Hot Spot Mutant p53 Proteins to Supercoiled DNA In Vitro and in Cells

Hot spot mutant p53 (mutp53) proteins exert oncogenic gain-of-function activities. Binding of mutp53 to DNA is assumed to be involved in mutp53-mediated repression or activation of several mutp53 target genes. To investigate the importance of DNA topology on mutp53-DNA recognition in vitro and in cells, we analyzed the interaction of seven hot spot mutp53 proteins with topologically different DNA substrates (supercoiled, linear and relaxed) containing and/or lacking mutp53 binding sites (mutp53BS) using a variety of electrophoresis and immunoprecipitation based techniques. All seven hot spot mutp53 proteins (R175H, G245S, R248W, R249S, R273C, R273H and R282W) were found to have retained the ability of wild-type p53 to preferentially bind circular DNA at native negative superhelix density, while linear or relaxed circular DNA was a poor substrate. The preference of mutp53 proteins for supercoiled DNA (supercoil-selective binding) was further substantiated by competition experiments with linear DNA or relaxed DNA in vitro and ex vivo. Using chromatin immunoprecipitation, the preferential binding of mutp53 to a sc mutp53BS was detected also in cells. Furthermore, we have shown by luciferase reporter assay that the DNA topology influences p53 regulation of BAX and MSP/MST1 promoters. Possible modes of mutp53 binding to topologically constrained DNA substrates and their biological consequences are discussed.

A dynamic programming algorithm for identification of triplex-forming sequences

MOTIVATION Current methods for identification of potential triplex-forming sequences in genomes and similar sequence sets rely primarily on detecting homopurine and homopyrimidine tracts. Procedures capable of detecting sequences supporting imperfect, but structurally feasible intramolecular triplex structures are needed for better sequence analysis. RESULTS We modified an algorithm for detection of approximate palindromes, so as to account for the special nature of triplex DNA structures. From available literature, we conclude that approximate triplexes tolerate two classes of errors. One, analogical to mismatches in duplex DNA, involves nucleotides in triplets that do not readily form Hoogsteen bonds. The other class involves geometrically incompatible neighboring triplets hindering proper alignment of strands for optimal hydrogen bonding and stacking. We tested the statistical properties of the algorithm, as well as its correctness when confronted with known triplex sequences. The proposed algorithm satisfactorily detects sequences with intramolecular triplex-forming potential. Its complexity is directly comparable to palindrome searching. AVAILABILITY Our implementation of the algorithm is available at http://www.fi.muni.cz/lexa/triplex as source code and a web-based search tool. The source code compiles into a library providing searching capability to other programs, as well as into a stand-alone command-line application based on this library. CONTACT lexa@fi.muni.cz SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex-forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures—some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3′UTR (but were also present in 5′UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements.

Transposable elements and G-quadruplexes

A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.

Plant growth modelling and the integration of shoot and root activities without communicating messengers : Opinion

In this paper, we consider the use of compartmental modelling to examine the integration of root and shoot resource allocation without the use of partitioning functions or communicating messengers. Emphasing overall growth and the partitioning of biomass and resources between shoots and roots, we discuss the use of modelling to explore mechanisms of control, to direct experimentation and to test physiological hypotheses concerning their regulation. We discuss how the interrelationships of allocation processes and growth might be considered by generating “mutants” of a basic model, and we suggest this approach as one general way to increase interactions between modellers and experimentalists.Recognizing that the meristematic origin of plant organs inherently limits the usefulness of two compartment (root and shoot) models, we consider three problems to be solved (both computationally and experimentally) in extending modelling to more complex simulations: the incorporation of direct root/shoot signaling for regulation of the shoot-shoot ratio (S/R), the modelling of growth of individual leaves, and the definition of shoots based on component leaves and internodes. Finally, we briefly consider the problem of nitrogen and the regulation of S/R as an example of experimentation directed by modelling.

Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators

Transposable elements (TEs) are ubiquitous genome inhabitants in eukaryotes. Increasing evidence shows that TEs are involved in regulatory networks of eukaryotic cells and contribute to genome evolution. Recently, we reported that many plant long-terminal repeat (LTR) retrotransposons contain DNA quadruplex-forming sequences at precise positions inside their LTRs and that quadruplexes are better preserved in evolutionary younger elements. As quadruplexes can modulate molecular processes, quadruplexes found at specific distances upstream and downstream from the endogenous TE promoter can affect transcription of the element. Moreover, quadruplexes found in solo LTRs, as well as in 3′ ends of 5′-truncated copies of LINE-1 elements, can affect expression of neighboring genes. Here, we propose that this way retrotransposons can serve as vehicles for spread of DNA quadruplexes. Quadruplexes can thus fulfill a dual regulatory role—to influence both the retrotransposons carrying them and the neighboring host genes, e.g., by direct effect on transcription or by modifying the local chromatin state. Additionally, four-stranded DNA structures may serve as hotspots for recombination-based genome rearrangements.

Gas Exchange: Models and Measurements

In this chapter, we use mathematical models of C3, photosynthesis from the chloroplast to the leaf level to consider the relationships between photosynthetic capacity and performance. The differences must reflect regulation of chloroplast processes under the influence of environmental limitations. Thus, we examine the means by which models handle regulation of individual processes and identify five critical areas of uncertainty. These are: stomatal interactions, mesophyll conductance, Rubisco activation, ribulose 1,5-bisphosphate regeneration and photoprotection. Each is discussed both with regard to modeling efforts which have been made, and experimental results which are yet to be fully assimilated. In all five cases, control is clearly dynamic, not static, and we note several areas in which current methods of data interpretation insufficiently take this into account.