MREPATT: detection and analysis of exact consecutive repeats in genomic sequences

Roset, Roman; Subirana, Juan A.; Messeguer, Xavier

doi:10.1093/bioinformatics/btg326

Cited by 13 publications

(8 citation statements)

References 16 publications

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“…These results clearly indicate that probe TC preferentially bound to the AT-rich genome of the parasite at very low concentrations. Collectively, these results suggest the selectivity of probe TC for AT-base pairs in dsDNA, fidelity to DNA over RNA and protein, non-toxicity, and preferential staining of malarial parasites in human erythrocytes, indicating that probe TC is a useful diagnostic and possibly therapeutic, red-fluorescence biomarker for AT-rich genomes4849.…”

Section: Resultsmentioning

confidence: 86%

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

Narayanaswamy

Kumar

Das

et al. 2014

Sci Rep

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Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based thiazole coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-activated cell sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology.

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Section: Resultsmentioning

confidence: 86%

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

Narayanaswamy

Kumar

Das

et al. 2014

Sci Rep

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“…Repetitive sequences were analyzed with the programs MREPATT [28] and CONREPP [11]. A new program (SATFIND) was also developed in order to determine the position of long tandem repeats (satellites).…”

Section: Methodsmentioning

confidence: 99%

A Satellite Explosion in the Genome of Holocentric Nematodes

Subirana

Messeguer

2013

PLoS ONE

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Centromere sequences in the genome are associated with the formation of kinetochores, where spindle microtubules grow in mitosis. Centromere sequences usually have long tandem repeats (satellites). In holocentric nematodes it is not clear how kinetochores are formed during mitosis; they are distributed throughout the chromosomes. For this reason it appeared of interest to study the satellites in nematodes in order to determine if they offer any clue on how kinetochores are assembled in these species. We have studied the satellites in the genome of six nematode species. We found that the presence of satellites depends on whether the nematode chromosomes are holocentric or monocentric. It turns out that holocentric nematodes are unique because they have a large number of satellites scattered throughout their genome. Their number, length and composition are different in each species: they apparently have very little evolutionary conservation. In contrast, no scattered satellites are found in the monocentric nematode Trichinella spiralis. It appears that the absence/presence of scattered satellites in the genome distinguishes monocentric from holocentric nematodes. We conclude that the presence of satellites is related to the holocentric nature of the chromosomes of most nematodes. Satellites may stabilize a higher order structure of chromatin and facilitate the formation of kinetochores. We also present a new program, SATFIND, which is suited to find satellite sequences.

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“…This program has been described elsewhere (8) and is freely available at our website (http://alggen.lsi.upc.edu). It works with genome sequences already stored in our website or introduced by the user.…”

Section: Methodsmentioning

confidence: 99%

The most frequent short sequences in non-coding DNA

Subirana

Messeguer

2009

Nucleic Acids Research

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The purpose of this work is to determine the most frequent short sequences in non-coding DNA. They may play a role in maintaining the structure and function of eukaryotic chromosomes. We present a simple method for the detection and analysis of such sequences in several genomes, including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. We also study two chromosomes of man and mouse with a length similar to the whole genomes of the other species. We provide a list of the most common sequences of 9–14 bases in each genome. As expected, they are present in human Alu sequences. Our programs may also give a graph and a list of their position in the genome. Detection of clusters is also possible. In most cases, these sequences contain few alternating regions. Their intrinsic structure and their influence on nucleosome formation are not known. In particular, we have found new features of short sequences in C. elegans, which are distributed in heterogeneous clusters. They appear as punctuation marks in the chromosomes. Such clusters are not found in either A. thaliana or D. melanogaster. We discuss the possibility that they play a role in centromere function and homolog recognition in meiosis.

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MREPATT: detection and analysis of exact consecutive repeats in genomic sequences

Abstract: MREPATT can be accessed on line at http://www.lsi.upc.es/~alggen under the RESEARCH and SEARCH links.

Cited by 13 publications

References 16 publications

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

A Satellite Explosion in the Genome of Holocentric Nematodes

The most frequent short sequences in non-coding DNA

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