Palindrome analyser – A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences

Brázda, Václav; Kolomazník, Jan; Lýsek, Jiří; Hároníková, Lucia; Coufal, Jan; Šťastný, Jiří

doi:10.1016/j.bbrc.2016.09.015

Cited by 70 publications

(63 citation statements)

References 34 publications

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“…The same software was also used for file conversions (including the creation of the GenBank file) and to generate tables with comparative mitogenomic statistics (including the file used to visualise gene orders in iTOL). Palindromes in the CR were predicted using Palindrome analyser [53]. The mitogenome is available from the GenBank repository under the accession number MH396438.…”

Section: Methodsmentioning

confidence: 99%

The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade

et al. 2018

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As a result of great diversity in life histories and a large number of described species, taxonomic and phylogenetic uncertainty permeates the entire crustacean order of Isopoda. Large molecular datasets capable of providing sufficiently high phylogenetic resolution, such as mitochondrial genomes (mitogenomes), are needed to infer their evolutionary history with confidence, but isopod mitogenomes remain remarkably poorly represented in public databases. We sequenced the complete mitogenome of Cymothoa indica, a species belonging to a family from which no mitochondrial genome was sequenced yet, Cymothoidae. The mitogenome (circular, 14484 bp, A+T = 63.8%) is highly compact, appears to be missing two tRNA genes (trnI and trnE), and exhibits a unique gene order with a large number of rearrangements. High compactness and the existence of palindromes indicate that the mechanism behind these rearrangements might be associated with linearization events in its evolutionary history, similar to those proposed for isopods from the Armadillidium genus (Oniscidea). Isopods might present an important model system to study the proposed discontinuity in the dynamics of mitochondrial genomic architecture evolution. Phylogenetic analyses (Bayesian Inference and Maximum Likelihood) conducted using nucleotide sequences of all mitochondrial genes resolved Oniscidea and Cymothoida suborders as paraphyletic. Cymothoa indica was resolved as a sister group (basal) to all remaining isopods, which challenges the accepted isopod phylogeny, where Cymothoida are the most derived, and Phreatoicidea the most basal isopod group. There is growing evidence that Cymothoida suborder might be split into two evolutionary distant clades, with parasitic species being the most basal split in the Isopoda clade, but a much larger amount of molecular resources carrying a high phylogenetic resolution will be needed to infer the remarkably complex evolutionary history of this group of animals with confidence.

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Section: Methodsmentioning

confidence: 99%

The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade

et al. 2018

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“…In contrast, the two preceding studies did not provide any maps. Although a web-based server for detecting palindromes has recently become available (Brázda et al 2016), it does not provide a comprehensive map. Another notable methodological difference is the genome partitioning.…”

Section: Discussionmentioning

confidence: 99%

Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses

2018

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Inverted repeat (IR) sequences are DNA sequences that read the same from 5′ to 3′ in each strand. Some IRs can form cruciforms under the stress of negative supercoiling, and these IRs are widely found in genomes. However, their biological significance remains unclear. The aim of the current study is to explore this issue further. We constructed the first Escherichia coli genome-wide comprehensive map of IRs with cruciform-forming potential. Based on the map, we performed detailed and quantitative analyses. Here, we report that IRs with cruciform-forming potential are statistically enriched in the following five regions: the adjacent regions downstream of the stop codon-coding sites (referred to as the stop codons), on and around the positions corresponding to mRNA ends (referred to as the gene ends), ~ 20 to ~45 bp upstream of the start codon-coding sites (referred to as the start codons) within the 5′-UTR (untranslated region), ~ 25 to ~ 60 bp downstream of the start codons, and promoter regions. For the adjacent regions downstream of the stop codons and on and around the gene ends, most of the IRs with a repeat unit length of ≥ 8 bp and a spacer size of ≤ 8 bp were parts of the intrinsic terminators, regardless of the location, and presumably used for Rho-independent transcription termination. In contrast, fewer IRs were present in the small region preceding the start codons. In E. coli, IRs with cruciform-forming potential are actively placed or excluded in the regulatory regions for the initiation and termination of transcription and translation, indicating their deep involvement or influence in these processes.Electronic supplementary materialThe online version of this article (10.1007/s00294-018-0815-y) contains supplementary material, which is available to authorized users.

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“…The length of this repeat should be six or more nucleotides [14,15]. High non-random occurrences of these inverted repeats were detected in the proximity of breakpoint junctions, promoters and sites of replication initiation [10,16,17] and the probability of cruciform formation can be analyzed by several informatics tools [18,19]. Cruciforms have the ability to affect DNA supercoiling, positioning of nucleosomes in vivo and also the formation and stabilization of other secondary DNA structures [20].…”

Section: Introductionmentioning

confidence: 99%

Recognition of Local DNA Structures by p53 Protein

Brázda

Coufal

2017

IJMS

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p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.

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Palindrome analyser – A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences

Cited by 70 publications

References 34 publications

The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade

The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade

Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses

Recognition of Local DNA Structures by p53 Protein

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