Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability

Čechová, Jana; Lýsek, Jiří; Bartas, Martin; Brázda, Václav

doi:10.1093/bioinformatics/btx729

Cited by 30 publications

(27 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…DNA cruciforms are formed by S-IRs and with their important roles in replication, transcription and DNA stability it is not surprising that S-IRs are also present in cpDNA genomes. Analyses of mtDNA genomes revealed that S-IR sequences are abundant and nonrandomly distributed in the mitochondrial genomes of all living organisms, with particular abundance in regulatory regions such as replication origin and D-loop region [ 12 ]. Here, we analyzed all available cpDNA genomes for the presence of S-IRs capable of forming cruciform structures.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

Brázda

Lýsek

Bartas

et al. 2018

BioMed Research International

Self Cite

View full text Add to dashboard Cite

Chloroplasts are key organelles in the management of oxygen in algae and plants and are therefore crucial for all living beings that consume oxygen. Chloroplasts typically contain a circular DNA molecule with nucleus-independent replication and heredity. Using “palindrome analyser” we performed complete analyses of short inverted repeats (S-IRs) in all chloroplast DNAs (cpDNAs) available from the NCBI genome database. Our results provide basic parameters of cpDNAs including comparative information on localization, frequency, and differences in S-IR presence. In a total of 2,565 cpDNA sequences available, the average frequency of S-IRs in cpDNA genomes is 45 S-IRs/per kbp, significantly higher than that found in mitochondrial DNA sequences. The frequency of S-IRs in cpDNAs generally decreased with S-IR length, but not for S-IRs 15, 22, 24, or 27 bp long, which are significantly more abundant than S-IRs with other lengths. These results point to the importance of specific S-IRs in cpDNA genomes. Moreover, comparison by Levenshtein distance of S-IR similarities showed that a limited number of S-IR sequences are shared in the majority of cpDNAs. S-IRs are not located randomly in cpDNAs, but are length-dependently enriched in specific locations, including the repeat region, stem, introns, and tRNA regions. The highest enrichment was found for 12 bp and longer S-IRs in the stem-loop region followed by 12 bp and longer S-IRs located before the repeat region. On the other hand, S-IRs are relatively rare in rRNA sequences and around introns. These data show nonrandom and conserved arrangements of S-IRs in chloroplast genomes.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Both chloroplasts and mitochondria retain their own genomes and transcription machinery. S-IRs in mitochondrial DNA (mtDNA) are located nonrandomly with high abundance in the replication origin, D-loop, and stem-loop sequences [ 12 ]. While mitochondria are present in all eukaryotes, chloroplasts are exclusive for algae and plants.…”

Section: Introductionmentioning

confidence: 99%

Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

Brázda

Lýsek

Bartas

et al. 2018

BioMed Research International

Self Cite

View full text Add to dashboard Cite

show abstract

“…Furthermore, several studies have demonstrated the important role of non-B-DNA structures in the context of gene regulation in bacteria [30,60,61]. For example, cruciforms have been shown to be important for dynamic genome organization [62], and for replication of the circular molecules of genomes, plasmids, mitochondrial DNAs [63], and chloroplast DNAs [64]. Cruciforms are targets for many architectural and regulatory proteins [10] and their importance has been demonstrated for the regulation of transcription of some genes [65].…”

Section: Biochemical and Cellular Impacts Of Simple Repeat Sequences mentioning

confidence: 99%

Structures and stability of simple DNA repeats from bacteria

Brázda

Fojta

Bowater

2020

Biochemical Journal

View full text Add to dashboard Cite

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

show abstract

“…First, Goios et al 2006 examined the human mitogenomes to identify the direct and inverted repeat sequences [40]. Second, the study of Čechová et al 2018, which identified variability in the number of mitochondrial inverted repeat sequences in plants and fungi compared with mammals [41]. Third, the database and software developed by Shamanskiy et al 2019 to identify degenerated direct and inverted repeat sequences in mitochondrial DNA [23].…”

Section: Introductionmentioning

confidence: 99%

Repetitive DNA profile of the amphibian mitogenome

et al. 2020

View full text Add to dashboard Cite

Background: Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians. Results: This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry. Conclusions: Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.

show abstract

Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability

Cited by 30 publications

References 29 publications

Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

Structures and stability of simple DNA repeats from bacteria

Repetitive DNA profile of the amphibian mitogenome

Contact Info

Product

Resources

About