Inverted Repeats in Viral Genomes

Spanò, M.; Lillo, Fabrizio; Miccichè, Salvatore; Mantegna, Rosario N.

doi:10.1142/s0219477505002550

Cited by 3 publications

(5 citation statements)

References 11 publications

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“…For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. Differently from our previous results reported in [13], we observe that the detected hairpin structures are preferentially located in the noncoding regions. Therefore an approach based on com-binatorial considerations such as the one of Ref.…”

Section: Discussioncontrasting

confidence: 99%

“…Therefore an approach based on com-binatorial considerations such as the one of Ref. [13] and a thermodynamically based approach like the present one lead to a different conclusion.…”

Section: Discussionmentioning

confidence: 75%

“…Hairpin structures have been investigated in quite different organims with a variety of methods. Examples of these studies can be found in Ref.s [5,6,7,8,9,10,11,12,13,14] In this paper we detect candidate RNA secondary structures which are characterized by a minimal value of the free energy of the strucure in the folded state. In a first investigation the free energy is estimated by using Mfold, which is a reference software for the estimation of the free energy of RNA secondary structures.…”

Section: Introductionmentioning

confidence: 99%

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Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

et al. 2008

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By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.

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Section: Discussioncontrasting

confidence: 99%

“…Therefore an approach based on com-binatorial considerations such as the one of Ref. [13] and a thermodynamically based approach like the present one lead to a different conclusion.…”

Section: Discussionmentioning

confidence: 75%

Section: Introductionmentioning

confidence: 99%

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Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

et al. 2008

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“…Inverted repeats are found in higher numbers in many viral genomes than is expected from a random occurrence of bases [ 46 ]. This is true for many different types of viruses, but we illustrate this using Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and adeno-associated viruses (AAV), which have single-stranded RNA and DNA genomes, respectively.…”

Section: Presence Of Inverted Repeats In Genomesmentioning

confidence: 99%

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids

Bowater

Bohálová

Brázda

2022

IJMS

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Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.

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“…DNA or RNA short sequences that may be associated to RNA secondary structures are present in genomes of different species of phages, viruses, bacteria and eukaryotes. Indication about the potential existence of RNA secondary structures can be inferred throughout the detection of short pair sequences having the characteristic of inverted repeats in the investigated genomes [10,11,12,13]. Also mirror repeats may have multiple biological roles.…”

Section: Introductionmentioning

confidence: 99%

Inverted and mirror repeats in model nucleotide sequences

Lillo

Spanò

2007

Phys. Rev. E

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We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and nonperfect repeats, i.e., repeats with mismatches and gaps. The considered sequence models are independent identically distributed (i.i.d.) sequences, Markov processes and long-range sequences. We show that the number of repeats in correlated sequences is significantly larger than in i.i.d. sequences and that this discrepancy increases exponentially with the repeat length for long-range sequences.

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Inverted Repeats in Viral Genomes

Cited by 3 publications

References 11 publications

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids

Inverted and mirror repeats in model nucleotide sequences

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