The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

Strawbridge, Eva; Benson, Gary; Gelfand, Yevgeniy; Benham, Craig J.

doi:10.1007/s00294-010-0302-6

Cited by 28 publications

(31 citation statements)

References 69 publications

(109 reference statements)

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“…For example, genome-wide bioinformatics surveys have shown that G-quadruplex motifs are conserved across different eukaryotic organisms and enriched in gene promoter regions (25–33). In certain eukaryotes, cruciform sequences are enriched in intergenic regions and are closely clustered at the 3′-ends of genes (34), whereas Z-DNA motifs have been found near their 5′-end (35,36). Importantly, the occurrence of a motif does not imply that the structure has to form in vivo , and in addition, some motifs (cruciform, G-quadruplex) may correspond to formation of structures in mRNA rather than in DNA.…”

Section: Introductionmentioning

confidence: 99%

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli

Wójtowicz

Bowers

et al. 2013

Nucleic Acids Research

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Although the right-handed double helical B-form DNA is most common under physiological conditions, DNA is dynamic and can adopt a number of alternative structures, such as the four-stranded G-quadruplex, left-handed Z-DNA, cruciform and others. Active transcription necessitates strand separation and can induce such non-canonical forms at susceptible genomic sequences. Therefore, it has been speculated that these non-B DNA motifs can play regulatory roles in gene transcription. Such conjecture has been supported in higher eukaryotes by direct studies of several individual genes, as well as a number of large-scale analyses. However, the role of non-B DNA structures in many lower organisms, in particular proteobacteria, remains poorly understood and incompletely documented. In this study, we performed the first comprehensive study of the occurrence of B DNA–non-B DNA transition-susceptible sites (non-B DNA motifs) within the context of the operon structure of the Escherichia coli genome. We compared the distributions of non-B DNA motifs in the regulatory regions of operons with those from internal regions. We found an enrichment of some non-B DNA motifs in regulatory regions, and we show that this enrichment cannot be simply explained by base composition bias in these regions. We also showed that the distribution of several non-B DNA motifs within intergenic regions separating divergently oriented operons differs from the distribution found between convergent ones. In particular, we found a strong enrichment of cruciforms in the termination region of operons; this enrichment was observed for operons with Rho-dependent, as well as Rho-independent terminators. Finally, a preference for some non-B DNA motifs was observed near transcription factor-binding sites. Overall, the conspicuous enrichment of transition-susceptible sites in these specific regulatory regions suggests that non-B DNA structures may have roles in the transcriptional regulation of specific operons within the E. coli genome.

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Section: Introductionmentioning

confidence: 99%

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli

Wójtowicz

Bowers

et al. 2013

Nucleic Acids Research

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“…The sequence randomization was performed by the method of Strawbridge et al (2010). Briefly, the nucleotides in the coding regions were collected together and then distributed randomly within all of the coding regions of the genome.…”

Section: Methodsmentioning

confidence: 99%

“…Genome-wide analyses can provide powerful clues toward clarifying the reasons for the existence of IRs with cruciform-forming potential. However, such studies have been limited, and the conclusions almost stay at the stage reporting the regional abundance of these IRs (Lillo et al 2002; Ladoukakis and Eyre-Walker 2008; Strawbridge et al 2010; Du et al 2013). To understand the implications of IRs with cruciform-forming potential in biological functions, more detailed analyses are required.…”

Section: Introductionmentioning

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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“…Inverted repeats are significantly enriched in eukaryotic genomes, suggesting that they are functionally important. 43,62,63 The majority of human inverted repeats are derived from SINEs. 43 These elements should therefore provide the most attractive structural models of mammalian pre-mRNA splicing, alleviating uncertainties in accuracy of RNA secondary structure predictions encountered with typical pre-mRNAs.…”

Section: Discussionmentioning

confidence: 99%

The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat

et al. 2015

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Splice-site selection is controlled by secondary structure through sequestration or approximation of splicing signals in primary transcripts but the exact role of even the simplest and most prevalent structural motifs in exon recognition remains poorly understood. Here we took advantage of a single-hairpin exon that was activated in a mammalian-wide interspersed repeat (MIR) by a mutation stabilizing a terminal triloop, with splice sites positioned close to each other in a lower stem of the hairpin. We first show that the MIR exon inclusion in mRNA correlated inversely with hairpin stabilities. Employing a systematic manipulation of unpaired regions without altering splice-site configuration, we demonstrate a high correlation between exon inclusion of terminal tri-and tetraloop mutants and matching tri-/ tetramers in splicing silencers/enhancers. Loop-specific exon inclusion levels and enhancer/silencer associations were preserved across primate cell lines, in 4 hybrid transcripts and also in the context of a distinct stem, but only if its loopclosing base pairs were shared with the MIR hairpin. Unlike terminal loops, splicing activities of internal loop mutants were predicted by their intramolecular Watson-Crick interactions with the antiparallel strand of the MIR hairpin rather than by frequencies of corresponding trinucleotides in splicing silencers/enhancers. We also show that splicing outcome of oligonucleotides targeting the MIR exon depend on the identity of the triloop adjacent to their antisense target. Finally, we identify proteins regulating MIR exon recognition and reveal a distinct requirement of adjacent exons for C-terminal extensions of Tra2a and Tra2b RNA recognition motifs.

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The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

Cited by 28 publications

References 69 publications

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli

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

The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat

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