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Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties.

Masoudi-Nejad A, Movahedi S, Jáuregui R - BMC Genomics (2011)

Bottom Line: By analyzing tandem repeats across the genome, we found that frequencies of repeats are higher in regions adjacent to those with high curvature value.Each CpG island appears in a local minimal curvature region, and CpG islands usually do not appear in the centromere or regions with high repeat frequency.This study represents the first systematic genome-scale analysis of DNA curvature, CpG islands and tandem repeats at the DNA sequence level in plant genomes, and finds that not all of the chromosomes in plants follow the same rules common to other eukaryote organisms, suggesting that some of these genomic properties might be considered as specific to plants.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics and COE in Biomathematics, University of Tehran, Iran. amasoudin@ibb.ut.ac.ir

ABSTRACT

Background: Due to its overarching role in genome function, sequence-dependent DNA curvature continues to attract great attention. The DNA double helix is not a rigid cylinder, but presents both curvature and flexibility in different regions, depending on the sequence. More in depth knowledge of the various orders of complexity of genomic DNA structure has allowed the design of sophisticated bioinformatics tools for its analysis and manipulation, which, in turn, have yielded a better understanding of the genome itself. Curved DNA is involved in many biologically important processes, such as transcription initiation and termination, recombination, DNA replication, and nucleosome positioning. CpG islands and tandem repeats also play significant roles in the dynamics and evolution of genomes.

Results: In this study, we analyzed the relationship between these three structural features within rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genomes. A genome-scale prediction of curvature distribution in rice and Arabidopsis indicated that most of the chromosomes of both genomes have maximal chromosomal DNA curvature adjacent to the centromeric region. By analyzing tandem repeats across the genome, we found that frequencies of repeats are higher in regions adjacent to those with high curvature value. Further analysis of CpG islands shows a clear interdependence between curvature value, repeat frequencies and CpG islands. Each CpG island appears in a local minimal curvature region, and CpG islands usually do not appear in the centromere or regions with high repeat frequency. A statistical evaluation demonstrates the significance and non-randomness of these features.

Conclusions: This study represents the first systematic genome-scale analysis of DNA curvature, CpG islands and tandem repeats at the DNA sequence level in plant genomes, and finds that not all of the chromosomes in plants follow the same rules common to other eukaryote organisms, suggesting that some of these genomic properties might be considered as specific to plants.

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Joint plot of curvature and CpG islands. Most CpG islands occur in regions with minimal curvature values. In centromeric regions, where curvature usually has its highest value, CpG islands disappear. The plot shows Arabidopsis chromosome 1 (top) and rice chromosome 9 (bottom).
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Figure 4: Joint plot of curvature and CpG islands. Most CpG islands occur in regions with minimal curvature values. In centromeric regions, where curvature usually has its highest value, CpG islands disappear. The plot shows Arabidopsis chromosome 1 (top) and rice chromosome 9 (bottom).

Mentions: Figure 4 shows a combined-plot of curvature and CpG islands for Arabidopsis chromosome 1 and rice chromosome 9. The plot shows a clear relationship between curvature and CpG islands, since most CpG islands occur in regions with minimal curvature value (MinCV). This behavior is consistently present in the majority of chromosomes of both genomes and concurrently in centromeric regions, where curvature usually has its highest value and where CpG islands are scarce. It has been shown that GC content impacts the structure of the DNA molecule and that curved regions tend to appear in GC poor regions [5], but GC content is not sufficient to determine the curvature profile of a DNA molecule. Since the curvature depends on the cumulative effects of the sequence in a long DNA region, it is possible to obtain two DNA fragments with exactly the same GC content but completely different curvature profiles, depending on the order on which the nucleotides appear. The evaluation of both CpG islands and curvature profile of second and third order Markov-chain permutations of chromosomes from Arabidopsis and Rice showed that the presence of both CpG islands and highly curved regions are non -random events that depend directly on the sequence order (see additional file 2 "Markov-plots", figures S1 and S2).


Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties.

Masoudi-Nejad A, Movahedi S, Jáuregui R - BMC Genomics (2011)

Joint plot of curvature and CpG islands. Most CpG islands occur in regions with minimal curvature values. In centromeric regions, where curvature usually has its highest value, CpG islands disappear. The plot shows Arabidopsis chromosome 1 (top) and rice chromosome 9 (bottom).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113785&req=5

Figure 4: Joint plot of curvature and CpG islands. Most CpG islands occur in regions with minimal curvature values. In centromeric regions, where curvature usually has its highest value, CpG islands disappear. The plot shows Arabidopsis chromosome 1 (top) and rice chromosome 9 (bottom).
Mentions: Figure 4 shows a combined-plot of curvature and CpG islands for Arabidopsis chromosome 1 and rice chromosome 9. The plot shows a clear relationship between curvature and CpG islands, since most CpG islands occur in regions with minimal curvature value (MinCV). This behavior is consistently present in the majority of chromosomes of both genomes and concurrently in centromeric regions, where curvature usually has its highest value and where CpG islands are scarce. It has been shown that GC content impacts the structure of the DNA molecule and that curved regions tend to appear in GC poor regions [5], but GC content is not sufficient to determine the curvature profile of a DNA molecule. Since the curvature depends on the cumulative effects of the sequence in a long DNA region, it is possible to obtain two DNA fragments with exactly the same GC content but completely different curvature profiles, depending on the order on which the nucleotides appear. The evaluation of both CpG islands and curvature profile of second and third order Markov-chain permutations of chromosomes from Arabidopsis and Rice showed that the presence of both CpG islands and highly curved regions are non -random events that depend directly on the sequence order (see additional file 2 "Markov-plots", figures S1 and S2).

Bottom Line: By analyzing tandem repeats across the genome, we found that frequencies of repeats are higher in regions adjacent to those with high curvature value.Each CpG island appears in a local minimal curvature region, and CpG islands usually do not appear in the centromere or regions with high repeat frequency.This study represents the first systematic genome-scale analysis of DNA curvature, CpG islands and tandem repeats at the DNA sequence level in plant genomes, and finds that not all of the chromosomes in plants follow the same rules common to other eukaryote organisms, suggesting that some of these genomic properties might be considered as specific to plants.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics and COE in Biomathematics, University of Tehran, Iran. amasoudin@ibb.ut.ac.ir

ABSTRACT

Background: Due to its overarching role in genome function, sequence-dependent DNA curvature continues to attract great attention. The DNA double helix is not a rigid cylinder, but presents both curvature and flexibility in different regions, depending on the sequence. More in depth knowledge of the various orders of complexity of genomic DNA structure has allowed the design of sophisticated bioinformatics tools for its analysis and manipulation, which, in turn, have yielded a better understanding of the genome itself. Curved DNA is involved in many biologically important processes, such as transcription initiation and termination, recombination, DNA replication, and nucleosome positioning. CpG islands and tandem repeats also play significant roles in the dynamics and evolution of genomes.

Results: In this study, we analyzed the relationship between these three structural features within rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genomes. A genome-scale prediction of curvature distribution in rice and Arabidopsis indicated that most of the chromosomes of both genomes have maximal chromosomal DNA curvature adjacent to the centromeric region. By analyzing tandem repeats across the genome, we found that frequencies of repeats are higher in regions adjacent to those with high curvature value. Further analysis of CpG islands shows a clear interdependence between curvature value, repeat frequencies and CpG islands. Each CpG island appears in a local minimal curvature region, and CpG islands usually do not appear in the centromere or regions with high repeat frequency. A statistical evaluation demonstrates the significance and non-randomness of these features.

Conclusions: This study represents the first systematic genome-scale analysis of DNA curvature, CpG islands and tandem repeats at the DNA sequence level in plant genomes, and finds that not all of the chromosomes in plants follow the same rules common to other eukaryote organisms, suggesting that some of these genomic properties might be considered as specific to plants.

Show MeSH
Related in: MedlinePlus