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

2.50
Hdl Handle:
http://hdl.handle.net/10033/620682
Title:
Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties
Authors:
Masoudi-Nejad, Ali; Movahedi, Sara; Jáuregui, Ruy
Abstract:
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.
Citation:
BMC Genomics. 2011 May 06;12(1):214
Issue Date:
6-May-2011
URI:
http://dx.doi.org/10.1186/1471-2164-12-214; http://hdl.handle.net/10033/620682
Type:
Journal Article
Appears in Collections:
publications of the research group microbial interactions and processes (MINP)

Full metadata record

DC FieldValue Language
dc.contributor.authorMasoudi-Nejad, Alien
dc.contributor.authorMovahedi, Saraen
dc.contributor.authorJáuregui, Ruyen
dc.date.accessioned2017-01-06T10:23:54Z-
dc.date.available2017-01-06T10:23:54Z-
dc.date.issued2011-05-06en
dc.identifier.citationBMC Genomics. 2011 May 06;12(1):214en
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-12-214en
dc.identifier.urihttp://hdl.handle.net/10033/620682-
dc.description.abstractAbstract 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.en
dc.titleGenome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic propertiesen
dc.typeJournal Articleen
dc.language.rfc3066enen
dc.rights.holderMasoudi-Nejad et al; licensee BioMed Central Ltd.en
dc.date.updated2015-09-04T08:23:33Zen
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