Conference paper

LEXA Matej, MARTÍNEK Tomáš and BRÁZDOVÁ Marie. Uneven distribution of potential triplex sequences in the human genome: In silico study using the R/Bioconductor package triplex. In: Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Angers: SciTePress - Science and Technology Publications, 2014, pp. 80-88. ISBN 978-989-758-012-3.
Publication language:english
Original title:Uneven distribution of potential triplex sequences in the human genome: In silico study using the R/Bioconductor package triplex
Title (cs):Nerovnoměrné rozložení potenciálních sekvencí tvořicích triplex v lidském genomu: Výpočetní studie s využitím balíčku triplex prostředí R/Bioconductor
Pages:80-88
Proceedings:Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms
Conference:International Conference on Bioinformatics Models, Methods and Algorithms
Place:Angers, FR
Year:2014
ISBN:978-989-758-012-3
Publisher:SciTePress - Science and Technology Publications
Keywords
Human genome; DNA sequence; Non-B-DNA; Triplex; Bioconductor; Repetitive sequences; Mobile DNA; Lexicographically minimal rotation
Annotation
Eukaryotic genomes are rich in sequences capable of forming non-B DNA structures. These structures are expected to play important roles in natural regulatory processes at levels above those of individual genes, such as whole genome dynamics or chromatin organization, as well as in processes leading to the loss of these functions, such as cancer development. Recently, a number of authors have mapped the occurrence of potential quadruplex sequences in the human genome and found them to be associated with promoters. In this paper, we set out to map the distribution and characteristics of potential triplex-forming sequences in human genome DNA sequences. Using the R/Bioconductor package triplex, we found these sequences to be excluded from exons, while present mostly in a small number of repetitive sequence classes, especially short sequence tandem repeats (microsatellites), Alu and combined elements, such as SVA. We also introduce a novel way of classifying potential triplex sequences, using a lexicographically minimal rotation of the most frequent k-mer to assign class membership automatically. Members of such classes typically have different propensities to form parallel and antiparallel intramolecular triplexes (H-DNA). We observed an interesting pattern, where the predicted third strands of antiparallel H-DNA were much less likely to contain a deletion against their duplex structural counterpart than were their parallel versions.
BibTeX:
@INPROCEEDINGS{
   author = {Matej Lexa and Tom{\'{a}}{\v{s}} Mart{\'{i}}nek and Marie
	Br{\'{a}}zdov{\'{a}}},
   title = {Uneven distribution of potential triplex sequences in the
	human genome: In silico study using the R/Bioconductor
	package triplex},
   pages = {80--88},
   booktitle = {Proceedings of the International Conference on
	Bioinformatics Models, Methods and Algorithms},
   year = {2014},
   location = {Angers, FR},
   publisher = {SciTePress - Science and Technology Publications},
   ISBN = {978-989-758-012-3},
   language = {english},
   url = {http://www.fit.vutbr.cz/research/view_pub.php.en.iso-8859-2?id=10566}
}

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