Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex.

LEXA, Matej, Tomáš MARTÍNEK and Marie BRÁZDOVÁ. Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex. In Oscar Pastor, Christine Sinoquet, Guy Plantier, Tanja Schultz, Ana L. N. Fred, Hugo Gamboa. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Angers, France: SciTePress, 2014, p. 80-88. ISBN 978-989-758-012-3. Available from: https://dx.doi.org/10.5220/0004824100800088.

Basic information

• Original name: Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex.
• Authors: LEXA, Matej (703 Slovakia, guarantor, belonging to the institution), Tomáš MARTÍNEK (203 Czech Republic) and Marie BRÁZDOVÁ (203 Czech Republic).
• Edition: Angers, France, Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, p. 80-88, 9 pp. 2014.
• Publisher: SciTePress

Other information

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: France
• Confidentiality degree: is not subject to a state or trade secret
• Publication form: printed version "print"
• WWW: URL
• RIV identification code: RIV/00216224:14330/14:00074890
• Organization unit: Faculty of Informatics
• ISBN: 978-989-758-012-3
• Doi: http://dx.doi.org/10.5220/0004824100800088
• Keywords in English: Human genome; DNA sequence; Non-B-DNA; Triplex; Bioconductor; Repetitive sequences; Mobile DNA; Lexicographically minimal rotation
• Tags: International impact, Reviewed

Abstract

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 {\it 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.

Links

• EE2.3.20.0189, research and development project: Name: Rozvoj výzkumné excelence v oblasti evoluční cytogenomiky, epigenetiky a buněčné signalizace