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

D 2014

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

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

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

France

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

References:

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

Abstract

V originále

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

Files attached

paper.pdf

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Citovat

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.

@inproceedings{1139452,
   author = {Lexa, Matej and Martínek, Tomáš and Brázdová, Marie},
   address = {Angers, France},
   booktitle = {Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms},
   doi = {http://dx.doi.org/10.5220/0004824100800088},
   editor = {Oscar Pastor, Christine Sinoquet, Guy Plantier, Tanja Schultz, Ana L. N. Fred, Hugo Gamboa},
   keywords = {Human genome; DNA sequence; Non-B-DNA; Triplex; Bioconductor; Repetitive sequences; Mobile DNA; Lexicographically minimal rotation},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Angers, France},
   isbn = {978-989-758-012-3},
   pages = {80-88},
   publisher = {SciTePress},
   title = {Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex.},
   url = {http://www.scitepress.org/DigitalLibrary/Link.aspx?doi=10.5220/0004824100800088},
   year = {2014}
}

TY  - JOUR
ID  - 1139452
AU  - Lexa, Matej - Martínek, Tomáš - Brázdová, Marie
PY  - 2014
TI  - Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex.
PB  - SciTePress
CY  - Angers, France
SN  - 9789897580123
KW  - Human genome
KW  - DNA sequence
KW  - Non-B-DNA
KW  - Triplex
KW  - Bioconductor
KW  - Repetitive sequences
KW  - Mobile DNA
KW  - Lexicographically minimal rotation
UR  - http://www.scitepress.org/DigitalLibrary/Link.aspx?doi=10.5220/0004824100800088
N2  - 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.
ER  -

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. \textit{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.

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