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 a Marie BRÁZDOVÁ

Základní údaje

Originální název

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

Autoři

LEXA, Matej (703 Slovensko, garant, domácí), Tomáš MARTÍNEK (203 Česká republika) a Marie BRÁZDOVÁ (203 Česká republika)

Vydání

Angers, France, Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, od s. 80-88, 9 s. 2014

Nakladatel

SciTePress

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Francie

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Odkazy

URL

Kód RIV

RIV/00216224:14330/14:00074890

Organizační jednotka

Fakulta informatiky

ISBN

978-989-758-012-3

DOI

http://dx.doi.org/10.5220/0004824100800088

Klíčová slova anglicky

Human genome; DNA sequence; Non-B-DNA; Triplex; Bioconductor; Repetitive sequences; Mobile DNA; Lexicographically minimal rotation

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 4. 2015 21:44, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

Návaznosti

EE2.3.20.0189, projekt VaV

Název: Rozvoj výzkumné excelence v oblasti evoluční cytogenomiky, epigenetiky a buněčné signalizace

Přiložené soubory

paper.pdf

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Citovat

LEXA, Matej, Tomáš MARTÍNEK a 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, s. 80-88. ISBN 978-989-758-012-3. Dostupné z: 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 a 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, s.~80-88. ISBN~978-989-758-012-3. Dostupné z: https://dx.doi.org/10.5220/0004824100800088.

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