Bisprimer—A Program for the Design of Primers for
Bisulfite-Based Genomic Sequencing of Both Plant and Mammalian
DNA Samples

J 2012

Bisprimer—A Program for the Design of Primers for Bisulfite-Based Genomic Sequencing of Both Plant and Mammalian DNA Samples

KOVÁČOVÁ, Viera a Bohuslav JANOUŠEK

Základní údaje

Originální název

Bisprimer—A Program for the Design of Primers for Bisulfite-Based Genomic Sequencing of Both Plant and Mammalian DNA Samples

Název česky

Bisprimer - program pro vytváření primerů určených na bisulfitové sekvencování pro rostlinné i savčí vzorky DNA

Autoři

KOVÁČOVÁ, Viera a Bohuslav JANOUŠEK

Vydání

Journal of Heredity, 2012, 0022-1503

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

Genetika a molekulární biologie

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL, URL

Impakt faktor

Impact factor: 1.995

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/12:00059285

Organizační jednotka

Přírodovědecká fakulta

DOI

https://doi.org/10.1093/jhered/esr137

UT WoS

000300723400017

Klíčová slova česky

bisulfit, metylace cytozinu, DNA metylace, genomické sekvencování, primery

Klíčová slova anglicky

bisulfite; cytosine methylation; DNA methylation; genomic sequencing; primers

Štítky

AKR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 9. 4. 2013 14:14, Ing. Andrea Mikešková

Anotace

V originále

Plants and animals differ in the sequence context of the methylated sites in DNA. Plants exhibit cytosine methylation in CG, CHG, and CHH sites, whereas CG methylation is the only form present in mammals (with an exception of the early embryonic development). This fact must be taken into account in the design of primers for bisulfite-based genomic sequencing because CHG and CHH sites can remain unmodified. Surprisingly, no user-friendly primer design program is publicly available that could be used to design primers in plants and to simultaneously check the properties of primers such as the potential for primer-dimer formation. For studies concentrating on particular DNA loci, the correct design of primers is crucial. The program, called BisPrimer, includes 2 different subprograms for the primer design, the first one for mammals and the second one for angiosperm plants. Each subprogram is divided into 2 variants. The first variant serves to design primers that preferentially bind to the bisulfite-modified primer-binding sites (C to U conversion). This type of primer preferentially amplifies the bisulfite-converted DNA strands. This feature can help to avoid problems connected with an incomplete bisulfite modification that can sometimes occur for technical reasons. The second variant is intended for the analysis of samples that are supposed to consist of a mixture of DNA molecules that have different levels of cytosine methylation (e.g., pollen DNA). In this case, the aim is to minimize the selection in favor of either less methylated or more methylated molecules.

Citovat

KOVÁČOVÁ, Viera a Bohuslav JANOUŠEK. Bisprimer—A Program for the Design of Primers for Bisulfite-Based Genomic Sequencing of Both Plant and Mammalian DNA Samples. Journal of Heredity. 2012, roč. 103, č. 2, s. 308 - 312. ISSN 0022-1503. Dostupné z: https://doi.org/10.1093/jhered/esr137.

@article{970036,
   author = {Kováčová, Viera and Janoušek, Bohuslav},
   article_number = {2},
   doi = {https://doi.org/10.1093/jhered/esr137},
   keywords = {bisulfite; cytosine methylation; DNA methylation; genomic sequencing; primers},
   language = {eng},
   issn = {0022-1503},
   journal = {Journal of Heredity},
   title = {Bisprimer—A Program for the Design of Primers for Bisulfite-Based Genomic Sequencing of Both Plant and Mammalian DNA Samples},
   url = {http://jhered.oxfordjournals.org/content/early/2012/01/13/jhered.esr137.abstract},
   volume = {103},
   year = {2012}
}

TY  - JOUR
ID  - 970036
AU  - Kováčová, Viera - Janoušek, Bohuslav
PY  - 2012
TI  - Bisprimer—A Program for the Design of Primers for Bisulfite-Based Genomic Sequencing of Both Plant and Mammalian DNA Samples
JF  - Journal of Heredity
VL  - 103
IS  - 2
SP  - 308 - 312
EP  - 308 - 312
SN  - 00221503
KW  - bisulfite
KW  - cytosine methylation
KW  - DNA methylation
KW  - genomic sequencing
KW  - primers
UR  - http://jhered.oxfordjournals.org/content/early/2012/01/13/jhered.esr137.abstract
L2  - http://jhered.oxfordjournals.org/content/early/2012/01/13/jhered.esr137.abstract
N2  - Plants and animals differ in the sequence context of the methylated sites in DNA. Plants exhibit cytosine methylation in CG, CHG, and CHH sites, whereas CG methylation is the only form present in mammals (with an exception of the early embryonic development). This fact must be taken into account in the design of primers for bisulfite-based genomic sequencing because CHG and CHH sites can remain unmodified. Surprisingly, no user-friendly primer design program is publicly available that could be used to design primers in plants and to simultaneously check the properties of primers such as the potential for primer-dimer formation. For studies concentrating on particular DNA loci, the correct design of primers is crucial. The program, called BisPrimer, includes 2 different subprograms for the primer design, the first one for mammals and the second one for angiosperm plants. Each subprogram is divided into 2 variants. The first variant serves to design primers that preferentially bind to the bisulfite-modified primer-binding sites (C to U conversion). This type of primer preferentially amplifies the bisulfite-converted DNA strands. This feature can help to avoid problems connected with an incomplete bisulfite modification that can sometimes occur for technical reasons. The second variant is intended for the analysis of samples that are supposed to consist of a mixture of DNA molecules that have different levels of cytosine methylation (e.g., pollen DNA). In this case, the aim is to minimize the selection in favor of either less methylated or more methylated molecules.
ER  -

KOVÁČOVÁ, Viera a Bohuslav JANOUŠEK. Bisprimer—A Program for the Design of Primers for Bisulfite-Based Genomic Sequencing of Both Plant and Mammalian DNA Samples. \textit{Journal of Heredity}. 2012, roč.~103, č.~2, s.~308 - 312. ISSN~0022-1503. Dostupné z: https://doi.org/10.1093/jhered/esr137.

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