Considerations and complications of mapping small RNA
high-throughput data to transposable elements

J 2017

Considerations and complications of mapping small RNA high-throughput data to transposable elements

BOUSIOS, A., B.S. GAUT a Nikos DARZENTAS

Základní údaje

Originální název

Considerations and complications of mapping small RNA high-throughput data to transposable elements

Autoři

BOUSIOS, A. (826 Velká Británie a Severní Irsko), B.S. GAUT (840 Spojené státy) a Nikos DARZENTAS (300 Řecko, garant, domácí)

Vydání

Mobile DNA, LONDON, BioMed Central, 2017, 1759-8753

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10603 Genetics and heredity

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.891

Kód RIV

RIV/00216224:14740/17:00095710

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1186/s13100-017-0086-z

UT WoS

000397749300001

Klíčová slova anglicky

Transposable elements; Small RNAs; High-throughput sequencing; siRNAs; Genome mapping; Annotation; Bioinformatics; RNA-seq

Štítky

OA, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 15. 3. 2018 14:47, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

Background: High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants. Results: Here, in an attempt to shed light on complications of mapping sRNAs to TEs, we focus on the 2,300 Mb maize genome, 85% of which is derived from TEs, and scrutinize methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiply mapping sRNAs, and the selection among sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and contrast their effect on low copy genomic regions and other popular HTS data. Conclusions: Based on our analyses, we share a series of take-home messages that may help with the design, implementation, and interpretation of high-throughput TE epigenetic studies specifically, but our conclusions may also apply to any work that involves analysis of HTS data.

Návaznosti

ED3.2.00/08.0144, projekt VaV

Název: CERIT Scientific Cloud

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

NV16-34272A, projekt VaV

Název: Encyklopedie CLL podskupin: unikátní znalostní databáze vybavená bioinformatickými nástroji použitelná v personalizované biomedicíně a klinické praxi

Citovat

BOUSIOS, A., B.S. GAUT a Nikos DARZENTAS. Considerations and complications of mapping small RNA high-throughput data to transposable elements. Mobile DNA. LONDON: BioMed Central, 2017, roč. 8, FEB, s. nestránkováno, 13 s. ISSN 1759-8753. Dostupné z: https://dx.doi.org/10.1186/s13100-017-0086-z.

@article{1411308,
   author = {Bousios, A. and Gaut, B.S. and Darzentas, Nikos},
   article_location = {LONDON},
   article_number = {FEB},
   doi = {http://dx.doi.org/10.1186/s13100-017-0086-z},
   keywords = {Transposable elements; Small RNAs; High-throughput sequencing; siRNAs; Genome mapping; Annotation; Bioinformatics; RNA-seq},
   language = {eng},
   issn = {1759-8753},
   journal = {Mobile DNA},
   title = {Considerations and complications of mapping small RNA high-throughput data to transposable elements},
   url = {https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-017-0086-z?site=mobilednajournal.biomedcentral.com},
   volume = {8},
   year = {2017}
}

TY  - JOUR
ID  - 1411308
AU  - Bousios, A. - Gaut, B.S. - Darzentas, Nikos
PY  - 2017
TI  - Considerations and complications of mapping small RNA high-throughput data to transposable elements
JF  - Mobile DNA
VL  - 8
IS  - FEB
SP  - nestránkováno
EP  - nestránkováno
PB  - BioMed Central
SN  - 17598753
KW  - Transposable elements
KW  - Small RNAs
KW  - High-throughput sequencing
KW  - siRNAs
KW  - Genome mapping
KW  - Annotation
KW  - Bioinformatics
KW  - RNA-seq
UR  - https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-017-0086-z?site=mobilednajournal.biomedcentral.com
L2  - https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-017-0086-z?site=mobilednajournal.biomedcentral.com
N2  - Background: High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants. Results: Here, in an attempt to shed light on complications of mapping sRNAs to TEs, we focus on the 2,300 Mb maize genome, 85% of which is derived from TEs, and scrutinize methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiply mapping sRNAs, and the selection among sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and contrast their effect on low copy genomic regions and other popular HTS data. Conclusions: Based on our analyses, we share a series of take-home messages that may help with the design, implementation, and interpretation of high-throughput TE epigenetic studies specifically, but our conclusions may also apply to any work that involves analysis of HTS data.
ER  -

BOUSIOS, A., B.S. GAUT a Nikos DARZENTAS. Considerations and complications of mapping small RNA high-throughput data to transposable elements. \textit{Mobile DNA}. LONDON: BioMed Central, 2017, roč.~8, FEB, s.~nestránkováno, 13 s. ISSN~1759-8753. Dostupné z: https://dx.doi.org/10.1186/s13100-017-0086-z.

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