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 and Nikos DARZENTAS

Basic information

Original name

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

Authors

BOUSIOS, A. (826 United Kingdom of Great Britain and Northern Ireland), B.S. GAUT (840 United States of America) and Nikos DARZENTAS (300 Greece, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10603 Genetics and heredity

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.891

RIV identification code

RIV/00216224:14740/17:00095710

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000397749300001

Keywords in English

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

Abstract

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.

Links

ED3.2.00/08.0144, research and development project

Name: CERIT Scientific Cloud

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

NV16-34272A, research and development project

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

Citovat

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

Detailed Information on Publication Record