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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F17%3A00095710" target="_blank" >RIV/00216224:14740/17:00095710 - isvavai.cz</a>

Result on the web

<a href="https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-017-0086-z?site=mobilednajournal.biomedcentral.com" target="_blank" >https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-017-0086-z?site=mobilednajournal.biomedcentral.com</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13100-017-0086-z" target="_blank" >10.1186/s13100-017-0086-z</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10603 - Genetics and heredity (medical genetics to be 3)

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Mobile DNA

ISSN

1759-8753

e-ISSN

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Volume of the periodical

8

Issue of the periodical within the volume

FEB

Country of publishing house

GB - UNITED KINGDOM

Number of pages

13

Pages from-to

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UT code for WoS article

000397749300001

EID of the result in the Scopus database

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