e-journal

EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing

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1. Research addressing the role of epigenetics in a diversity of experimental and natural systems is rapidly accumulating.
Diverse methods have been developed to study epigenetic states, including bisulphite sequencing and
AFLP-based approaches. However, existing methods are sometimes difficult to apply to non-traditional model
organisms that lack genomic resources (bisulphite sequencing), and can fail to be economical and readily scalable
to diverse research questions because of reliance on traditional Sanger sequencing (AFLP approaches).
2. Here we develop a reduced-representation library-based approach that is scalable and economical to quantitatively
compare patterns of genomewide methylation. This approach shares substantial similarity to the now
widely used double digest restriction-site associated DNA sequencing-based method (ddRADseq), except that it
utilizes a methylation-sensitive restriction enzyme. This method therefore identifies changes in the genomic
methylation state of cytosine (to 5-methylcytosine; 5mC) by sampling loci (via next-generation sequencing) that
are not methylated within a sample. We test this method to identify shifts in the epigenome of clonal water fleas
(Daphnia ambigua) in response to exposure to fish predator cues, which are known to induce transgenerational
changes in life-history traits.
3. We found evidence for differential transgenerational responses (inferred via significant shifts in the methylation state of sampled loci) to predator cues among our treatment groups and remarkably consistent responses
within treatment groups. Our results demonstrate that this method is capable of producing highly repeatable
results even without the use of a reference genome.
4. Applications of this general method are broad and diverse and include the analysis of epigenetic shifts in both
experimental and natural study systems.

Key-words: CpG methylation, Daphnia, epigenetics, high-throughput methylation measurement,restriction-site associatedDNAsequencing, transgenerational shift

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Ketersediaan

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Informasi Detail

Judul Seri

Methods in Ecology and Evolution

No. Panggil

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Penerbit

: British Ecological Society., 2016

Deskripsi Fisik

Methods in Ecology and Evolution 2016, 7, 60–69

Bahasa

English

ISBN/ISSN

doi: 10.1111/2041-21

Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

Lampiran Berkas

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