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The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Standard

The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth. / Malinowska, Marta; Nagy, Istvan; Wagemaker, Cornelis A. M.; Ruud, Anja K.; Svane, Simon F.; Thorup-Kristensen, Kristian; Jensen, Christian S.; Eriksen, Birger; Krusell, Lene; Jahoor, Ahmed; Jensen, Jens; Eriksen, Lars Bonde; Asp, Torben.

I: The Plant Genome, Bind 13, Nr. 3, 20049, 2020.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Malinowska, M, Nagy, I, Wagemaker, CAM, Ruud, AK, Svane, SF, Thorup-Kristensen, K, Jensen, CS, Eriksen, B, Krusell, L, Jahoor, A, Jensen, J, Eriksen, LB & Asp, T 2020, 'The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth', The Plant Genome, bind 13, nr. 3, 20049. https://doi.org/10.1002/tpg2.20049

APA

Malinowska, M., Nagy, I., Wagemaker, C. A. M., Ruud, A. K., Svane, S. F., Thorup-Kristensen, K., Jensen, C. S., Eriksen, B., Krusell, L., Jahoor, A., Jensen, J., Eriksen, L. B., & Asp, T. (2020). The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth. The Plant Genome, 13(3), [20049]. https://doi.org/10.1002/tpg2.20049

Vancouver

Malinowska M, Nagy I, Wagemaker CAM, Ruud AK, Svane SF, Thorup-Kristensen K o.a. The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth. The Plant Genome. 2020;13(3). 20049. https://doi.org/10.1002/tpg2.20049

Author

Malinowska, Marta ; Nagy, Istvan ; Wagemaker, Cornelis A. M. ; Ruud, Anja K. ; Svane, Simon F. ; Thorup-Kristensen, Kristian ; Jensen, Christian S. ; Eriksen, Birger ; Krusell, Lene ; Jahoor, Ahmed ; Jensen, Jens ; Eriksen, Lars Bonde ; Asp, Torben. / The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth. I: The Plant Genome. 2020 ; Bind 13, Nr. 3.

Bibtex

@article{6010d167a62649558ac6647ea6d90974,
title = "The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth",
abstract = "Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgareL.) genome across several commercial and historical cultivars. This study adapted a genotyping-by-sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context-specific DNA methylation at the single-base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10-fold higher levels than those inArabidopsis thaliana(L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long-terminal repeats (LTR) retrotransposonsGypsyandCopia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome-level structural and functional aspects of methylation in barley.",
keywords = "DNA-METHYLATION, EPIGENETIC MUTATION, GENOME, PLANTS, LIBRARIES, MODEL, SUITE, RNA",
author = "Marta Malinowska and Istvan Nagy and Wagemaker, {Cornelis A. M.} and Ruud, {Anja K.} and Svane, {Simon F.} and Kristian Thorup-Kristensen and Jensen, {Christian S.} and Birger Eriksen and Lene Krusell and Ahmed Jahoor and Jens Jensen and Eriksen, {Lars Bonde} and Torben Asp",
year = "2020",
doi = "10.1002/tpg2.20049",
language = "English",
volume = "13",
journal = "The Plant Genome",
issn = "1940-3372",
publisher = "crop science society of america",
number = "3",

}

RIS

TY - JOUR

T1 - The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth

AU - Malinowska, Marta

AU - Nagy, Istvan

AU - Wagemaker, Cornelis A. M.

AU - Ruud, Anja K.

AU - Svane, Simon F.

AU - Thorup-Kristensen, Kristian

AU - Jensen, Christian S.

AU - Eriksen, Birger

AU - Krusell, Lene

AU - Jahoor, Ahmed

AU - Jensen, Jens

AU - Eriksen, Lars Bonde

AU - Asp, Torben

PY - 2020

Y1 - 2020

N2 - Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgareL.) genome across several commercial and historical cultivars. This study adapted a genotyping-by-sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context-specific DNA methylation at the single-base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10-fold higher levels than those inArabidopsis thaliana(L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long-terminal repeats (LTR) retrotransposonsGypsyandCopia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome-level structural and functional aspects of methylation in barley.

AB - Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgareL.) genome across several commercial and historical cultivars. This study adapted a genotyping-by-sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context-specific DNA methylation at the single-base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10-fold higher levels than those inArabidopsis thaliana(L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long-terminal repeats (LTR) retrotransposonsGypsyandCopia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome-level structural and functional aspects of methylation in barley.

KW - DNA-METHYLATION

KW - EPIGENETIC MUTATION

KW - GENOME

KW - PLANTS

KW - LIBRARIES

KW - MODEL

KW - SUITE

KW - RNA

U2 - 10.1002/tpg2.20049

DO - 10.1002/tpg2.20049

M3 - Journal article

C2 - 33217208

VL - 13

JO - The Plant Genome

JF - The Plant Genome

SN - 1940-3372

IS - 3

M1 - 20049

ER -

ID: 249767851