Comparison of EM-seq and PBAT methylome library methods for low-input DNA
DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1–10ng) from two methylome library prepar...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2022-10-01
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| Series: | Epigenetics |
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| Online Access: | http://dx.doi.org/10.1080/15592294.2021.1997406 |
| _version_ | 1797678810231996416 |
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| author | Yanan Han Galina Yurevna Zheleznyakova Yanara Marincevic-Zuniga Majid Pahlevan Kakhki Amanda Raine Maria Needhamsen Maja Jagodic |
| author_facet | Yanan Han Galina Yurevna Zheleznyakova Yanara Marincevic-Zuniga Majid Pahlevan Kakhki Amanda Raine Maria Needhamsen Maja Jagodic |
| author_sort | Yanan Han |
| collection | DOAJ |
| description | DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1–10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples. |
| first_indexed | 2024-03-11T23:05:20Z |
| format | Article |
| id | doaj.art-452abb58e35a4e1a873635961ec6d97d |
| institution | Directory Open Access Journal |
| issn | 1559-2294 1559-2308 |
| language | English |
| last_indexed | 2024-03-11T23:05:20Z |
| publishDate | 2022-10-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Epigenetics |
| spelling | doaj.art-452abb58e35a4e1a873635961ec6d97d2023-09-21T13:23:11ZengTaylor & Francis GroupEpigenetics1559-22941559-23082022-10-0117101195120410.1080/15592294.2021.19974061997406Comparison of EM-seq and PBAT methylome library methods for low-input DNAYanan Han0Galina Yurevna Zheleznyakova1Yanara Marincevic-Zuniga2Majid Pahlevan Kakhki3Amanda Raine4Maria Needhamsen5Maja Jagodic6Karolinska Institutet, Center for Molecular Medicine, Karolinska University HospitalKarolinska Institutet, Center for Molecular Medicine, Karolinska University HospitalScience for Life Laboratory, Uppsala UniversityKarolinska Institutet, Center for Molecular Medicine, Karolinska University HospitalScience for Life Laboratory, Uppsala UniversityKarolinska Institutet, Center for Molecular Medicine, Karolinska University HospitalKarolinska Institutet, Center for Molecular Medicine, Karolinska University HospitalDNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1–10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples.http://dx.doi.org/10.1080/15592294.2021.1997406low input dnamethylomeem-seqpbat |
| spellingShingle | Yanan Han Galina Yurevna Zheleznyakova Yanara Marincevic-Zuniga Majid Pahlevan Kakhki Amanda Raine Maria Needhamsen Maja Jagodic Comparison of EM-seq and PBAT methylome library methods for low-input DNA Epigenetics low input dna methylome em-seq pbat |
| title | Comparison of EM-seq and PBAT methylome library methods for low-input DNA |
| title_full | Comparison of EM-seq and PBAT methylome library methods for low-input DNA |
| title_fullStr | Comparison of EM-seq and PBAT methylome library methods for low-input DNA |
| title_full_unstemmed | Comparison of EM-seq and PBAT methylome library methods for low-input DNA |
| title_short | Comparison of EM-seq and PBAT methylome library methods for low-input DNA |
| title_sort | comparison of em seq and pbat methylome library methods for low input dna |
| topic | low input dna methylome em-seq pbat |
| url | http://dx.doi.org/10.1080/15592294.2021.1997406 |
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