Improved detection of methylation in ancient DNA

Susanna Sawyer; Pere Gelabert; Benjamin Yakir; Alejandro Llanos-Lizcano; Alessandra Sperduti; Luca Bondioli; Olivia Cheronet; Christine Neugebauer-Maresch; Maria Teschler-Nicola; Mario Novak; Ildikó Pap; Ildikó Szikossy; Tamás Hajdu; Vyacheslav Moiseyev; Andrey Gromov; Gunita Zariņa; Eran Meshorer; Liran Carmel; Ron Pinhasi

doi:10.1186/s13059-024-03405-5

Improved detection of methylation in ancient DNA

Susanna Sawyer, Pere Gelabert, Benjamin Yakir, Alejandro Llanos-Lizcano, Alessandra Sperduti, Luca Bondioli, Olivia Cheronet, Christine Neugebauer-Maresch, Maria Teschler-Nicola, Mario Novak, Ildikó Pap, Ildikó Szikossy, Tamás Hajdu, Vyacheslav Moiseyev, Andrey Gromov, Gunita Zariņa, Eran Meshorer, Liran Carmel, Ron Pinhasi

The Hebrew University of Jerusalem

Research output: Contribution to journal › Article › peer-review

Abstract

Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.

Original language	English
Pages (from-to)	261
Number of pages	1
Journal	GENOME BIOLOGY
Volume	25
Issue number	1
DOIs	https://doi.org/10.1186/s13059-024-03405-5
State	Published - 10 Oct 2024

Keywords

Ancient DNA
Bisulfite treatment
Enzymatic methylation treatment
Methylation
Paleogenomics

All Science Journal Classification (ASJC) codes

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/s13059-024-03405-5

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Sawyer, S., Gelabert, P., Yakir, B., Llanos-Lizcano, A., Sperduti, A., Bondioli, L., Cheronet, O., Neugebauer-Maresch, C., Teschler-Nicola, M., Novak, M., Pap, I., Szikossy, I., Hajdu, T., Moiseyev, V., Gromov, A., Zariņa, G., Meshorer, E., Carmel, L., & Pinhasi, R. (2024). Improved detection of methylation in ancient DNA. GENOME BIOLOGY, 25(1), 261. https://doi.org/10.1186/s13059-024-03405-5

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abstract = "Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.",

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doi = "10.1186/s13059-024-03405-5",

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Sawyer, S, Gelabert, P, Yakir, B, Llanos-Lizcano, A, Sperduti, A, Bondioli, L, Cheronet, O, Neugebauer-Maresch, C, Teschler-Nicola, M, Novak, M, Pap, I, Szikossy, I, Hajdu, T, Moiseyev, V, Gromov, A, Zariņa, G, Meshorer, E , Carmel, L & Pinhasi, R 2024, 'Improved detection of methylation in ancient DNA', GENOME BIOLOGY, vol. 25, no. 1, pp. 261. https://doi.org/10.1186/s13059-024-03405-5

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AU - Sawyer, Susanna

AU - Gelabert, Pere

AU - Yakir, Benjamin

AU - Llanos-Lizcano, Alejandro

AU - Sperduti, Alessandra

AU - Bondioli, Luca

AU - Cheronet, Olivia

AU - Neugebauer-Maresch, Christine

AU - Teschler-Nicola, Maria

AU - Novak, Mario

AU - Pap, Ildikó

AU - Szikossy, Ildikó

AU - Hajdu, Tamás

AU - Moiseyev, Vyacheslav

AU - Gromov, Andrey

AU - Zariņa, Gunita

AU - Meshorer, Eran

AU - Carmel, Liran

AU - Pinhasi, Ron

PY - 2024/10/10

Y1 - 2024/10/10

N2 - Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.

AB - Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.

KW - Ancient DNA

KW - Bisulfite treatment

KW - Enzymatic methylation treatment

KW - Methylation

KW - Paleogenomics

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U2 - 10.1186/s13059-024-03405-5

DO - 10.1186/s13059-024-03405-5

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SN - 1474-7596

VL - 25

SP - 261

JO - GENOME BIOLOGY

JF - GENOME BIOLOGY

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ER -

Improved detection of methylation in ancient DNA

Abstract

Keywords

All Science Journal Classification (ASJC) codes

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