Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX

Research output: Contribution to journalJournal articleResearchpeer-review

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Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX. / Hanghøj, Kristian Ebbesen; Seguin-Orlando, Andaine; Schubert, Mikkel; Madsen, Tobias; Pedersen, Jakob Skou; Willerslev, Eske; Orlando, Ludovic Antoine Alexandre.

In: Molecular Biology and Evolution, Vol. 33, No. 12, 2016, p. 3284-3298.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Hanghøj, KE, Seguin-Orlando, A, Schubert, M, Madsen, T, Pedersen, JS, Willerslev, E & Orlando, LAA 2016, 'Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX', Molecular Biology and Evolution, vol. 33, no. 12, pp. 3284-3298. https://doi.org/10.1093/molbev/msw184

APA

Hanghøj, K. E., Seguin-Orlando, A., Schubert, M., Madsen, T., Pedersen, J. S., Willerslev, E., & Orlando, L. A. A. (2016). Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX. Molecular Biology and Evolution, 33(12), 3284-3298. https://doi.org/10.1093/molbev/msw184

Vancouver

Hanghøj KE, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E et al. Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX. Molecular Biology and Evolution. 2016;33(12):3284-3298. https://doi.org/10.1093/molbev/msw184

Author

Hanghøj, Kristian Ebbesen ; Seguin-Orlando, Andaine ; Schubert, Mikkel ; Madsen, Tobias ; Pedersen, Jakob Skou ; Willerslev, Eske ; Orlando, Ludovic Antoine Alexandre. / Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX. In: Molecular Biology and Evolution. 2016 ; Vol. 33, No. 12. pp. 3284-3298.

Bibtex

@article{07023f13623a423bba92599a619b8e75,
title = "Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX",
abstract = "The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.",
author = "Hangh{\o}j, {Kristian Ebbesen} and Andaine Seguin-Orlando and Mikkel Schubert and Tobias Madsen and Pedersen, {Jakob Skou} and Eske Willerslev and Orlando, {Ludovic Antoine Alexandre}",
note = "{\circledC} The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.",
year = "2016",
doi = "10.1093/molbev/msw184",
language = "English",
volume = "33",
pages = "3284--3298",
journal = "Molecular Biology and Evolution",
issn = "0737-4038",
publisher = "Oxford University Press",
number = "12",

}

RIS

TY - JOUR

T1 - Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX

AU - Hanghøj, Kristian Ebbesen

AU - Seguin-Orlando, Andaine

AU - Schubert, Mikkel

AU - Madsen, Tobias

AU - Pedersen, Jakob Skou

AU - Willerslev, Eske

AU - Orlando, Ludovic Antoine Alexandre

N1 - © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

PY - 2016

Y1 - 2016

N2 - The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.

AB - The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.

U2 - 10.1093/molbev/msw184

DO - 10.1093/molbev/msw184

M3 - Journal article

C2 - 27624717

VL - 33

SP - 3284

EP - 3298

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

SN - 0737-4038

IS - 12

ER -

ID: 172510759