TY - JOUR
T1 - Improved detection of methylation in ancient DNA
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
N1 - Publisher Copyright:
© The Author(s) 2024.
PY - 2024/12
Y1 - 2024/12
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
UR - http://www.scopus.com/inward/record.url?scp=85206063702&partnerID=8YFLogxK
U2 - 10.1186/s13059-024-03405-5
DO - 10.1186/s13059-024-03405-5
M3 - Article
C2 - 39390557
AN - SCOPUS:85206063702
SN - 1474-7596
VL - 25
JO - Genome Biology
JF - Genome Biology
IS - 1
M1 - 261
ER -