RoAM: computational reconstruction of ancient methylomes and identification of differentially methylated regions

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-09-04 DOI:10.1186/s13059-025-03702-7

Yoav Mathov, Naomi Rosen, Chen Leibson, Eran Meshorer, Benjamin Yakir, Liran Carmel

引用次数: 0

Abstract

We present a new and considerably improved version of RoAM (Reconstruction of Ancient Methylation), a flexible tool for reconstructing ancient methylomes and identifying differentially methylated regions (DMRs) between populations. Through a series of filtering and quality control steps, RoAM produces highly reliable DNA methylation maps, making it a valuable tool for paleoepigenomics studies. We apply RoAM to pre-and post-Neolithic transition Balkan samples, and uncover DMRs in genes related to sugar metabolism. Notably, we observe post-Neolithic hypermethylation of PTPRN2, a regulator of insulin secretion. These results are compatible with hypoinsulinism in pre-Neolithic hunter-gatherers.

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RoAM：古代甲基组的计算重建和差异甲基化区域的鉴定

我们提出了一个新的和显著改进版本的RoAM（古代甲基化重建），这是一个灵活的工具，用于重建古代甲基组和识别种群之间的差异甲基化区域（DMRs）。通过一系列的过滤和质量控制步骤，RoAM生成高度可靠的DNA甲基化图谱，使其成为古表观基因组学研究的宝贵工具。我们将RoAM应用于前新石器时代和后新石器时代过渡的巴尔干样本，并发现与糖代谢相关的基因中的DMRs。值得注意的是，我们观察到新石器时代后PTPRN2的高甲基化，这是胰岛素分泌的调节剂。这些结果与新石器时代前狩猎采集者的低胰岛素症相一致。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

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