Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency

Anna Chanou, Matthias Weiβ, Karoline Holler, Atiqa Sajid, Tobias Straub, Jana Krietsch, Andrea Sanchi, Henning Ummethum, Clare S.K. Lee, Elisabeth Kruse, Manuel Trauner, Marcel Werner, Maxime Lalonde, Massimo Lopes, Antonio Scialdone and Stephan Hamperl  (2023) Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency. Nucleic Acids Research 1-22. https://doi.org/10.1093/nar/gkad1022

Abstract cited directly from the article:

Stochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of four specific genomic loci. MATAC-Seq relies on preferential modification of accessible DNA by methyltransferases combined with Nanopore-Sequencing for direct readout of methylated DNA-bases. Applying MATAC-Seq to selected early-efficient and late-inefficient yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an accessible nucleosome-free region in combination with well-positioned +1 and +2 nucleosomes as a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during eukaryotic DNA replication. Consequently, our single-molecule chromatin accessibility assay will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.