Abstract
BackgroundEarly DNA replication occurs within actively transcribed chromatin compartments in mammalian cells, raising the immediate question of how early DNA replication coordinates with transcription to avoid collisions and DNA damage.ResultsWe develop a high-throughput nucleoside analog incorporation sequencing assay and identify thousands of early replication initiation zones in both mouse and human cells. The identified early replication initiation zones fall in open chromatin compartments and are mutually exclusive with transcription elongation. Of note, early replication initiation zones are mainly located in non-transcribed regions adjacent to transcribed regions. Mechanistically, we find that RNA polymerase II actively redistributes the chromatin-bound mini-chromosome maintenance complex (MCM), but not the origin recognition complex (ORC), to actively restrict early DNA replication initiation outside of transcribed regions. In support of this finding, we detect apparent MCM accumulation and DNA replication initiation in transcribed regions due to anchoring of nuclease-dead Cas9 at transcribed genes, which stalls RNA polymerase II. Finally, we find that the orchestration of early DNA replication initiation by transcription efficiently prevents gross DNA damage.ConclusionRNA polymerase II redistributes MCM complexes, but not the ORC, to prevent early DNA replication from initiating within transcribed regions. This RNA polymerase II-driven MCM redistribution spatially separates transcription and early DNA replication events and avoids the transcription-replication initiation collision, thereby providing a critical regulatory mechanism to preserve genome stability.
Highlights
DNA replication occurs within actively transcribed chromatin compartments in mammalian cells, raising the immediate question of how early DNA replication coordinates with transcription to avoid collisions and DNA damage
Inducing a disordered cell cycle via overexpression of oncogenes (c-MYC or cyclin E) results in DNA replication initiation in gene bodies, which promotes chromosomal translocation and tumorigenesis [13]. In this context, employing RNA polymerase II to exclude inactive maintenance complex (MCM) double hexamers from active gene bodies is a superbly effective strategy by which cells initiate DNA replication while maintaining robust gene transcription. Both early DNA replication initiation and transcription occur in active chromatin compartments; the mechanisms through which these pivotal cellular processes coordinate remain unclear, especially in mammalian cells
We report our development of the NAIL-seq method to monitor the interplay between early replication initiation and transcription, which allowed us to reveal that transcription actively shapes early DNA replication initiation in mammalian cells
Summary
DNA replication occurs within actively transcribed chromatin compartments in mammalian cells, raising the immediate question of how early DNA replication coordinates with transcription to avoid collisions and DNA damage. Liu et al Genome Biology (2021) 22:176 transcription both occur within active chromatin compartments, raising the pivotal question of how these processes are spatially and temporally coordinated to avoid replication-transcription collisions and subsequent DNA damage [6,7,8,9]. Okazaki fragments (OK) generated during DNA replication have been employed to identify initiation zones that harbor one or more origin(s) within each zone [10, 24] These methods reveal that early DNA replication initiation occurs in active chromatin compartments in which transcription occurs [7]
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