Genome-wide mapping and profiling of γH2AX binding hotspots in response to different replication stress inducers.
BACKGROUND
Replication stress (RS) gives rise to DNA damage that threatens genome stability. RS can originate from different sources that stall replication by diverse mechanisms. However, the mechanism underlying how different types of RS contribute to genome instability is unclear, in part due to the poor understanding of the distribution and characteristics of damage sites induced by different RS mechanisms.


RESULTS
We use ChIP-seq to map γH2AX binding sites genome-wide caused by aphidicolin (APH), hydroxyurea (HU), and methyl methanesulfonate (MMS) treatments in human lymphocyte cells. Mapping of γH2AX ChIP-seq reveals that APH, HU, and MMS treatments induce non-random γH2AX chromatin binding at discrete regions, suggesting that there are γH2AX binding hotspots in the genome. Characterization of the distribution and sequence/epigenetic features of γH2AX binding sites reveals that the three treatments induce γH2AX binding at largely non-overlapping regions, suggesting that RS may cause damage at specific genomic loci in a manner dependent on the fork stalling mechanism. Nonetheless, γH2AX binding sites induced by the three treatments share common features including compact chromatin, coinciding with larger-than-average genes, and depletion of CpG islands and transcription start sites. Moreover, we observe significant enrichment of SINEs in γH2AX sites in all treatments, indicating that SINEs may be a common barrier for replication polymerases.


CONCLUSIONS
Our results identify the location and common features of genome instability hotspots induced by different types of RS, and help in deciphering the mechanisms underlying RS-induced genetic diseases and carcinogenesis.
['Lyu|Xinxing|X|', 'Chastain|Megan|M|', 'Chai|Weihang|W|']
D016590:Aphidicolin D001665:Binding Sites D002460:Cell Line D002874:Chromosome Mapping D004261:DNA Replication D015894:Genome, Human D042822:Genomic Instability D006657:Histones D006801:Humans D006918:Hydroxyurea D013312:Stress, Physiological D013441:Sulfinic Acids
γH2AX Replication stress Genome stability Fragile sites