They say that timing is everything – from the perfect golf shot to the most cutting joke – and now, a well-timed study establishes that DNA replication timing is everything when it comes to maintaining the global epigenetic state of human cells!
Studies had previously described a link between the temporal order of DNA replication with the definition of chromatin profiles and three-dimensional genome architecture – early-replicating chromatin contains active histone modifications and is located in the nuclear interior, while late-replicating DNA chromatin contains more repressive histone modifications and is instead located in the periphery. However, we previously lacked the ability to manipulate the replication timing program at a genome-wide scale and thereby define a mechanistic link between replication timing and the maintenance of the global epigenetic state during the cell cycle.
In a timely new advance, researchers led by David M. Gilbert (Florida State University, Tallahassee) now describe how knocking out the principal regulator of replication timing (Replication Timing Regulatory Factor 1 or RIF1) led them to mechanistically link replication timing and the maintenance of the global epigenetic state in human embryonic stem and cancer cells.
Time’s a wastin! So let’s hear what Klein, Zhao, Lyu, and colleagues discovered in this perfectly-timed study:
- RIF1 knockout human cells exhibit genome-wide aberrations in replication timing, as shown by the disruption in early- and late-replicating chromatin domains
- The disruption suggests that the derepression of late-replicating chromatin regions increases competition for the limited number of replication initiation factors and delays replication timing of early-replicating chromatin regions
- High-resolution Repli-seq, which provides high-accuracy profiles of replication timing, uncovered that RIF1 knockout leads to a significant increase in the heterogeneity of replication timing across a cell population
- This heterogeneity in replication timing then prompts the widespread redistribution of active and repressive histone modifications (ChIP-seq for H3K9me3, H3K27me3, and H3K27ac) and alterations in genome architecture (Hi-C assays)
- Disruptions to chromatin profiles and architecture require DNA replication, and disruptions become magnified with successive cycles of altered replication timing
- Interestingly, RIF1 knockout causes only a limited number of gene expression alterations and few shared changes across cell types, suggesting an indirect effect
Overall, this on-time study suggests the overall importance of RIF1 to replication timing and provides the long sought-after mechanistic evidence that supports a crucial role for replication timing in orchestrating the maintenance of the global epigenetic state and genome compartmentalization.
Gilbert shares, “Why would cells care about the order in which they replicate DNA? After all – all cells need to replicate all their DNA. Our hypothesis has been that it’s not just DNA that replicates, but all of the regulatory molecules that read the DNA replicate as well. Mother nature would not squander this opportunity to control how the DNA is read. The time at which you replicate provides an ideal time at which to choose whether to maintain all the regulatory factors and continue with the same functional interpretation of the information in DNA or change it to elicit new functions. We and others have shown previously that the program is altered in many diseases. Our lab recently showed specific patterns of altered timing that were linked statistically to poor outcomes in pediatric leukemia, and in another study to diseases of premature aging.”
Time for a quick read of the details? Head over to Science, April 2021.