Homologous recombination-based mechanisms have been implicated in replication re-initiation at sites of collapsed replication forks and double strand breaks.
Human ACF has been implicated in replication of heterochromatin during S-phase, and RNAi-mediated depletion causes a delay in cell cycle progression through late S-phase [13].
However, in certain mammalian cell lines, fork reversal has been implicated in replication restart mechanisms under conditions causing replication stress (Berti et al., 2013; Zellweger et al., 2015).
Homolog of Afd1 encodes protein associated with the cohesion complex, which establishes sister chromatid cohesion [ 33- 35], while RPA70 is implicated in replication, repair, and transcription [ 36].
Very recently, Rpd3L-C proteins were implicated in replication timing events in yeast [ 52], so a plausible explanation for epistasis between these complexes could be based on the coordination of DNA replication or the regulation of gene expression or both.
A distant homolog of the Whirlies, the TIF1 protein from the protist Tetrahymena thermophyla has been implicated in replication of DNA as well as in the faithful intergenerational transmission of genetic information and is required for activation of an intra-S-phase checkpoint triggered by DNA-damage [ 32- 34].
XRCC1 and PARP-1-containing complexes have also been implicated in replication-associated repair, a process that is critical for preventing the incorporation of damaged bases into the DNA.
The annotation of the prophage found 44% proteins to be implicated in DNA replication and bacterial or/and phage metabolism, 37% were annotated as bacteriophage proteins (including structural, integration and terminase) and 14% proteins had no functional annotation.
These are present immediately upstream of the OH and are suggested to be implicated in the initiation of the H-strand replication [54], [55].
