DNA damage response and repair proteins are centrally involved in genome 
maintenance pathways. Yet, little is known about their functional role under 
non-DNA damage-inducing conditions. Here we show that Rad9 checkpoint protein, 
known to mediate the damage signal from upstream to downstream essential 
kinases, interacts with Aft1 transcription factor in the budding yeast. Aft1 
regulates iron homeostasis and is also involved in genome integrity having 
additional iron-independent functions. Using genome-wide expression and 
chromatin immunoprecipitation approaches, we found Rad9 to be recruited to 16% 
of the yeast genes, often related to cellular growth and metabolism, while 
affecting the transcription of ∼2% of the coding genome in the absence of 
exogenously induced DNA damage. Importantly, Rad9 is recruited to fragile 
genomic regions (transcriptionally active, GC rich, centromeres, meiotic 
recombination hotspots and retrotransposons) non-randomly and in an 
Aft1-dependent manner. Further analyses revealed substantial genome-wide 
parallels between Rad9 binding patterns to the genome and major activating 
histone marks, such as H3K36me, H3K79me and H3K4me. Thus, our findings suggest 
that Rad9 functions together with Aft1 on DNA damage-prone chromatin to 
facilitate genome surveillance, thereby ensuring rapid and effective response to 
possible DNA damage events.