Replisome assembly at eukaryotic replication forks connects the DNA helicase to 
DNA polymerases and many other factors. The helicase binds the leading-strand 
polymerase directly, but is connected to the Pol α lagging-strand polymerase by 
the trimeric adaptor Ctf4. Here, we identify new Ctf4 partners in addition to 
Pol α and helicase, all of which contain a "Ctf4-interacting-peptide" or 
CIP-box. Crystallographic analysis classifies CIP-boxes into two related groups 
that target different sites on Ctf4. Mutations in the CIP-box motifs of the Dna2 
nuclease or the rDNA-associated protein Tof2 do not perturb DNA synthesis 
genome-wide, but instead lead to a dramatic shortening of chromosome 12 that 
contains the large array of rDNA repeats. Our data reveal unexpected complexity 
of Ctf4 function, as a hub that connects multiple accessory factors to the 
replisome. Most strikingly, Ctf4-dependent recruitment of CIP-box proteins 
couples other processes to DNA synthesis, including rDNA copy-number regulation.