Updated publication reference for PubMed record(s): 33767140. Biogenesis of eukaryotic box C/D snoRNPs initiates co-transcriptionally and requires the action of an assembly machinery including the HSP90/R2TP complex, Rsa1p:Hit1p (NUFIP1:ZNHIT3 in human) heterodimer and the Bcd1 protein (ZNHIT6 in human). We identified genetic interactions between the Rsa1p-encoding gene and genes involved in chromatin organization including RTT106 that codes for the H3-H4 histone chaperone Rtt106p controlling H3K56ac deposition. We show that Bcd1p binds Rtt106p directly. Whereas the interaction does not appear to contribute or interfere with known Bcd1p functions during snoRNP biogenesis, we show that Bcd1p controls the transcription-dependent recruitment of Rtt106p by reducing its association with RNA polymerase II, modulating H3K56ac levels at gene body. We reveal the 3D structures of the free and Rtt106p-bound forms of Bcd1p using NMR and X-ray crystallography, and we studied the interaction by a combination of biophysical and proteomic techniques. Bcd1p interacts with a region in the PH1 domain of Rtt106p that is distinct from the interaction interface between the histone chaperone and histone H3. Our results are evidence for a new protein interaction interface for Rtt106p that controls its transcription-associated activity.