August 30, 2016 – Ribosomal Protein (RP) genes are co-regulated in the genome, under the control of multiple regulators: Rap1, Fhl1, Ifh1, Sfp1, and Hmo1. A majority of RP genes contain a Rap1 motif upstream of the TSS. It has been shown that Rap1 acts as a master regulator, recruiting other TFs to mediate RPG regulation. Since the RP genes are so highly co-regulated, it is expected that they are subject to similar transcriptional control. Yet the precise mechanism of this transcriptional control has been lacking, and how these factors interact to orchestrate RP gene regulation remains elusive.

Dr. Pugh’s lab used ChIP-exo, a high-resolution protein-binding assay, to explore the organization of the RP gene regulators. They found that the RP genes organized their regulatory machinery around the Rap1 site. This confirmed Rap1 as an organizing centre for RPG regulation. While each of the other TFs were present in all the Rap1 bound sites, only a subset of RP genes showed Hmo1 enrichment. This enrichment was spread over a large 20-50 base pair window, upstream of the Transcription Start Site. Interestingly, it was seen that during gene repression, Hmo1 was lost. This loss coincided with the upstream movement of the +1 nucleosome, suggesting that Hmo1 de-localization acts as a barrier to nucleosomal occupancy. A loss of Hmo1 alters nucleosome positioning, thus leading to RP gene repression.

This study shows how fine grained regulation plays an important role in transcriptional control. At the same time, it also highlights the importance of resolution in looking at protein-DNA binding, focusing on the power of ChIP-exo technology to study the positional organization of protein-DNA complexes.

To follow up with this technique, here’s the ChIP-exo paper!

To read more about RP gene regulatory mechanisms, go here!