Pocket Protein Complexes Are Recruited to Distinct Targets in Quiescent and Proliferating Cells

Abstract

Biochemical and genetic studies have determined that retinoblastoma protein (pRB) tumor suppressor family members have overlapping functions. However, these studies have largely failed to distinguish functional differences between the highly related p107 and p130 proteins. Moreover, most studies pertaining to the pRB family and its principal target, the E2F transcription factor, have focused on cells that have reinitiated a cell cycle from quiescence, although recent studies suggest that cycling cells exhibit layers of regulation distinct from mitogenically stimulated cells. Using genome-wide chromatin immunoprecipitation, we show that there are distinct classes of genes directly regulated by unique combinations of E2F4, p107, and p130, including a group of genes specifically regulated in cycling cells. These groups exhibit both distinct histone acetylation signatures and patterns of mammalian Sin3B corepressor recruitment. Our findings suggest that cell cycle-dependent repression results from recruitment of an unexpected array of diverse complexes and reveals specific differences between transcriptional regulation in cycling and quiescent cells. In addition, factor location analyses have, for the first time, allowed the identification of novel and specific targets of the highly related transcriptional regulators p107 and p130, suggesting new and distinct regulatory networks engaged by each protein in continuously cycling cells.

ACKNOWLEDGMENTS

We thank I. Sanchez, L. Gardner, A. Blais, M. Tsikitis, and members of the Dynlacht laboratory for critical input and suggestions. We are grateful to Michael S. Huh for the help with MEFs. We are grateful to the NYU Cancer Institute Genomics Facility for providing necessary instrumentation and expertise.

N.H.L. was initially supported by an NRSA postdoctoral fellowship (1F32-AG025617-01) and is now supported by a Susan G. Komen postdoctoral fellowship (PDF0504345). This work was initiated and completed using funds from the American Cancer Society (#RSG-0034204CCG) and NIH (2R01 CA77245-07), respectively, to B.D.D.