1. Department of Molecular and Cell Biology, Howard Hughes Medical Institute, 401 Barker Hall, University of California, Berkeley, California 94720-3204, USA
2. Present address: Sangamo BioSciences, Inc., Point Richmond Tech Center, 501 Canal Blvd., Richmond, California 94804, USA.

Correspondence to: Robert Tjian Correspondence and requests for materials should be addressed to R.T. (e-mail: Email: jmlim@uclink4.berkeley.edu).

Abstract

Drosophila TATA-box-binding protein (TBP)-related factor 2 (TRF2) is a member of a family of TBP-related factors present in metazoan organisms. Recent evidence suggests that TRF2s are required for proper embryonic development and differentiation^{1, 2, 3, 4, 5}. However, true target promoters and the mechanisms by which TRF2 operates to control transcription remain elusive. Here we report the antibody affinity purification of a Drosophila TRF2-containing complex that contains components of the nucleosome remodelling factor (NURF) chromatin remodelling complex as well as the DNA replication-related element (DRE)-binding factor DREF. This latter finding led us to potential target genes containing TRF2-responsive promoters. We have used a combination of in vitro and in vivo assays to show that the DREF-containing TRF2 complex directs core promoter recognition of the proliferating cell nuclear antigen (PCNA) gene. We also identified additional TRF2-responsive target genes involved in DNA replication and cell proliferation. These data suggest that TRF2 functions as a core promoter-selectivity factor responsible for coordinating transcription of a subset of genes in Drosophila.