Multiple N-CoR complexes contain distinct histone deacetylases

N-CoR (nuclear receptor corepressor) is a corepressor for multiple transcri ption factors including unliganded thyroid hormone receptors (TRs). In vitr o, N-CoR can interact with the Sin3 corepressor, which in turn binds to the histone deacetylase Rpd3 (HDAC1), predicting the existence of a corepresso r complex containing N-CoR, Sin3, and histone deacetylase. However, previou s biochemical studies of endogenous Sin3 complexes have failed to find an N CoR association. Xenopus laevis eggs and oocytes contain all of the necess ary components for transcriptional repression by unliganded TRs. In this st udy, we report the biochemical fractionation of three novel macromolecular complexes containing N-CoR, two of which possess histone deacetylase activi ty, from Xenopus egg extract. One complex contains Sin3, Rpd3, and RbAp48; the second complex contains a Sin3-independent histone deacetylase; and the third complex lacks histone deacetylase activity. This study describes the first biochemical isolation of endogenous N-CoR-containing HDAC complexes and illustrates that N-CoR associates with distinct histone deacetylases th at are both dependent and independent of Sin3. Immunoprecipitation studies show that N-CoR binds to unliganded TR expressed in the frog oocyte, confir ming that N-CoR complexes are involved in repression by unliganded TR. Thes e results suggest that N-CoR targets transcriptional repression of specific promoters through at least two distinct histone deacetylase pathways.