The present invention relates to isolated polynucleotides encoding a family of silencing mediators of retinoic acid and thyroid hormone receptor (SMRT) isoforms, including vertebrate and invertebrate isoforms thereof. The invention also relates to polypeptide SMRT co-repressors encoded by invention SMRT polynucleotides, and to peptide portions thereof that can modulate transcriptional potential of a nuclear receptor. In addition, the invention relates to chimeric molecules and to complexes containing a SMRT co-repressor or peptide portion thereof, to antibodies that specifically bind such compositions, and to methods for identifying an agent that modulates the repressor potential of a SMRT co-repressor. The invention also provides methods for identifying an agent that modulates a function of a SMRT co-repressor; for modulating the transcriptional potential of a nuclear receptor in a cell using the compositions of the invention; and for identifying a molecule that interacts specifically with a SMRT co-repressor.