The telomerase holoenzyme consists of two essential components, a reverse transcriptase, TERT (telomerase reverse transcriptase), and an RNA molecule, TR (telomerase RNA, also known as TERC), that contains the template for the synthesis of new telomeric repeats. Telomerase RNA has been isolated from 32 different vertebrates, and a common secondary structure has been proposed (Chen, J.-L., Blasco, M. A., and Greider, C. W. (2000) Cell 100, 503-514). We have generated 25 mutants in the four conserved structural domains of the mouse telomerase RNA molecule, mTR, and assayed their ability to reconstitute telomerase activity in mTR(-/-) cells in vivo. We found that the pseudoknot and the CR4/CR5 domains are required for telomerase activity but are not essential for mTR stability in the cell, whereas mutations in the BoxH/ACA and the CR7 domains affect mTR accumulation in the cell. We have also identified mTR mutants that are able to inhibit wild type telomerase in vivo.