Transcriptional elongation is regulated by both positive and negative transcription elongation factors and is recognized as an important target for transcriptional regulation (37). The human positive transcription elongation factor b (P-TEFb) is composed of a 43-kDa catalytic subunit, CDK9 (previously known as PITALRE) (13), and an 87-kDa regulatory subunit, cyclin T1 (33, 46). Cyclin T1 is the predominant cyclin associated with CDK9 in HeLa nuclear extracts, although CDK9 is also present in complexes with cyclins T2 and K (9, 33). Cyclin T1 is most closely related to the C-type cyclins, which, paired with their associated CDKs, function in transcriptional regulation by phosphorylating the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII) (6). P-TEFb was originally identified by its ability to stimulate RNAPII transcriptional elongation in vitro (29, 30). The CTD of RNAPII present in preinitiation complexes and early elongation complexes is hypophosphorylated but becomes hyperphosphorylated during productive elongation (25). P-TEFb is proposed to facilitate the transition from abortive to productive elongation by hyperphosphorylating the RNAPII CTD. Removal of the CTD in early elongation complexes abolished P-TEFb function, suggesting that the CTD is the target of P-TEFb function (28). CDK9 has been shown to phosphorylate the RNAPII CTD in vitro and is sensitive to 5,6-dichloro-1-β-d-ribofuranosyl-benzimidazole (DRB), which is a known inhibitor of transcriptional elongation (28, 49). Ubiquitin-dependent proteolysis plays an essential role in a number of cellular processes, including cell cycle progression, transcription, and signal transduction (reviewed in reference 5). Proteins destined for degradation by the proteasome are recognized and ubiquitinated in a process that requires a conserved cascade of enzymatic reactions (reviewed in reference 21). The ubiquitin-activating enzyme E1 and an E2 ubiquitin-conjugating enzyme function with E3 ubiquitin-protein ligases to covalently attach ubiquitin to lysine residues in substrate proteins. A polyubiquitin chain is synthesized by transfer of additional ubiquitin molecules to the assembling ubiquitin chain. Polyubiquinated substrates are targeted by the 26S proteasome for degradation. The SCF E3 ubiquitin ligase system mediates the ubiquitination of many cellular proteins. SCF is named for three of its core components, p19SKP1, CDC53/cullin, and an F-box containing protein. p19SKP1 and F-box proteins interact through the F-box motif (1), while CDC53 bridges this complex to an E2 enzyme, CDC34 (47). An additional component, Rbx1/Roc1, enhances the recruitment of CDC34 (38). Substrates targeted for ubiquitination are recognized by different E3 ligases via specific motifs. One such motif is the PEST (rich in proline, glutamate, serine, and threonine) sequence (35), which is found in many proteins whose abundance is regulated by proteolysis, including cyclin D1, IκBα, fos, jun, myc, and p53 (reviewed in reference 34). F-box proteins are responsible for substrate recognition by different SCF E3 ligases. Here, we report that CDK9 is a novel target for SCFSKP2-dependent ubiquitination and degradation by the proteasome. CDK9 ubiquitination represents a unique example in which the SCF complex is recruited by the regulatory subunit, cyclin T1, while ubiquitination proceeds on its partner protein, CDK9. Our results have important implications for the regulation of P-TEFb activity in vivo.