Targeted protein degradation reveals direct roles of SPT6 in POL2 elongation and termination

SPT6 is both, an important histone chaperone and POL2 elongation factor but its primary role on transcription in mammalian cells remains open, as no acute depletion system is available. We used targeted protein degradation to rapidly deplete SPT6 and analyzed defects in POL2 behavior by a multi-omics approach and estimated POL2 processivity, elongation rates and termination and compared it to gene transcription. Our data indicate that SPT6 is a crucial factor for POL2 elongation. Unexpectedly, SPT6 has also a vital role in POL2 termination, as acute depletion induces POL2 read through at most protein coding genes. In contrast, acute depletion did not induce spurious intragenic initiation, while this behavior can be induced by long-term depletion of SPT6 and can therefore be attributed to its function as a histone chaperone. In conclusion, targeted protein degradation of SPT6 allows the kinetic discrimination of its function as a histone chaperone and POL2 elongation factor. Overall design: 4sU-seq, ChIP-seq (SPT6, Ser2 Pol2 and Total Pol2), DRB-4sU-seq and SLAM-seq in presence or absence of SPT6 ChIP-seq (CSTF2,H3,TFIIF,TBP,pH2AX) in presence or absence of SPT6