The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. The turnover of RNAPII permits the subsequent recruitment of an elongation-competent RNAPII complex, leading to productive elongation. In contrast, enhancers require INTS11 catalysis not to evict paused RNAPII but rather to terminate enhancer RNA transcription beyond the +1 nucleosome. These findings are supported by the differential occupancy of negative elongation factor (NELF), SPT5, and tyrosine-1-phosphorylated RNAPII. This study elucidates the role of Integrator in mediating transcriptional elongation at human promoters through the endonucleolytic cleavage of nascent transcripts and the dynamic turnover of RNAPII. Overall design: ChIP-seq of RNAPII and INTS11 in INTS11-depleted in HeLa shINTS11 cells in duplicates. ATAC-seq in HeLa shINTS11 cells in duplicates. Total RNA-seq of INTS11-depleted in HeLa shINTS11 cells in duplicates. small RNA-seq INTS11-depleted or control in HeLa shINTS11, shGFP, WT and E203Q mutant INTS11 cells in duplicates. CAGE-seq control in HeLa shGFP cells in duplicates. ChIP-seq of RNAPII and INTS11 in INTS11-depleted in HeLa shINTS11 cells in duplicates. ATAC-seq in HeLa shINTS11 cells in duplicates. Total RNA-seq of INTS11-depleted in HeLa shINTS11 cells in duplicates. small RNA-seq INTS11-depleted or control in HeLa shINTS11, shGFP, WT and E203Q mutant INTS11 cells in duplicates. CAGE-seq control in HeLa shGFP cells in duplicates.