The Integrator Complex Is Essential for Erythropoiesis

Erythropoiesis is a finely orchestrated process that involves the generation of a ~2.5 million red blood cells per second to maintain homeostasis and prevent anemia. During terminal maturation, erythroid precursors upregulate erythroid-specific genes while silencing non-erythroid genes in the setting of a cell that is rapidly dividing, and nucleus that is condensing in preparation for enucleation. Our group has shown that regulation of RNAPII activity is an essential determinant of erythroid cell function. During terminal erythroid maturation, RNA polymerase II (RNAPII) levels decline dramatically, becoming a scarce resource allocated to erythroid genes, such as alpha and beta globin (Murphy Blood 2021). The mechanism(s) by which RNAPII is removed from genes unnecessary to erythroid differentiation and shunted to produce mRNA essential for red blood cell function are unknown. The Integrator Complex (INT) is a modular and multi-subunit machinery that binds to paused RNAPII and promotes promoter-proximal termination. INT is highly expressed in maturing erythroid cells, although little is known about the function of INT during erythropoiesis. We hypothesize that INT facilitates promoter-proximal termination at non-erythroid genes to maintain RNAPII availability during terminal erythroid maturation.

The balance between kinase and phosphatase activity is a key regulator of RNAPII activity. Phosphorylation of the c-terminal domain of RNAPII by pTEFb facilitates RNAPII pause release, and promotes active transcription. Alternatively, subunit 8 of INT (INTS8) can dephosphorylate the c-terminal domain of RNAPII through association with protein phosphatase 2a (PP2A) (Huang Mol Cell 2020), enforcing RNAPII pausing and antagonizing pTEFb activity. Integrator subunit 11 then cleaves the nascent RNA causing promoter-proximal transcriptional termination (Wu PNAS 2017). To gain insights into the function of INT in erythropoiesis, we utilized the RNP method of Crispr/Cas 9 genome editing (Gundry Cell Reports 2016) to delete INTS8 from CD34+ HSPCs, and then subjected them to erythroid differentiation and colony forming assays. Disruption of INTS8 significantly impaired erythroid proliferation and viability. It also delayed erythroid maturation, evident by delayed GPA expression, less mature morphology, and lower rates of benzidine positivity. Moreover, INTS8 disruption led to a decline in erythroid colony-forming ability and decreased expression of alpha and beta globin. Together these data indicate that INT function is essential for erythropoiesis.

Integrator subunit 1 (INTS1) serves as a molecular scaffold for the complex, and can be used as an indicator of INT levels and occupancy. Western blotting demonstrated that INTS1 protein increased after CD36 selection and remained high throughout terminal erythroid maturation. To delineate the genomic targets of INT we performed CUT&RUN for INTS1 on day 7 and day 9 of erythroid culture following CD36 selection (as described in Gautier, Cell Reports 2016), corresponding to the basophilic and polychromatic stages of erythroid maturation. Approximately 50% of sites of INT occupancy were located at transcription start sites at both time points. Motif analyses of sites of INTS1 occupancy were enriched for transcription factors involved in signaling, including STAT5 (p1e-189) and SMAD2 (p1e-170), and INTS1 was present at several known STAT5 target genes including MYC and CCNB1. Interestingly, ~74% of genes with stably paused RNAPII, as indicated by a pausing index (PI) >4, were occupied by INTS1. Further, the level of INTS1 occupancy was significantly higher at genes with a PI >4 than genes with PI <4. The genomic occupancy of INTS increased from day 7 to day 9. Transcription start sites that gained INTS1 occupancy during maturation lost RNPII, suggesting a role for INT in promoting RNAPII eviction at these loci. Collectively, our findings identify a critical role for INT in governing erythroid maturation and gene expression, and provide novel insights into the transcriptional regulation of erythropoiesis.