Phosphorylation-dependent regulation of Eleven Lysine Rich Leukemia (ELL) uncovered by quantitative global phosphoproteomic analysis.

Transcription elongation represents a key regulatory checkpoint that controls RNA polymerase II processivity and gene expression output. The human Eleven-nineteen lysine-rich leukemia (ELL) protein functions as a conserved RNA polymerase II elongation factor that enhances productive transcription by suppressing transient polymerase pausing and uniquely serves as the only Super Elongation Complex component capable of directly stimulating transcription elongation in vitro; however, the mechanisms governing its regulation through phosphorylation remain poorly defined. Here, we systematically curated and analysed the publicly available global phosphoproteomics datasets to characterise the phosphorylation landscape of ELL. Serine 309 (S309) emerged as the most frequently detected and consistently regulated phosphosite across multiple datasets. Phosphosite-specific co-regulation analysis identified coordinated phosphorylation patterns across ELL (S309) and proteins involved in transcriptional regulation and DDR, including PBRM1 (S648), where phosphorylation at S648 is associated with Double Strand Break induced transcriptional silencing. Additionally, ATM (S1885) and TP53 (S392), the core proteins associated with DNA damage response and previously identified binary interactors of ELL, show consistent co-regulation with (S309), along with several phosphosites reported in cancer-related datasets. Together, our findings explore the phosphorylation landscape of ELL by identifying S309 as its predominant phosphosite and establish a framework for future studies to define how the ELL phosphorylation contributes to transcriptional regulation, DNA damage response pathways and tumor-associated processes.