PHF3 regulates RNA stability through PHD and TLD domains - ChIPseq CNOT

Transcription and RNA processing are tightly coupled and precisely coordinated to ensure appropriate levels of mature transcripts. The C-terminal domain (CTD) of RNA polymerase II (Pol II) is phosphorylated differentially during the transcription cycle and serves as a landing pad for a variety of transcriptional regulators and RNA processing proteins. PHD finger protein 3 (PHF3) binds to the serine-2 phosphorylated Pol II CTD with its Spen Paralogue and Orthologue C-terminal (SPOC) domain and regulates transcription elongation and mRNA stability. Here we show that PHF3 binds target RNAs by recognizing a G-rich motif prone to form G-quadruplexes (G4s). Two PHF3 zinc finger domains, PHD (plant homeo domain) and TLD (TFIIS-like domain) act in concert to bind and destabilize target RNAs and their deletion in HEK293T cells causes massive deregulation of gene expression. Together these results establish PHF3 as a Pol II and an RNA-binding protein that coordinates transcription elongation with RNA decay to regulate neuronal gene expression.