Poster abstracts
Poster number 55 submitted by Chuyue Zhang
Identification of novel RNA-protein binding events through a covalent tag
Chuyue Zhang (MB&B, Yale University), Karla Neugebauer (MB&B, Yale University)
Abstract:
RNA-protein interactions are fundamental regulators of a multitude of biological processes. Perturbation of ribonucleoprotein (RNP) complexes has been implicated in diseases including neurodegenerative disorders and cancer. To investigate nuclear RNP biology across distinct pathways, I profiled the RNA substrates of three proteins through covalent linkage and affinity purification (CLAP-seq), where HaloTag was employed to enable more efficient and stringent capture of their respective RNA interactome. COIL, the Cajal body scaffold protein, is found to primarily bind small nuclear and small nucleolar RNAs (sn/snoRNAs), consistent with its role as the biogenesis hub of these noncoding RNAs. On the other hand, the poly(A) binding protein PABPN1 almost exclusively interacts with mRNAs. Surprisingly, I observed PABPN1 binding to mRNA introns, distinct from its canonical poly(A) binding activity at 3’ ends. Given PABPN1’s established role in nuclear RNA retention and PAXT-dependent mRNA degradation, I analyzed a publicly available PABPN1 siRNA knockdown dataset. In line with prior publications, PABPN1 binds to members of the snoRNA host gene (SNHG) family and downregulates their expression. In contrast, genes with PABPN1 intronic binding have their expression downregulated or unchanged upon PABPN1 depletion, suggesting a PAXT-independent role of PABPN1. Using CLAP-seq, I also uncovered novel binding events for the telomerase Cajal body protein 1 (TCAB1) on mRNA exons besides its known snoRNA binding properties. Taken together, these data uncover novel RNA binding events for PABPN1 and TCAB1 and suggest RNA regulation mechanisms beyond their canonical functions.
Keywords: RNA-protein interaction, CLAP-seq, PABPN1