# RNA Binding to CCRRM of PABPN1 Induces Conformation Change

## TL;DR

This study shows how RNA binding changes the structure of a key region in the PABPN1 protein, which may affect RNA processing and gene regulation.

## Contribution

The study reveals that RNA binding induces conformational changes in the CCRRM fragment of PABPN1, potentially enhancing RNA interaction and specificity.

## Key findings

- The CCRRM fragment of PABPN1 binds strongly to poly(A) RNA and moderately to GU-rich and CU-rich sequences.
- RNA binding causes structural changes in the CC region of CCRRM, as shown by small-angle X-ray scattering.
- These conformational changes may improve RNA interaction and specificity, suggesting a role in mRNA regulation.

## Abstract

PABPN1 is a highly conserved nuclear poly(A)-binding protein in eukaryotes. This study utilized electrophoretic mobility shift assays, biolayer interferometry, and selective 2′-hydroxyl acylation analyzed by primer extension to confirm the RNA-binding capacity. We found that the CCRRM fragment of PABPN1 exhibits high affinity for poly(A) RNA, displays moderate affinity for GU-rich and CU-rich sequences, and shows minimal binding to AU-rich and CA-rich sequences. Furthermore, small-angle X-ray scattering was employed to analyze the solution conformations of CCRRM in its RNA-free and RNA-bound states. The results revealed that RNA binding induces conformational changes, primarily in the CC region. This local structural adjustment may enhance the protein’s ability to interact with RNA, thereby improving binding specificity.

Poly(A) Binding Protein Nuclear 1 (PABPN1) is a nuclear poly(A)-binding protein that is highly conserved in eukaryotes. It plays multifaceted roles in RNA processing and metabolism, with its dysregulation closely linked to various diseases. PABPN1 contains an alanine-rich N-terminus, a central coiled-coil domain (CC), a conserved RNA recognition motif (RRM) and a C-terminal extension. PABPN1 influences mRNA splicing and stability through its RNA-binding capabilities, thereby modulating gene expression. While PABPN1 is known to interact with RNA, the molecular mechanism underlying this interaction with RNA awaits further investigation. Here, we designed and purified a PABPN1 fragment encompassing the RNA-binding domain (CCRRM fragment, amino acids 114–254). Using a combination of 3D modeling, small-angle X-ray scattering (SAXS) and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) assay, our result indicated that CCRRM exhibits a high affinity for poly(A) RNA, a moderate affinity for GU-rich and CU-rich sequences, and negligible binding to AU-rich and CA-rich sequences. RNA binding induces conformation change in the CC. These results suggest that PABPN1 could potentially be involved in cytoplasmic polyadenylation and may influence the regulation of mRNA translation and degradation, although further investigation is required to confirm this role.