XRN2-DDX23 cooperation in avoiding r-loop-induced genomic instability

The National Institute of General Medical Sciences (NIGMS), through its Biomedical Research and Research Training program (CFDA 93.859), awarded a $355,584 Project Grant to the New Mexico Institute of Mining and Technology (New Mexico Tech) on August 18, 2023. This funding will support research to determine the biochemical basis and functional implications of the interaction between the proteins XRN2 and DDX23, and explore their cooperative role in regulating RNA-DNA hybrid structures (R-loops) to maintain genomic integrity. The research aims to provide mechanistic insights into how XRN2 and DDX23 work together to avoid R-loop-induced genomic instability, which can contribute to diseases like neurodegenerative disorders, autoimmune diseases, and cancer. The project will run through July 31, 2026.

Abstract

Compromised genomic integrity results in several debilitating diseases such as neurodegenerative disorders, autoimmune diseases, and cancer. Persistent nucleic acid structures containing RNA-DNA hybrids with a displaced single-stranded DNA (r-loops) are a potent source of genomic instability. One of the major sources of r-loops is impaired regulation of RNA polymerase II (rnapii) at transcription termination sites of protein coding genes. In humans, the 5'-3'-exoribonuclease 2 (XRN2) is essential for genome-wide timely termination of rnapii downstream of poly(a) sites. In essence, XRN2's role in RNA metabolism is well understood. However, its role in genome maintenance remains elusive and there is lack of functional information regarding its molecular contributions in coordinating DNA repair, resolving replication stress, and promoting cell survival. Our long-term research goal is to define the roles of transcription termination factors including XRN2, in preventing r-loop-induced genomic instability and identify avenues to target their vulnerabilities. For this research program, we will primarily focus on delineating the interplay of XRN2 and dead (ASP-GLU-ALA-ASP) box helicase 23 (DDX23). We recently defined the interactome of XRN2 and identified molecular links that connect IT to DNA double-strand break (DSB) repair and cell cycle control of chromosomal replication. Our data support XRN2 and DDX23 interaction and a potential interplay of these two enzymes in r-loop metabolism and genome maintenance. We hypothesize that XRN2-DDX23 interaction enables them to cooperatively suppress r-loop-induced genomic instability and deficiencies of these enzymes engage central DNA damage sensor protein poly(ADP-ribose) polymerase 1 (PARP1) to coordinate repair of dsbs emanating from impaired r-loop homeostasis. We will pursue following specific aims to test our hypothesis; aim 1: determine the biochemical basis and functional implications of XRN2 and DDX23 interaction. Aim 2: determine the biological significance of XRN2-DDX23 interplay in r-loop metabolism and genome maintenance. Collectively, our studies will provide mechanistic insights into XRN2-DDX23 cooperation in avoiding r-loop-induced genomic instability, and establish potential avenues for targeting XRN2 and DDX23 vulnerabilities.