FOXD3 promotes homologous recombination repair and genomic stability by facilitating MRE11-mediated DNA end resection

Abstract

Homologous recombination (HR) is crucial for the high-fidelity repair of DNA double-strand breaks (DSBs), ensuring the maintenance of genome stability. In this study, we show that FOXD3 interacts with poly (ADP-ribose) polymerase 1 (PARP1) and is recruited to DSBs in a PARP1-dependent manner. FOXD3 directly binds to the DSB repair protein MRE11 and promotes its recruitment to DSB sites, ensuring proper end resection. Inhibition of FOXD3 expression compromises HR-mediated DSB repair and chromosome stability and sensitizes cancer cells to ionizing radiation. Collectively, our findings demonstrate that FOXD3 promotes HR-mediated DSB repair and genome stability.

1. Introduction

Genomic DNA is constantly under attack by a variety of environmental and endogenous factors, as one unrepaired DNA double-strand break (DSB) is sufficient to trigger apoptosis, and the accumulation of error-prone repair can lead to genomic instability [1,2]. Genomic instability facilitates the rapid acquisition of genetic diversity, contributing to the development of diverse cancer phenotypes, and is crucial for cancer progression and recurrence [3]. In general, DSBs, the most detrimental among the resulting DNA lesions, can be repaired by two major pathways, namely, non-homologous end joining (NHEJ) and homologous recombination (HR) [4]. HR repair utilizes the sister chromatid as a template; thus, it only occurs in the S/G2 phase of the cell cycle and has high fidelity. NHEJ can be further divided into error-prone canonical NHEJ (c-NHEJ), which re-ligates broken DNA ends after limited end resection and thus can occur throughout the cell cycle, and more mutagenic microhomology-mediated end joining, which utilizes the internal microhomologies of 2–6 base pairs within the DNA as a repairing template, mainly in mitosis [5–7]. These pathways are promising targets for cancer therapy [8,9].

In DSB sensing, the Mre11/Rad50/Nbs1 (MRN) complex is among the earliest factors recruited to DSB ends, promoting the activation of the DNA damage response (DDR) core kinase ataxia telangiectasia mutated (ATM) [10,11] and initiating limited end resection of DSBs in conjunction with CtBP-interacting protein/CtIP and BRCA1 during HR [12–14]. This resection is attributed mainly to MRE11, which possesses both single-stranded DNA (ssDNA) endonuclease activity and double-stranded DNA 3′→5′ exonuclease activity [15–17]. The resulting 3′ ssDNA overhang is coated by replication protein A (RPA) until it is replaced by Rad51, leading to strand invasion into homologous DNA sequences for pairing [18,19]. Although Rad17-mediated or MDC1-mediated MRN complex accumulation and retention at DSBs are well established [20–22], the precise mechanism of MRN complex recruitment at an early stage of DDR is still obscure.

Forkhead box D3 (FOXD3), which belongs to the family of FOXD transcription factors, acts as a transcriptional activator or repressor [23,24]. The FOXD3 protein reportedly has a tumor suppressor function in a variety of tumors, including liver cancer, malignant melanoma, stomach cancer, nasopharyngeal cancer, breast cancer, lung cancer, colorectal cancer, and thyroid cancer [25–32]. It also plays an important role in maintaining genome integrity through the transient inhibition of transcription during S phase entry, enabling faithful DNA replication in pluripotent cells [33]. However, it remains unknown whether FOXD3 also plays a role in the DNA damage response independent of its transcription factor function.