ALC1/eIF4A1-mediated regulation of CtIP mRNA stability controls DNA end resection

During repair of DNA double-strand breaks, resection of DNA ends influences how these lesions will be repaired. If resection is activated, the break will be channeled through homologous recombination; if not, it will be simply ligated using the non-homologous end-joining machinery. Regulation of resection relies greatly on modulating CtIP, which can be done by modifying: i) its interaction partners, ii) its post-translational modifications, or iii) its cellular levels, by regulating transcription, splicing and/or protein stability/degradation. Here, we have analyzed the role of ALC1, a chromatin remodeler previously described as an integral part of the DNA damage response, in resection. Strikingly, we found that ALC1 affects resection independently of chromatin remodeling activity or its ability to bind damaged chromatin. In fact, it cooperates with the RNA-helicase eIF4A1 to help stabilize the most abundant splicing form of CtIP mRNA. This function relies on the presence of a specific RNA sequence in the 5 ' UTR of CtIP. Therefore, we describe an additional layer of regulation of CtIP-at the level of mRNA stability through ALC1 and eIF4A1. Author summary The DNA molecule is constantly threatened by the appearance of physical or chemical modifications that endanger the integrity of the genetic information. Among them, the breakage of the DNA molecule is the most challenging to deal with. In order to minimize such risks, cells have developed multiple DNA repair mechanisms that take care of broken chromosomes. The regulation of the usage of each different mechanism is extremely important for the safekeeping of the genetic material. CtIP is a key protein of pivotal importance in the decision between different broken DNA repair pathways. Here we show a novel regulatory mechanism that controls the abundance of this protein by controlling the stability of the different mRNA molecules produced by the CtIP gene. In brief, we show that the factors ALC1 and eIF4A1 affect the stability of some, but not all, CtIP mRNA variants. This effect is dependent on the presence or absence of a specific RNA structure, called a G-quartet or G-quadruplex, in a non-coding portion of the mRNA.