Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin

Abstract

DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.

DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling

“…These data indicate a functional antagonism between Fun30 and Rad9. Notably, also in human cells SMARCAD1 acts as resection activator, while the Rad9 orthologue 53BP1 is a resection inhibitor ( Lazzaro et al, 2008 ; Bunting et al, 2010 ; Bothmer et al, 2011 ; Costelloe et al, 2012 ; Densham et al, 2016 ), suggesting that the antagonism of both factors is conserved throughout eukaryotic evolution (please see ( Sanchez et al, 2021 )) in this issue for a detailed review on the interaction between 53BP1 and BRCA1 in the DSB repair decision). Notably, Rad9, 53BP1, as well as the fission yeast orthologue Crb2 associate with chromatin and have all been shown to bind to nucleosomes, where they recognize specific histone modifications ( Huyen et al, 2004 ; Nakamura et al, 2004 ; Sanders et al, 2004 ; Wysocki et al, 2005 ; Botuyan et al, 2006 ; Du et al, 2006 ; Toh et al, 2006 ; Grenon et al, 2007 ; Hammet et al, 2007 ; Fradet-Turcotte et al, 2013 ; Wilson et al, 2016 ; Hu et al, 2017 ; Kilic et al, 2019 ).…”

“…Depletion of SMARCAD1 stabilizes 53BP1 around DSB sites ( Densham et al, 2016 ). However, resection regulation in human cells is more complex compared to yeast as besides SMARCAD1 a second resection promoting factor exist, the BRCA1-BARD1 complex (reviewed in Densham and Morris, 2019 ; Sanchez et al, 2021 ). BRCA1-BARD1 form an E3 ubiquitin-ligase complex that mediates ubiquitylation of H2A ( Kalb et al, 2014 ; Densham et al, 2016 ; Leung et al, 2017 ; Nakamura et al, 2019 ).…”

“…Notably, resection destroys the substrate for repair by NHEJ and increasing amounts of 3′ single-stranded DNA (ssDNA) predisposes for repair by different mechanisms (alt EJ < HR < SSA, Blier et al, 1993 ; Falzon et al, 1993 ; Ira et al, 2004 ). The enzymatic process of resection has been subject of excellent reviews in this issue and elsewhere ( Symington and Gautier, 2011 ; Cejka and Symington, 2021 ; Elbakry and Löbrich, 2021 ; Sanchez et al, 2021 ). Here we focus on how resection and thereby the repair pathway decision is regulated by nucleosomes and nucleosome remodelers, enzymes that can evict, position and edit nucleosomes.…”

“…Nucleosomes form obstacles to the resection nucleases ( Figure 1 ). Initial short-range resection is carried out by the Mre11-complex (Mre11-C in the following, consisting of Mre11-Rad50-Xrs2 with the Sae2 activator in budding yeast, and analogously of MRE11-RAD50-NBS1 with CtIP in human) ( Symington and Gautier, 2011 ; Cejka and Symington, 2021 ; Elbakry and Löbrich, 2021 ; Sanchez et al, 2021 ). Endonucleolytic cleavage by Mre11-C occurs preferentially within nucleosome-free linker DNA, suggesting that nucleosomal DNA is protected and/or that chromatin binding of Mre11-C is guided by nucleosomes ( Mimitou et al, 2017 ; Wang et al, 2017 ).…”

Joining the PARty: PARP Regulation of KDM5A during DNA Repair (and Transcription?)

“…Integrative signaling between both the DDR and chromatin is necessary to ensure both repair efficiency and epigenome stability to maintain the fidelity of the underlying genetic sequence and its function. [ 15 ]…”