ATRX proximal protein associations boast roles beyond histone deposition

Abstract

The ATRX ATP-dependent chromatin remodelling/helicase protein associates with the DAXX histone chaperone to deposit histone H3.3 over repetitive DNA regions. Because ATRX-protein interactions impart functions, such as histone deposition, we used proximity-dependent biotinylation (BioID) to identify proximal associations for ATRX. The proteomic screen captured known interactors, such as DAXX, NBS1, and PML, but also identified a range of new associating proteins. To gauge the scope of their roles, we examined three novel ATRX-associating proteins that likely differed in function, and for which little data were available. We found CCDC71 to associate with ATRX, but also HP1 and NAP1, suggesting a role in chromatin maintenance. Contrastingly, FAM207A associated with proteins involved in ribosome biosynthesis and localized to the nucleolus. ATRX proximal associations with the SLF2 DNA damage response factor help inhibit telomere exchanges. We further screened for the proteomic changes at telomeres when ATRX, SLF2, or both proteins were deleted. The loss caused important changes in the abundance of chromatin remodelling, DNA replication, and DNA repair factors at telomeres. Interestingly, several of these have previously been implicated in alternative lengthening of telomeres. Altogether, this study expands the repertoire of ATRX-associating proteins and functions.

Inhibition of p53 and ATRX increases telomeric recombination in primary fibroblasts

“…In particular, we observed an increase in crossover products, but a much higher increase in noncrossover products. This is in agreement with the observation of Scott et al [51], but in disagreement with Elbakry et al [48], which observed that ATRX inhibition increases SDSA at the expenses of SCE. We also observed a correlation (although we did not demonstrate causality) between telomeric cohesion and recombination.…”

Effects of p53 and ATRX inhibition on telomeric recombination in aging fibroblasts

“…Moreover, upon depletion of ATRX in HeLa and HEK293 cells (which both have inactive p53), Scott et al. ( 55 ) found increased levels of telomeric H2AX, PML, POLD3 and decreased levels of telomeric BRCA2, a picture similar to the one seen in ALT models. The authors also found evidence of ATRX-mediated recruitment of SLF2 (a member of the SMC5/6 complex) to telomeres and found that the loss of these proteins causes an increase of T-SCE and “telomere exchanges” (a kind of T-SCE showing an exchange on a chromatid and a single signal on the other chromatid, see Figure 5 ).…”

Actionable loss of SLF2 drives B‐cell lymphomagenesis and impairs the DNA damage response

“…SLF2 has no known function in cancer yet has been identified as a DNA repair factor that acts as a localization factor of the SMC5/6 complex and other DNA damage and DNA repair factors at DNA damage sites (Raschle et al , 2015 ; Scott et al , 2021 ). To validate the function of SLF2 in the DDR, we generated CRISPR/Cas9‐mediated knockouts (KO) of SLF2 in U‐2‐OS cells.…”

“…To unravel the molecular mechanism which leads to impaired CHK1 activation following SLF2 loss, we undertook an unbiased mass spectrometry‐based approach on SU‐DHL‐5 parental and SLF2 KO cells. Considering that SLF2 is best characterized as a chromatin recruitment factor for DNA repair and chromatin remodeling factor (Raschle et al , 2015 ; Scott et al , 2021 ), we aimed to understand how loss of SLF2 affects the chromatin landscape. To this end, we studied the chromatin proteome of the parental and SLF2‐deficient SU‐DHL‐5 cells.…”