ATRX proximal protein associations boast roles beyond histone deposition
Open Access
- 15 November 2021
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLoS Genetics
- Vol. 17 (11), e1009909
- https://doi.org/10.1371/journal.pgen.1009909
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. ATRX is a protein that is needed to keep repetitive DNA regions organized. It does so in part by binding the DAXX histone chaperone to deposit histone proteins on DNA and assemble structures known as nucleosomes. While important, ATRX has additional functions that remain understudied. To better understand its various biological roles, we first identified the other proteins that are found in its proximity. ATRX-associating proteins were implicated in a range of functions, in addition to histone deposition. Our results suggest that ATRX-associating proteins likely help compact DNA after it is assembled into nucleosomes, and also promote its stability. We then examined the effect of ATRX on telomeres (repetitive DNA regions at the end of chromosomes). ATRX and at least one of its associating proteins suppressed spurious DNA exchanges at telomeres. To understand why, we then identified proteomic changes that occur at telomeres when ATRX was deleted. Loss of ATRX altered the enrichment of a surprising number of proteins at telomeres, including several DNA damage response and chromatin remodelling proteins.Funding Information
- Canadian Institutes of Health Research (scholarship)
- Natural Sciences and Engineering Research Council of Canada (fellowship)
- Canadian Institutes of Health Research (PJT-159683)
- Natural Sciences and Engineering Research Council of Canada (RGPIN-2016-05559)
- Cancer Research Society
- Garron Family Cancer Center
- Cancer Research UK (C17183/A23303)
- Canada Foundation for Innovation
- Genome Canada
- Ontario Genomics (OGI-139)
- Natural Sciences and Engineering Research Council of Canada (fellowship)
- University of Birmingham and CR-UK Ph.D. studentship (C17422/A25154)
This publication has 114 references indexed in Scilit:
- A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cellsThe Journal of cell biology, 2012
- iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error EstimatesMolecular & Cellular Proteomics, 2011
- Prevalence of the Alternative Lengthening of Telomeres Telomere Maintenance Mechanism in Human Cancer SubtypesThe American Journal of Pathology, 2011
- Characterization of a 8q21.11 Microdeletion Syndrome Associated with Intellectual Disability and a Recognizable PhenotypeAmerican Journal of Human Genetics, 2011
- ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndromeNature Structural & Molecular Biology, 2011
- Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeresProceedings of the National Academy of Sciences of the United States of America, 2010
- Protein Complex of Drosophila ATRX/XNP and HP1a Is Required for the Formation of Pericentric Beta-heterochromatin in VivoOnline Journal of Public Health Informatics, 2010
- Purification of Proteins Associated with Specific Genomic LociCell, 2009
- A Novel Small Molecule That Alters Shelterin Integrity and Triggers a DNA-Damage Response at TelomeresJournal of the American Chemical Society, 2008
- Interaction between chromatin proteins MECP2 and ATRX is disrupted by mutations that cause inherited mental retardationProceedings of the National Academy of Sciences of the United States of America, 2007