The ATRXt Protein Represses rDNA Transcription While Mirroring ATRX Interactions and Heterochromatin Localization

The ATRX gene encodes an SWI/SNF-type chromatin remodeling protein that is critical for proper development of the mammalian central nervous system and musculoskeletal system. While significant progress has been made in understanding the molecular functions of the full-length (FL) ATRX protein, there is still very little known about its conserved alternative spliceoform, ATRXt. ATRXt is a truncated isoform of ATRX which lacks the entire SWI/SNF domain due to the retention of intron 10, which results in the in-frame addition of 61 unique amino acids (exon 10a) at its C-terminus. Here, we demonstrate that ATRXt accounts for 5-20% of total ATRX protein levels, while showing tissue- and differentiation-specific changes in expression levels compared to its full-length counterpart. ATRXt shows enriched localization at H3K9me3-positive heterochromatin but not at PML-nuclear bodies, while physically interacting with the known FL-ATRX protein partners, DAXX and HP1α. Exon 10a can target a GFP-fusion protein to the nucleolus, but removal of exon 10a from ATRXt does not prevent nucleolar localization. Finally, re-introducing ATRXt into the ATRX-negative U2OS cell line reduced rRNA transcription and severely hampered cell growth, similar to previous studies using FL-ATRX. Our study highlights that ATRXt has many of the same properties as FL-ATRX, suggesting that some roles of ATRX do not require remodeling activity, while highlighting the need to distinguish ATRXt's functions from those of the full-length protein.