Research On The Effect Of ATRX On Chromatin Openness And Gene Expression Regulation

The ATRX gene,which encodes a component of SWI/SNF-like chromatin remodeling complex,plays pivotal roles in heterochromatin maintenance and gene transcriptional regulation.Frequent mutations in ATRX have been identified in a variety of tumors,including pancreatic neuroendocrine tumors,adult lower-grade gliomas,pediatric glioblastoma multiforme,pediatric adrenocortical carcinoma,osteosarcoma,neuroblastoma and hepatocellular carcinoma.In tumors and cancer cell lines,ATRX loss has been associated to alternative lengthening of telomere(ALT),which is a telomerase-independent way to enable telomere extension.However,the functional impact of ATRX binding on heterochromatin in human cancer cells has not been fully investigated.To elucidate ATRX-mediated epigenomics changes in cancer cells,we utilized ATAC-seq to generate the accessibility profiles for both ATRX intact and ATRX knockout cells in a human liver cancer cell line PLC/PRF/5.With an analysis focusing on repetitive regions,we identified 503 repetitive DNA elements with differential chromatin accessibilities.Strikingly,we found that loss of ATRX led to a significant increase in open chromatin at telomeric and centromeric regions,and a significant reduction at repetitive regions containing certain retrotransposons.We uncovered a positive correaltion between the GC content in repetitive regions and chromatin accessibility change.For other regions of the genome,a total of 14381 genomic regions with significant changes in chromatin accessibility were identified,of which 8829 regions had enhanced accessibilities,while the remaining 5552 regions had decreased accessibilities.Combining accessibility profiles with gene expression data,we identified 1691 potential links of DNA regulatory elements to genes,and found the activation of TGF-?signaling and the downregulation of CDH family driven by ATRX loss.In addition,we noticed that some cancer-related genes,such as MUC16 and CXCL8 were significantly up-regulated after ATRX loss through increased opening of chromatin regions in these gene loci.Collectively,these findings suggest that global changes in chromatin accessibility and transcription after ATRX inactivation might be involved in promoting tumorigenesis.