GSE87585 The Aneuploid Multiple Myeloma 3D Genome Reveals Spatial Genome Disorganization Associated with Copy Number Variations and Gene Expression

Contributors : Tingting Li ; Lumeng Jia ; Ruifeng Li ; Pengze WuSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Genome variation profiling by high throughput sequencingOrganism : Homo sapiensHi-C technique has been widely applied to study the three-dimensional architecture of the whole genome. Genome structures such as compartment A/B, TAD (topologically associated domain) and chromatin loops can be identified from Hi-C data in both normal cells of human and other species, and are found to be associated with features such as epigenetic markers, DNA-binding proteins and gene expression. But such technique had been rarely used in cancer studies. Here we used Hi-C to study the aneuploid cancer genomic architecture in multiple myeloma cells. Our results indicate that Hi-C interaction matrix of cancer cells is affected by CNVs and should be adjusted for copy number. After correcting this CNV bias, we found a significant overlapping between the boundaries of CNV blocks and boundaries of TADs, which suggests that TAD boundaries are fragile sites for CNV breakpoints. In addition, the compartment A/B switching is associated with differential gene expression, from which we found important genes that are related with multiple myeloma. We build a 3D structure model of the aneuploidy genome and found that there are great changes both in the whole genome spatial interactome and local chromosome territ...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Genome variation profiling by high throughput sequencing Homo sapiens Source Type: research