Spatial genome organization during T-cell differentiation

Abstract

The spatial organization of genomes within the mammalian cell nucleus is non-random. The functional relevance of spatial genome organization might be in influencing gene expression programs as cells undergo changes during development and differentiation. To gain insight into the plasticity of genomes in space and time and to correlate the activity of specific genes with their nuclear position, we systematically analyzed the spatial genome organization in differentiating mouse T-cells. We find significant global reorganization of centromeres, chromosomes and gene loci during the differentiation process. Centromeres were repositioned from a preferentially internal distribution in undifferentiated cells to a preferentially peripheral position in differentiated CD4+ and CD8+ cells. Chromosome 6, containing the differentially expressed T-cell markers CD4 and CD8, underwent differential changes in position depending on whether cells differentiated into CD4+ or CD8+ thymocytes. Similarly, the two marker loci CD4 and CD8 showed distinct behavior in their position relative to the chromosome 6 centromere at various stages of differentiation. Our results demonstrate that significant spatial genome reorganization occurs during differentiation and indicate that the relationship between dynamic genome topology and single gene regulation is highly complex.

Gene expression, chromosome position and lamin A/C mutations

“…Interestingly, both loci were Whole chromosome movement has been noted during erythroid differentiation, adipogenesis, T-cell differentiation and keratinocyte differentiation. [8][9][10][11] Recent work has shown that there are dramatic changes in the interactions between chromatin and the nuclear lamina during terminal differentiation. 12 Regions of the genome that associate with the nuclear lamina can be marked using DNA adenine methylase (Dam) referred to as DamID.…”

Chromosomal rearrangements after ex vivo Epstein–Barr virus (EBV) infection of human B cells

“…For Q-FISH, cells were fixed in a way that preserves the shape of 3D nuclei (Chuang et al, 2004;Kim et al, 2004;Caporali et al, 2007). Briefly, cell pellets were submitted to a hypotonic shock for 10 min in 0.075 M KCl at room temperature.…”

Novel automated three‐dimensional genome scanning based on the nuclear architecture of telomeres

“…Prior to the hybridization the samples were equilibrated for 1 h in 70% formamide (Fluka-Sigma Aldrich, St Louis, MO), 23 SSC at room temperature. The slides were hybridized with Cy3-labeled telomere-specific PNA probe (DAKO) and washed as previously published (34)(35)(36). DAPI (4 0 ,6-diamidino-2-phenylindole) was purchased from Sigma Aldrich (Oakville, ON) and used at 0.1 lg ml 21 to counterstain the nuclei on the slides (31,35).…”