Abstract
Most of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis.
Highlights
Nuclei obtained from histologically normal colonic tissue in patients with an adenoma show an increase in heterogeneity of structure, with variations in aggregate clusters forming throughout the nucleus immediately observable in the formation of large heterochromatin and euchromatin domains (Fig. 1B). These qualitative differences in topology extend to the nanoscopic texture of chromatin: with sub-regions of nuclei from control patients appearing more diffuse/homogeneous (Fig. 1C and D) in comparison to sub-regions of nuclei from patients with an adenoma (Fig. 1E and F). Owing to this finding[18] and previous studies showing that the spatial organization of chromatin is well described as a fractal at length scales that range below that formed by chromatin loops[18,26,28,29,30,31], we explored from the mathematical point of view whether these changes in fractal dimension could provide quantitative insight into the interplay between the physical structure of chromatin and transcription[2,12,26]
As the false discovery rate (FDR) in microarray analysis can be high for individual genes and our primary aim was to test our model between the fractal topology of chromatin and the global pattern of gene transcription, we focused on general patterns of the differentially expressed genes by performing comparative analysis across all possible pairwise groups
Expression of genes responsible for oxidation, stress response (Stress), actin remodeling (Actin), and protein regulation are suppressed as Ld increases
Summary
We utilized microarray analysis to measure changes in gene expression and PWS microscopy to measure the changes in chromatin heterogeneity in colonic HT-29 cells under different growth conditions. In order to test experimentally if such a relationship exists between the physical structure of chromatin and transcription globally, we performed PWS microscopy to measure physical topology and microarray gene analysis to measure gene expression in colonic HT-29 cells grown under different conditions.
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