Abstract
For studying the 3D structure formed by consecutive genomic regions of chromosomes we propose using statistical shape theory in conjunction with registration methods. In contrast to earlier work, where the 3D chromatin structure was analyzed indirectly, we here directly exploit the 3D locations of genomic regions to determine the large-scale structure of chromatin fiber. Our study is based on 3D microscopy images of the X-chromosome where four consecutive genomic regions (BACs) have been simultaneously labeled by multicolor FISH. To allow unique reconstruction of the 3D shape, image data with sets of four consecutive BACs have been acquired with an overlap of three BACs between the different sets. We have statistically analyzed the data and it turned out that for all datasets the 3D structure is non-random. In addition, we found that the shapes of active and inactive X-chromosomal genomic regions are statistically independent. Moreover, we reconstructed the 3D structure of chromatin in a small genomic region based on five BACs resulting from two overlapping four BACs. We also found that spatial normalization of cell nuclei using non-rigid image registration has a significant influence on the location of the genomic regions.
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Yang, S. et al. (2011). Statistical Shape Theory and Registration Methods for Analyzing the 3D Architecture of Chromatin in Interphase Cell Nuclei. In: Adams, N., Freemont, P. (eds) Advances in Nuclear Architecture. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9899-3_4
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DOI: https://doi.org/10.1007/978-90-481-9899-3_4
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