Structural analysis of interphase X-chromatin based on statistical shape theory
Autor: | Siwei Yang, Karl Rohr, Roel van Driel, Roland Eils, Thomas Cremer, Boris Joffe, Doris Illner, Kathrin Teller, Irina Solovei |
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Přispěvatelé: | Synthetic Systems Biology (SILS, FNWI) |
Rok vydání: | 2008 |
Předmět: |
Normalization (statistics)
Image registration Genomic region Non-rigid image registration Biology Cell nuclei Chromosome (genetic algorithm) Humans Point (geometry) Interphase Molecular Biology In Situ Hybridization Fluorescence Genetics Chromosomes Human X Models Statistical Models Genetic business.industry Pattern recognition Cell Biology Statistical shape theory Chromatin Shape theory 3D chromatin structure Geometrical morphometrics Shape normalization Nucleic Acid Conformation Female Shape distribution Artificial intelligence 3D multicolor FISH microscopy business Multicolor fish |
Zdroj: | Biochimica et Biophysica Acta-Molecular Cell Research, 1783(11), 2089-2099. Elsevier |
ISSN: | 0167-4889 |
DOI: | 10.1016/j.bbamcr.2008.08.007 |
Popis: | The 3D folding structure formed by different genomic regions of a chromosome is still poorly understood. So far, only relatively simple geometric features, like distances and angles between different genomic regions, have been evaluated. This work is concerned with more complex geometric properties, i.e., the complete shape formed by genomic regions. Our work is based on statistical shape theory and we use different approaches to analyze the considered structures, e.g., shape uniformity test, 3D point-based registration, Fisher distribution, and 3D non-rigid image registration for shape normalization. We have applied these approaches to analyze 3D microscopy images of the X-chromosome where four consecutive genomic regions (BACs) have been simultaneously labeled by multicolor FISH. We have acquired two sets of four consecutive genomic regions with an overlap of three regions. From the experimental results, it turned out that for all data sets the complete 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 average 3D structure of chromatin in a small genomic region (below 4 Mb) based on five BACs resulting from two overlapping four BAC regions. We found that geometric normalization with respect to the nucleus shape based on non-rigid image registration has a significant influence on the location of the genomic regions. |
Databáze: | OpenAIRE |
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