The nucleus is a highly structured and organized cellular compartment. The genome is not randomly organized inside the nucleus, each chromosome occupies a particular space called the chromosomal territory (CT). Within CTs genes of particular interest may occupy particular localization and move during expression. Repeated DNA sequences located in the centromeric regions of mammalian chromosomes are thought to organize the genome by interacting with each other or with specific nuclear compartments such as the nucleolus or the lamina. In order to analyze nuclear organization, a statistical study needs to be run on a large population of cells. Modern microscopes allows to acquire a large amount of fields. Thanks to software such as ImageJ it is possible to automate analysis including filtering and quantitative measurements. Unfortunately in ImageJ available processing and measurements are only for 2D images. Furthermore since different users may need different settings for filtering and analyses, the use of macros has its limitation. We have developed TANGO (Tool for Analysis of Nuclear Genome Organization) to analyze thousands of nuclei in 3D. All images, settings and results are stored in a database (mongo-DB, powerful multi-platform object-oriented DB), a customizable processing chain can be set up for each different experiments using available plugin in ImageJ and new ones have been developed like 3D spatial statistics. The visualization of the 3D images and results benefits from the development of powerful 3D interfaces such as Image5D and 3D Viewer.
Nuclear Organization, 3D, Segmentation, High-Throughput, mongoDB
In 2010, I graduated from Ecole Polytechnique (Paris, France) and Université Pierre et Marie Curie (Paris, France), where I specialized in molecular and cellular biology, in 2010. Since 2010 I am a PhD Student in the interdisciplinarity and life sciences doctoral school, and performing my experimental work at at the Muséum National d'Histoire Naturelle (Paris, France). I am studying the role of repeated DNA sequences in nuclear genome organization, and regulation of gene expression. This work requires high-throughput processing of 3D images for the analysis of the localization of various nuclear structures.This is the reason why I undertook the development of TANGO which is now operative.
Presenting author: Jean Ollion
Organisation: Muséum National d'Histoire Naturelle, Paris, France
co-authors: Julien Cochennec, Christophe Escudé, Thomas Boudier