<p> Reconstruction and visualization of 2D and 3D arrangement of Drosophila sperm genome</p><p>V.A.Stepanenko,</p><p>Laboratory of Information Technologies, Joint Institute for Nuclear Research, 141980 Dubna, Moscow region, Russia E.-mail: [email protected]</p><p>M.V.Alexandrova, I.D.Alexandrov</p><p>Dzhelepov Laboratory of Nuclear Problems, Joint Institute for Nuclear Research, 141980 Dubna, Moscow region, Russia E.-mail: [email protected]</p><p>Abstract. The modern models (Yokota et al., 1995; Misteli, 2005; Horowitz-Scherer, 2006) of spatial macroorganization (macroarchitecture) of interphase chromosomes in animal and plant somatic cells reproduce or detail the classical Rabl’s configuration (Rabl, 1885) according to which interphase chromosomes maintain an anaphase-like (polar for centromere and telomere) orientation and remain in distinct domains throughout the cell cycle (“chromosome territories” in modern terms, Verschure, 2004).The spatial organization of chromosomes in postmeiotic animal germ cells throughout the spermiogenesis is enigmatic so far and it is mainly due to the lack of suitable methods for detailed observation and analyses without disruption of the existing organization. To study this issue, a patterns of radiation-induced locus-specific inversions and translocations in the Drosophila sperm nuclei were investigated and non-random distribution of the second exchange breakpoints over entire a large autosomes 2 and 3 was determined showing that specific euchromatin regions interacting with the pericentromeric heterochromatin were non-randomly spatially close to each other forming a loopy-like structures of different sizes (Alexandrov et al., 2007, 2008). Starting from these data, the reconstruction and visualization of this unusual configuration of Drosophila sperm genome were carried out employing the computer modeling based on a software program complex elaborated for 2D and 3D simulations (http://www.discreet.com/products/gmax ; http;//www.blender.org ). An example of general 3D models for chromosomes 2 and 3 in Drosophila sperm nucleus defined as a highly specific megarosette-loop structures is depicted as image submitted. Figure 1. An example of a general 2D models for both Drosophila autosomes 2 and 3 as an unitary entity based on (A) “hot” inversion/translocation breakpoints and (B) the same breakpoints plus extra inversion ones. Black body – the heterochromatic compartment; the b and vg - gene-loci mark the putative “sensitive” microvolumes and are positioned in spatial proximity relative to heterochromatic compartment; the number 21…60 and 61… 100 denote the relevant sections of autosome 2 and 3, respectively. </p>