Computational, Chemical, and Biological Characterization of Ultraconserved Elements (UCEs) in Plants
We aim to answer the question of how secondary DNA structures may be involved in inter-chromosomal interactions and possibly chromosome copy counting.
In this project a genome-wide map of interacting sequences in Arabidopsis will be generated. Chromatin Conformation Capture (3C) (Dekker, Rippe et al. 2002) is being modified to isolate interacting DNA sequences. A mixture of different plant tissues, which contain cells at different stages of the cell cycle, will allow us to cover a large part of the genomic interaction events occurring in planta. 3C technology enables the identification of such interactions in cis and trans. Chromatin is cross-linked, digested, and religated to obtain hybrid sequences containing both interacting partners. We are interested in inter-chromosomal interactions in order to obtain more information about how chromosomes are paired and copy numbers can be preserved through generations. Within the pool of interacting sequences, we will specifically search for sequences that fulfill the criteria to possibly form G-quadruplex structures. Subsequently, the potential of candidate sequences to form G-quadruplex structures will be analyzed employing dyes that specifically bind to G-quadruplex structures in vivo. Therefore, a genome-wide map of interacting DNA sequences promises to provide a powerful tool for the study of homologous pairing and copy counting.
Keywords: 4C, Hi-C, Chromatinback