Non-B DNA structures spatially and sequence-specifically associated with individual centromeres in the human interphase nucleus

Abstract

Chromosome domains such as centromeres and telomeres occupy specific nuclear compartments supporting spatial organization of chromosomal DNA in the interphase nucleus. Telomere repeat-sequences can form a non-B quadruplex structure, presumably to support telomere-telomere association [1]. Several sequences abundant in human centromeres are also known to have the potential to form non-B structures, that are thought to support the ordered arrangement of centromeric repeat sequences and also chromosomal DNA. In the human genome there exists many polypurine/polypyrimidine tract sequences (pur/pyr tracts), each several hundred bp in length and scattered along the genome [2]. Interest in pur/pyr tracts has increased due to thein vitroobservation that these sequences can form a triple-helix (triplex) structure even under physiological conditions [3, 4]. Triplex formation is thought to be important as a molecular mechanism determining spatial organization in an interphase nucleus [5, 6, 7]. In triplex formation, single-stranded DNA is left unpaired, and it can hybridize with other single-stranded DNA and RNA with sufficient complementarity under physiological conditions. This enables distantly-spaced DNA regions along the genome to associate with each other in the nucleus. It is also conceivable that distantly-spaced DNAs can form trans-molecular triplexes organizing themselves into an ordered array. The purpose of this paper is to show that non-B structures such as triplexes are present in the human interphase nucleus and introduce methods for their investigation. One of the pur/pyr tracts of interest is that found in the DNA-replication switch region described below.