The parameters of nuclear architecture include the sequence of gene regulatory elements, chromatin structure, and higher order organization of the transcriptional regulatory machinery into subnuclear domains.
SMC complexes facilitate higher order organization of chromosomes by their ability to tether together two different regions of DNA, either within the same chromosome or between different chromosomes My laboratory has shown that different types of higher order chromosome organization are coordinated because the function of SMC complexes are highly interdependent.
Several interdependent processes are currently classified as epigenetic, such as DNA methylation, nuclear positioning and covalent modifications of histone proteins, interaction with non-coding RNA species, and higher order organization of nucleic acid in the nucleus.
However, a PFGE study of the C. reinhardtii chloroplast genome did not reveal the higher order organization that was observed previously for higher plant cpDNAs [18].
In contrast, algal cpDNAs, like their higher plant counterparts, have circular restriction maps, and higher order organization (such as multimeric or anomalous forms) has not been identified in algal cpDNAs to date [7].
However, our study demonstrated that multimeric forms of cpDNA also exist in the IR-lacking chloroplast genome, which suggests that the higher order organization of the chloroplast genome maybe less related to the presence of IRs than was previously thought.
Furthermore, our cytogenomic investigations using pulsed-field gel electrophoresis (PFGE) and southern blotting methods showed that the B. hypnoides cpDNA had multimeric forms, including monomer, dimer, trimer, tetramer, and even higher multimers, which is similar to the higher order organization observed previously for higher plant cpDNA.
