Abstract
DNA topoisomerase II (topo II) catalyzes a strand passage reaction in that one duplex is passed through a transient brake or gate in another. Completion of late stages of neuronal development depends on the presence of active β isoform (topo IIβ). The enzyme appears to aid the transcriptional induction of a limited number of genes essential for neuronal maturation. However, this selectivity and underlying molecular mechanism remains unknown. Here we show a strong correlation between the genomic location of topo IIβ action sites and the genes it regulates. These genes, termed group A1, are functionally biased towards membrane proteins with ion channel, transporter, or receptor activities. Significant proportions of them encode long transcripts and are juxtaposed to a long AT-rich intergenic region (termed LAIR). We mapped genomic sites directly targeted by topo IIβ using a functional immunoprecipitation strategy. These sites can be classified into two distinct classes with discrete local GC contents. One of the classes, termed c2, appears to involve a strand passage event between distant segments of genomic DNA. The c2 sites are concentrated both in A1 gene boundaries and the adjacent LAIR, suggesting a direct link between the action sites and the transcriptional activation. A higher-order chromatin structure associated with AT richness and gene poorness is likely to serve as a silencer of gene expression, which is abrogated by topo IIβ releasing nearby genes from repression. Positioning of these genes and their control machinery may have developed recently in vertebrate evolution to support higher functions of central nervous system.
Highlights
In the cell division cycle, gated passage for chromosomal DNA strands is an essential requirement for disentanglement of the DNA link between post-mitotic sister chromatids prior to segregation
The group A1 that makes up only 2.6% is the primary target of the present study since these genes are up-regulated depending on topo IIb
Under the conditions used in the eTIP procedure, the enzyme-DNA intermediate is converted mainly to a form with a single-strand breakage at the site of action, suggesting that the cleavage sites on G-segments are concentrated in the P1 DNA fraction (Figure 3A)
Summary
In the cell division cycle, gated passage for chromosomal DNA strands is an essential requirement for disentanglement of the DNA link between post-mitotic sister chromatids prior to segregation. Two research groups, including our own, reported the evidence supporting this notion by showing that topo IIb is required in the late stage of neural differentiation probably through transcriptional induction of neuronal genes [2,3,4]. Use of expression arrays indicated that transcript levels of only a subset of genes are susceptible to depletion of topo IIb in differentiating neural tissues [3,7]. Why the enzyme controls only a fraction of genes remained unclear To answer this question and to elucidate the mechanism of gene regulation by topo IIb, we hypothesized that relative topographical relationship between topoisomerase action sites and the location of genes controlled by the enzyme should provide an important clue
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