Topoisomerase IIβ Activates a Subset of Neuronal Genes that Are Repressed in AT-Rich Genomic Environment

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.

Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci

“…We developed a procedure to comprehensively map TOP2A cleavage sites genome-wide by high-throughput sequencing of DNA ends released from immunopurified cleavage complexes that surmounts inherent limitations in cellular approaches to study TOP2 cleavage (Sano et al 2008;Iacovoni et al 2010;Crosetto et al 2013;Baranello et al 2014;Pang et al 2015). The procedure identifies +1 positions in cleavage complexes at single-base precision by coupling a new use of the phosphodiesterase activity in Table S4; The ENCODE Project Consortium 2012) were converted from GRCh37/hg19 to GRCh38/hg38 using liftOver (http://genome.sph.umich.edu/wiki/LiftOver) (Hinrichs et al 2006).…”

“…General techniques to map DNA breaks in cells are not TOP2 specific, have low spatial resolution (Iacovoni et al 2010;Pang et al 2015), and may not detect TOP2 cleaved DNA ends protected by the enzyme (Crosetto et al 2013;Baranello et al 2014). A tiling array of select genomic regions used to analyze murine TOP2B cleavage did not distinguish double-strand breaks (DSBs) from single-strand nicks (SSNs) (Sano et al 2008). Furthermore, in a cell line study employing TDP2 (Tyrosyl-DNA phosphodiesterase 2) to remove the DNA from TOP2, genome-wide data were not reported (Cowell et al 2012).…”

Topoisomerase IIβ is required for lamina-specific targeting of retinal ganglion cell axons and dendrites

“…Possibly, each of these DNA-modifying enzymes might cooperate with topological modifications by Top2b to adjust the availability of target genes for transcription. The sites of action of Top2b are not distributed randomly throughout the genome; mammalian Top2b might preferentially associate with matrix attachment regions (MARs) (Martins and Krawetz, 2007;Sano et al, 2008). Conformational changes at or near MARs might position sections of chromatin in regions with higher or lower transcriptional activity.…”

“…Transcription factors collaborate with epigenetic regulators that modify the structure and accessibility of regions of DNA to the transcriptional machinery. The accessibility of a DNA template to transcription can change following modification of a number of topological parameters: location within the nucleus (Martins and Krawetz, 2007), the types of histones present , acetylation of local histones (Weaver et al, 2004), methylation of cytosines in the template (Levenson et al, 2006) and local looping of the DNA strand (Sano et al, 2008).…”

Regulation of DNA Topoisomerase IIβ through RNA-dependent Association with Heterogeneous Nuclear Ribonucleoprotein U (hnRNP U)

“…Recently, using DNA microarray techniques we have extended the catalogue of genes that are regulated by topo II␤ (referred to as A1 genes) and analyzed genomic sites targeted by the enzyme (10). Two distinct classes of topo II␤ action sites (termed c1 and c2 toposites) were discriminated.…”