Genomic Regions Targeted by DNA Topoisomerase IIβ Frequently Interact With a Nuclear Scaffold/Matrix Protein hnRNP U/SAF‐A/SP120

Abstract

Type II DNA topoisomerases (topo II) play critical roles in some cellular events through repeated cleavage/rejoining of nuclear DNA. The β isoform (topo IIβ) is essential for the transcriptional induction of neuronal genes in terminal differentiation. Genomic sites targeted by the enzyme are nonrandom. Although previous studies have claimed that topo II cleavage sites are close to the nuclear scaffold/matrix attachment region (S/MAR), it is still unclear whether this view can be generalized. We report here that a library of cloned genomic DNA fragments targeted by topo IIβ in vivo frequently contains S/MAR and binding sites for hnRNP U/SAF‐A/SP120. Binding assays in vitro showed that a large proportion of the target DNAs bound to SP120 but their affinity to the nuclear scaffold/matrix varied significantly. Topo IIβ targets were extremely AT‐rich and often located in gene‐poor long intergenic regions (so‐called gene desert) that are juxtaposed to long genes expressed in neurons under differentiation. Sequence analysis revealed that topo IIβ targets are not just AT‐rich but are enriched with short tracts of A's and T's (termed A/T‐patches). Their affinity to the nuclear scaffold/matrix showed a moderate positive correlation with the coverage rate of A/T‐patches. The results suggest that the interaction of topo IIβ/SP120 with target regions modulates their proximity to the nuclear scaffold/matrix in a dynamic fashion and that A/T‐patch is a sequence motif assisting this process. J. Cell. Biochem. 116: 677–685, 2015. © 2014 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals, Inc.

Chromosome territories and the global regulation of the genome

“…Several proteins associated with isolated nuclear matrix have been identified as potential factors involved at chromatin loop S/MAR attachment sites and/or higher order CD. These include topoisomerase II, CTCF, cohesin, matrin 3 (also called as P‐130 nuclear scaffold protein), HnRNP‐U (also called as SAF‐A, for Scaffold/Matrix attachment region factor), SAF‐B, ARBP (Attachment Region Binding Protein), SAT‐B, and nuclear lamins . Recent proteomic approaches have further confirmed the S/MAR binding activities of SAF‐A, matrin 3, and nuclear lamins .…”

Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to induce chromatin opening

“…Our previous study demonstrated that SP120 is a partner protein of topo IIβ that activates and stabilizes the enzyme through RNA-dependent association 23 . We have also shown that randomly cloned genomic targets of topo IIβ are frequently enriched with SP120-binding sites, suggesting that these proteins bind DNA within close distance 24 . Ts3 toposites frequently overlap with SP120 sites but very little with Ts2 sites, indicating the distinctiveness of these toposites (Fig.…”

Genome-Wide Anaplasma phagocytophilum AnkA-DNA Interactions Are Enriched in Intergenic Regions and Gene Promoters and Correlate with Infection-Induced Differential Gene Expression

“…MARs and their binding partners are often found associated with the nuclear matrix and lamina as part of their genome organization and coordinate regulation functions (Rudd et al, 2004 ; Cai et al, 2006 ; Kohwi-Shigematsu et al, 2012 ; Pathak et al, 2014 ; Patrushev and Kovalenko, 2014 ; Yokota and Kanakura, 2014 ; Miyaji et al, 2015 ). There was a significant ( p < 0.0021) genome-wide association between intersections of individual AnkA fold-enriched binding sites and haploid KBM-7 clone 14 lamina-associated domains (LADs; 6528 sites; p < 0.001; Figure 5A ), and at individual chromosomes 1–4, 6, 9, 11, 13, 14, and X (Supplementary Table 2A and Figure S2A ).…”

“…MARs are also highly represented among non-coding DNA, where they serve as tether sites for proteins that bring distant co-regulated sites together in chromatin loops extending from the nuclear matrix (Kisseljova et al, 2014 ; Patrushev and Kovalenko, 2014 ; Pathak et al, 2014 ; Kind et al, 2015 ). Such sites are often located in long AT-rich intergenic regions separated by as much as 200 kb (Miyaji et al, 2015 ). Other potentially important epigenetic factors include DNA methylation, regulated miRNA and lincRNA, among other possibilities.…”