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

Mary Miyaji, Ryohei Furuta, Kuniaki Sano, Kimiko M. Tsutsui, Ken Tsutsui

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)677-685
Number of pages9
JournalJournal of Cellular Biochemistry
Volume116
Issue number4
DOIs
Publication statusPublished - Apr 1 2015

Fingerprint

Heterogeneous-Nuclear Ribonucleoprotein U
Nuclear Matrix-Associated Proteins
Nuclear Matrix
Type II DNA Topoisomerase
Scaffolds
Matrix Attachment Regions
Genes
DNA
Intergenic DNA
Neurons
Assays
Protein Isoforms
Binding Sites
Genomic Library
Syntex adjuvant formulation
Sequence Analysis
Enzymes

Keywords

  • hnRNP U
  • NEURONAL DIFFERENTIATION
  • NUCLEAR SCAFFOLD/MATRIX
  • TOPOISOMERASE II

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Genomic Regions Targeted by DNA Topoisomerase IIβ Frequently Interact with a Nuclear Scaffold/Matrix Protein hnRNP U/SAF-A/SP120. / Miyaji, Mary; Furuta, Ryohei; Sano, Kuniaki; Tsutsui, Kimiko M.; Tsutsui, Ken.

In: Journal of Cellular Biochemistry, Vol. 116, No. 4, 01.04.2015, p. 677-685.

Research output: Contribution to journalArticle

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