Mi-sun Kim

DNA demethylation in hormone-induced transcriptional derepression

Epigenetic modifications at the histone level affect gene regulation in response to extracellular signals. However, regulated epigenetic modifications at the DNA level, especially active DNA demethylation, in gene activation are not well understood. Here we report that DNA methylation/demethylation is hormonally switched to control transcription of the cytochrome p450 27B1 (CYP27B1) gene. Reflecting vitamin-D-mediated transrepression of the CYP27B1 gene by the negative vitamin D response element (nVDRE), methylation of CpG sites (5mCpG) is induced by vitamin D in this gene promoter. Conversely, treatment with parathyroid hormone, a hormone known to activate the CYP27B1 gene, induces active demethylation of the 5mCpG sites in this promoter. Biochemical purification of a complex associated with the nVDRE-binding protein (VDIR, also known as TCF3) identified two DNA methyltransferases, DNMT1 and DNMT3B, for methylation of CpG sites, as well as a DNA glycosylase, MBD4 (ref. 10). Protein-kinase-C-phosphorylated MBD4 by parathyroid hormone stimulation promotes incision of methylated DNA through glycosylase activity, and a base-excision repair process seems to complete DNA demethylation in the MBD4-bound promoter. Such parathyroid-hormone-induced DNA demethylation and subsequent transcriptional derepression are impaired in Mbd4-/- mice. Thus, the present findings suggest that methylation switching at the DNA level contributes to the hormonal control of transcription.

Transrepression by a liganded nuclear receptor via a bHLH activator through co-regulator switching

Vitamin D receptor (VDR) is essential for ligand-induced gene repression of 25(OH)D3 1α-hydroxylase (1α(OH)ase) in mammalian kidney, while this gene expression is activated by protein kinase A (PKA) signaling downstream of the parathyroid hormone action. The mapped negative vitamin D response element (1αnVDRE) in the human 1α(OH)ase gene promoter (around 530 bp) was distinct from those of the reported DR3-like nVDREs, composed of two E-box-like motifs. Unlike the reported nVDREs, no direct binding of VDR/RXR heterodimer to 1αnVDRE was detected. A bHLH-type factor, designated VDIR, was identified as a direct sequence-specific activator of 1αnVDRE. The transactivation function of VDIR was further potentiated by activated-PKA signaling through phosphorylation of serine residues in the transactivation domains, with the recruitment of a p300 histone acetyltransferase co-activator. The ligand-dependent association of VDR/RXR heterodimer with VDIR bound to 1αnVDRE caused the dissociation of p300 co-activators from VDIR, and the association of HDAC co-repressor complex components resulting in ligand-induced transrepression. Thus, the present study deciphers a novel mechanism of ligand-induced transrepression by nuclear receptor via co-regulator switching.

Two-dimensional normal-state quantum oscillations in a superconducting heterostructure

Semiconductor heterostructures provide an ideal platform for studying high-mobility, low-density electrons in reduced dimensions. The realization of superconductivity in heavily doped diamond, silicon, silicon carbide and germanium suggests that Cooper pairs eventually may be directly incorporated in semiconductor heterostructures, but these newly discovered superconductors are currently limited by their extremely large electronic disorder. Similarly, the electron mean free path in low-dimensional superconducting thin films is usually limited by interface scattering, in single-crystal or polycrystalline samples, or atomic-scale disorder, in amorphous materials, confining these examples to the extreme ‘dirty limit’. Here we report the fabrication of a high-quality superconducting layer within a thin-film heterostructure based on SrTiO3 (the first known superconducting semiconductor). By selectively doping a narrow region of SrTiO3 with the electron-donor niobium, we form a superconductor that is two-dimensional, as probed by the anisotropy of the upper critical magnetic field. Unlike in previous examples, however, the electron mobility is high enough that the normal-state resistance exhibits Shubnikov–de Haas oscillations that scale with the perpendicular field, indicating two-dimensional states. These results suggest that delta-doped SrTiO3 provides a model system in which to explore the quantum transport and interplay of both superconducting and normal electrons. They also demonstrate that high-quality complex oxide heterostructures can maintain electron coherence on the macroscopic scales probed by transport, as well as on the microscopic scales demonstrated previously.

Ligand-induced transrepression by VDR through association of WSTF with acetylated histones

We have previously shown that the novel ATP‐dependent chromatin‐remodeling complex WINAC is required for the ligand‐bound vitamin D receptor (VDR)‐mediated transrepression of the 25(OH)D3 1α‐hydroxylase (1α(OH)ase) gene. However, the molecular basis for VDR promoter association, which does not involve its binding to specific DNA sequences, remains unclear. To address this issue, we investigated the function of WSTF in terms of the association between WINAC and chromatin for ligand‐induced transrepression by VDR. Results of in vitro experiments using chromatin templates showed that the association of unliganded VDR with the promoter required physical interactions between WSTF and both VDR and acetylated histones prior to VDR association with chromatin. The acetylated histone‐interacting region of WSTF was mapped to the bromodomain, and a WSTF mutant lacking the bromodomain served as a dominant‐negative mutant in terms of ligand‐induced transrepression of the 1α(OH)ase gene. Thus, our findings indicate that WINAC associates with chromatin through a physical interaction between the WSTF bromodomain and acetylated his tones, which appears to be indispensable for VDR/promoter association for ligand‐induced transrepression of 1α(OH)ase gene expression.

RETRACTED: 1α,25(OH)2D3-induced DNA methylation suppresses the human CYP27B1 gene

CYP27B 1 is a critical enzyme of Vitamin D biosynthesis that hydroxylates 25(OH)D 3 at the final step of the biosynthetic pathway. The CYP27B 1 gene is expressed primarily in kidney and negatively controlled by Vitamin D receptor. We have characterized the negative vitamin D response element and its binding protein, a bHLH transcription factor. This factor directly binds to the lanVDRE and activates transcription, but its transcriptional activity is suppressed by the ligand-activated Vitamin D receptor through recruitment of histone deacetylase. We have shown that histone deacetylation is a critical step for chromatin structure remodeling in suppression of the CYP27B 1 gene. We have further demonstrated that, in addition to histone acetylation, this transrepression by VDR requires DNA methylation in the CYP27B 1 gene promoter. Thus, transcriptional regulation of the CYP27B 1 gene appears to be mediated by dual epigenetic modifications.

Enhancing the electron mobility via delta-doping in SrTiO3

We fabricated high-mobility {delta}-doped structures in SrTiO{sub 3} thin films in order to investigate the low temperature electronic transport properties of confined carriers in this system. An enhancement of the electron mobility above the bulk value was observed as the doped layer thickness decreased. High-field Hall measurements revealed that this mobility enhancement originates from higher-mobility electrons in the undoped clean regions, which have quantum-mechanically broadened from the doped layer. Because of the absence of apparent lattice misfit between the layers, this structure is highly suitable for investigating two-dimensional electron gases in SrTiO{sub 3}

RETRACTED: Ligand-induced transrepressive function of VDR requires a chromatin remodeling complex, WINAC

We have previously shown that the novel ATP-dependent chromatin remodeling complex WINAC is required for the ligand-bound Vitamin D receptor (VDR)-mediated transrepression of the 25(OH)D(3) 1alpha-hydroxylase [1alpha(OH)ase] gene. However, the molecular basis for VDR promoter association, which does not involve its binding to specific DNA sequences, remains unclear. To address this issue, we investigated the function of WSTF in terms of the association between WINAC and chromatin for ligand-induced transrepression by VDR. Results of in vitro experiments using chromatin templates showed that the association of unliganded VDR with the promoter required physical interactions between WSTF and both VDR and acetylated histones prior to VDR association with chromatin. The acetylated histone-interacting region of WSTF was mapped to the bromodomain, and a WSTF mutant lacking the bromodomain served as a dominant-negative mutant in terms of ligand-induced transrepression of the 1alpha(OH)ase gene. Thus, our findings indicate that WINAC associates with chromatin through a physical interaction between the WSTF bromodomain and acetylated histones, that appears to be indispensable for VDR/promoter association for ligand-induced transrepression of 1alpha(OH)ase gene expression.

Mechanisms of transcriptional repression by 1,25(OH)2 vitamin D.

Purpose of reviewVitamin D has diverse biological actions, and consequently the mechanisms behind how it regulates gene transcription are diverse. Unlike its well described positive effects on gene transcription, little is known about how vitamin D induces transcriptional repression. Recent findingsVitamin D-induced transcriptional repression of several negative vitamin D receptor target genes has been studied on a molecular level. A new class of negative vitamin D response elements, which are E-box-type motifs, bind the bHLH-type transcriptional activator (VDIR) together with a histone acetyltransferase coactivator. The vitamin D receptor, activated by vitamin D, does not directly bind to the negative vitamin D response elements, but instead associates with VDIR. This leads to the dissociation of the histone acetyltransferase coactivator and recruitment of a histone deacetylase corepressor to transrepress transcription of the target gene promoter. SummaryHistone inactivation induced by histone deacetylase co-repressors appears to facilitate vitamin D-induced transcriptional repression via the vitamin D receptor. Following vitamin D binding, structural alteration of the DNA-unbound vitamin D receptor triggers transcriptional repression. Given this, the mechanisms behind vitamin D-induced transcriptional repression are probably more complex than those of vitamin D-induced transactivation.

Fermi Surface and Superconductivity in Low-Density High-Mobility delta-Doped SrTiO3

The electronic structure of low-density n-type SrTiO3 δ-doped heterostructures is investigated by angular dependent Shubnikov-de Haas oscillations. In addition to a controllable crossover from a three- to two-dimensional Fermi surface, clear beating patterns for decreasing dopant layer thicknesses are found. These indicate the lifting of the degeneracy of the conduction band due to subband quantization in the two-dimensional limit. Analysis of the temperature-dependent oscillations shows that similar effective masses are found for all components, associated with the splitting of the light electron pocket. The dimensionality crossover in the superconducting state is found to be distinct from the normal state, resulting in a rich phase diagram as a function of dopant layer thickness.

Double PHD Fingers Protein DPF2 Recognizes Acetylated Histones and Suppresses the Function of Estrogen-related Receptor α through Histone Deacetylase 1

Reiko Matusyama, Ichiro Takada, Atsushi Yokoyama, Sally Fujiyma-Nakamura, Naoya Tsuji, Hirochika Kitagawa, Ryoji Fujiki, Misun Kim, Madoka Kouza-Fujita, Tetsu Yano, and Shigeaki Kato This article has been retracted by the publisher. An investigation by the University of Tokyo has identified inappropriate image manipulation in Figs. 1D and 2C. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 290, NO. 8, p. 4816, February 20, 2015