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The genome consists of non-B-DNA structures such as G-quadruplexes (G4) that are involved in the regulation of genome stability and transcription. Telomeric-repeat containing RNA (TERRA) is capable of folding into G-quadruplex and interacting with chromatin remodeler ATRX. Here we show that TERRA modulates ATRX occupancy on repetitive sequences and over genes, and maintains DNA G-quadruplex structures at TERRA target and non-target sites in mouse embryonic stem cells. TERRA prevents ATRX from binding to subtelomeric regions and represses H3K9me3 formation. G4 ChIP-seq reveals that G4 abundance decreases at accessible chromatin regions, particularly at transcription start sites (TSS) after TERRA depletion; such G4 reduction at TSS is associated with elevated ATRX occupancy and differentially expressed genes. Loss of ATRX alleviates the effect of gene repression caused by TERRA depletion. Immunostaining analyses demonstrate that knockdown of TERRA diminishes DNA G4 signals, whereas silencing ATRX elevates G4 formation. Our results uncover an epigenetic regulation by TERRA that sequesters ATRX and preserves DNA G4 structures.

More than 90% of the human genome is transcribed into noncoding RNAs, but their functional characterization has lagged behind. A major bottleneck in the understanding of their functions and mechanisms has been a dearth of systematic methods for identifying interacting protein partners. There now exist several methods, including identification of direct RNA interacting proteins (iDRiP), chromatin isolation by RNA purification (ChIRP), and RNA antisense purification, each previously applied towards identifying a proteome for the prototype noncoding RNA, Xist. iDRiP has recently been modified to successfully identify proteomes for two additional noncoding RNAs of interest, TERRA and U1 RNA. Here we describe the modified protocol in detail, highlighting technical differences that facilitate capture of various noncoding RNAs. The protocol can be applied to short and long RNAs in both cultured cells and tissues, and requires ~1 week from start to finish. Here we also perform a comparative analysis between iDRiP and ChIRP. We obtain partially overlapping profiles, but find that iDRiP yields a greater number of specific proteins and fewer mitochondrial contaminants. With an increasing number of essential long noncoding RNAs being described, robust RNA-centric protein capture methods are critical for the probing of noncoding RNA function and mechanism. This protocol describes how to identify direct protein targets of noncoding RNAs—Xist, TERRA and U1—and outlines modifications specific to each noncoding RNA and its partners.

In collaboration with the American College of Veterinary Radiology

Protein and DNA have been considered as the major components of chromatin. But beyond that, an increasing number of studies show that RNA occupies a large amount of chromatin and acts as a regulator of nuclear architecture. A significant fraction of long non-coding RNAs (lncRNAs) prefers to stay in the nucleus and cooperate with protein complexes to modulate epigenetic regulation, phase separation, compartment formation, and nuclear organization. An RNA strand also can invade into double-stranded DNA to form RNA:DNA hybrids (R-loops) in living cells, contributing to the regulation of gene expression and genomic instability. In this review, we discuss how nuclear lncRNAs orchestrate cellular processes through their interactions with proteins and DNA and summarize the recent genome-wide techniques to study the functions of lncRNAs by revealing their interactomes in vivo.

Plasmonics have been well investigated on photodetectors, particularly in IR and visible regimes. However, for a wide range of ultraviolet (UV) applications, plasmonics remain unavailable mainly because of the constrained optical properties of applicable plasmonic materials in the UV regime. Therefore, an epitaxial single‐crystalline aluminum (Al) film, an abundant metal with high plasma frequency and low intrinsic loss is fabricated, on a wide bandgap semiconductive gallium nitride (GaN) to form a UV photodetector. By deliberately designing a periodic nanohole array in this Al film, localized surface plasmon resonance and extraordinary transmission are enabled; hence, the maximum responsivity (670 A W−1) and highest detectivity (1.48 × 1015 cm Hz1/2 W−1) is obtained at the resonance wavelength of 355 nm. In addition, owing to coupling among nanoholes, the bandwidth expands substantially, encompassing the entire UV range. Finally, a Schottky contact is formed between the single‐crystalline Al nanohole array and the GaN substrate, resulting in a fast temporal response with a rise time of 51 ms and a fall time of 197 ms. To the best knowledge, the presented detectivity is the highest compared with those of other reported GaN photodetectors., Aluminum plasmonics is merged as an advancement tool to boost GaN a superior complementary metal oxide semiconductor (CMOS) compatible UV photodetector. By introducing a single‐crystalline Al nanohole array on a GaN substrate, it enables ultraviolet plasmons and Schottky barrier, and thus demonstrates excellent performance in entire UV regime: maximum responsivity (670 A W−1), highest detectivity (1.48 × 1015 cm Hz1/2 W−1), and fast temporal response.

BaPbO/sub 3/-based thick film resistors were fabricated using BaPbO/sub 3/ powders and alkali glass frits. From microstructure observations, the conductive mechanisms are assumed to be related to the contact conditions between particles, and by means of EMT (effective-medium theory) approximation for some possible distributions, a more possible conductive model is proposed. This model is composed of trinary conductive channels, i.e., continuous, semi-continuous, and discontinuous, corresponding to a distribution function of the contact conductance, which is composed of trinary contact conditions, i.e., good contact, poor contact (both with same probability density) and no contact between BaPbO/sub 3/ particles. This model can explain the blending curve, temperature dependence and field dependence of resistivity of the specimens. >

A thick-film resistor system that does not use a rare-earth or a transitional element was fabricated with semi-metallic BaPbO/sub 3/ and alkali glass powders. Its characteristics are comparable to conventional thick-film resistors such as those in the RuO/sub 2/-based system, while the cost is much lower. The relationship between glass-frit content and sheet resistivity is approximated by an exponential equation, and an almost one-order increase in resistivity was observed for every 10 wt.% increase in glass content. A conduction model consisting of three different types of conducting channels is proposed to explain both the blending curve and temperature coefficient of resistivity (TCR) characteristics. A high-Pb content in the raw BaPbO/sub 3/ material is essential to avoid the degradation of resistor characteristics by moisture. Silver was found to be a TCR modifier and can also improve stability in the BaPbO/sub 3/-based resistor system. >

BaPbO 3 ceramics are fabricated with BaCO 3 and PbO powders. Phase transitions and the physical properties of BaPbO 3 fabricated with different Pb/Ba mole ratios are studied. The metallic conduction behavior of BaPbO 3 can be understood by either the unfilled d orbital of Pb 4+ or the substitution of Ba by Pb. However, the model of a unit cell structure with PbO 2 layers ‘inserted’ between BaO layers together with unfilled d orbital of Pb 4+ seems more appropriate. BaPbO 3 is also proved to be stable in water, but not so stable in the presence of both water and air (moisture). Increasing the Pb content can improve the resistance of BaPbO 3 to moisture.