TET1: A UNIQUE DNA DEMETHYLASE FOR MAINTENANCE OF DNA METHYLATION PATTERN

DNA methylation at the C5 position of cytosine (5-methylcytosine, 5mC) is a crucial epigenetic modification of the genome and has been implicated in numerous cellular processes in mammals, including embryonic development, transcription, X chromosome inactivation, genomic imprinting and chromatin structure. Like histone modifications, DNA methylation is also dynamic and reversible. However, in contrast to well defined DNA methyltransferases, the enzymes responsible for erasing DNA methylation still remain to be studied. The ten-eleven translocation family proteins (TET1/2/3) were recently identified as Fe(II)/2-oxoglutarate (2OG)-dependent 5mC dioxygenases, which consecutively convert 5mC into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine and 5-carboxylcytosine both in vitro and in mammalian cells. Based on their potent oxidative activities on 5mC, TET proteins have shown great potential as the long-sought DNA demethylases that induce DNA demethylation through multiple potential mechanisms. Here, we show that overexpression of TET1 catalytic domain alone (TET1-CD) but not full length TET1 (TET1-FL) induces global DNA demethylation in HEK293T cells. Genome-wide mapping of 5hmC further reveals a unique regulation pattern of 5mC by TET1-FL, where its 5hmC production is relatively inhibited as local basal DNA methylation level increases. By contrast, overexpression of TET1-CD exhibited a strong positive correlation between 5hmC production and basal DNA methylation level. In support of it, we interestingly found that through CXXC domain TET1 specifically binds hypomethylated but not hypermethylated CpG-rich regions. Moreover, overexpression of TET1-FL specifically decreased DNA methylation levels to certain extent only in hypomethylated CpG sites (methylation level ≤ 10%). To further investigate the effect of TET1, we also developed a lentiviral shRNA mediated TET1 knockdown in HEK293T cells, which originally have a comparable TET1 expression level as human embryonic stem cells. Knockdown of TET1 significantly induced an increase of DNA methylation in the pre-methylated edges, but not unmethylated edges and center regions of CpG islands (CGIs), indicating that TET1 can efficiently maintain the DNA hypomethylated state of CGIs by inhibiting the spreading of de novo DNA methylation from the pre-methylated edges of CGIs. Finally, with the use of the inducible TET1-CD overexpression system in HEK293T cells, we found that knockdown or inhibition of APEX1, the key player of DNA base excision repair pathway (BER), did not impair DNA demethylation induced by TET1-CD overexpression, suggesting that TET-mediated DNA demethylation is independent on BER. Moreover, our results also suggest that the replication-dependent passive pathway is not the primary mechanism for TET-mediated DNA demethylation. In conclusion, our results demonstrated that TET1 is a unique DNA demethylase which cannot significantly change DNA methylation levels, but rather specifically maintains the DNA hypomethylation state in CpG-rich regions by removing aberrant de novo DNA methylation. Moreover, neither BER nor DNA replication is required for TET-mediated DNA demethylation. Future studies focusing on potential 5-carboxylcytosine decarboxylases are necessary to elucidate the underlying mechanism

Simulation of Particle Mixing and Separation in Multi-Component Fluidized Bed Using Eulerian-Eulerian Method: A Review

In practical engineering applications, the mixing and separation behavior of multi-component particles is importance to the fluidized bed operation. The development of many practical processes is inseparable from the knowledge of particle mixing and separation, such as material processing of ash-soluble coal gasification, multi-phase flow in boilers, and petrochemical catalytic processes. In recent years, due to the obvious advantages of the Eulerian–Eulerian model, many researchers at home and abroad have used it to study the mixing and separation behavior of particles. The paper reviews the use of Eulerian–Eulerian model to study the mixing and separation of multi-component particles in fluidized beds. The Eulerian–Eulerian model describes the gas-phase and each of the individual particles as continuums. The mechanism of particle mixing and separation, the influence of different factors on the particle mixing and separation including differences in particle size and density, the differences in apparent air velocity, the differences in model factors are discussed. Finally, an outlook for the use of Eulerian–Eulerian model to study the mixing and separation behavior of three component particles and related research on the drag model between particles

Data set for cloning and characterization of heterologous transporters in Saccharomyces cerevisiae and identification of important amino acids for xylose utilization

AbstractThe efficient uptake is important for the xylose utilization by Saccharomyces cerevisiae. A heterogenous transporter Mgt05196p was cloned from Meyerozyma guilliermondii and expressed in Saccharomyces cerevisiae [1]. This data article contains the transport characteristics of Mgt05196p in S. cerevisiae. The fluorescence of fusion protein Mgt05196p-GFP expressing strain was located on the cell surface demonstrated that the heterogenous transporter Mgt05196p was targeted to the plasma membrane of S. cerevisiae. The expressing of Mgt05196p in the hxt null S. cerevisiae endowed the strain with the glucose and d-xylose absorption capacity, as well as expressing the native d-xylose transporter Gal2p. The transmembrane domains of Mgt05196p were predicted and compared with the XylEp, whose crystal structure was revealed. And then, the homologous modeling of Mgt05196p was built basing on the XylEp to find out the crucial amino acid residues for sugars binding and transport

Determination of beam incidence conditions based on the analysis of laser interference patterns

Beam incidence conditions in the formation of two-, three- and four-beam laser interference patterns are presented and studied in this paper. In a laser interference lithography (LIL) process, it is of importance to determine and control beam incidence conditions based on the analysis of laser interference patterns for system calibration as any slight change of incident angles or intensities of beams will introduce significant variations of periods and contrasts of interference patterns. In this work, interference patterns were captured by a He-Ne laser interference system under different incidence conditions, the pattern period measurement was achieved by cross-correlation with, and the pattern contrast was calculated by image processing. Subsequently, the incident angles and intensities of beams were determined based on the analysis of spatial distributions of interfering beams. As a consequence, the relationship between the beam incidence conditions and interference patterns is revealed. The proposed method is useful for the calibration of LIL processes and for reverse engineering applications