Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers.

In Metazoans, transcription of most genes is driven by the use of multiple alternative promoters. Although the precise regulation of alternative promoters is important for proper gene expression, the mechanisms that mediates their differential utilization remains unclear. Here, we investigate how the two alternative promoters (P1, P2) that drive MYC expression are regulated. We find that P1 and P2 can be differentially regulated across cell-types and that their selective usage is largely mediated by distal regulatory sequences. Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation

Hydrodynamic Equation for the Breakdown of the Quantum Hall Effect in a Uniform Current

The hydrodynamic equation for the spatial and temporal evolution of the electron temperature T_e in the breakdown of the quantum Hall effect at even-integer filling factors in a uniform current density j is derived from the Boltzmann-type equation, which takes into account electron-electron and electron-phonon scatterings. The derived equation has a drift term, which is proportional to j and to the first spatial derivative of T_e. Applied to the spatial evolution of T_e in a sample with an abrupt change of the width along the current direction, the equation gives a distinct dependence on the current direction as well as a critical relaxation, in agreement with the recent experiments.Comment: 4 pages, 1 Postscript figure, corrected equations, to be published in J. Phys. Soc. Jpn. 70 (2001) No.

Electronic Processes at the Breakdown of the Quantum Hall Effect

Microscopic processes giving the energy gain and loss of a two-dimensional electron system in long-range potential fluctuations are studied theoretically at the breakdown of the quantum Hall effect in the case of even-integer filling factors. The Coulomb scattering within a broadened Landau level is proposed to give the gain, while the phonon scattering to give the loss. The energy balance equation shows that the electron temperature T_e and the diagonal conductivity sigma_{xx} exhibit a bistability above the lower critical electric field E_{c1}. Calculated values of E_{c1} as well as T_e and sigma_{xx} at E_{c1} are in agreement with the observed values in their orders of magnitude.Comment: 4 pages, 2 Postscript figures, submitted to the Journal of the Physical Society of Japa

Ground State at Low Landau Level Filling Factors in Two-Dimensional Systems of GaAs/AlGaAs Heterostructures in Strong Magnetic Fields(Research in High Magnetic Fields)

Integer and fractional quantum Hall effects are interesting phenomena in two-dimensional electron systems (2DES) in strong magnetic fields. In this paper, breakdown of the integer quantum Hall effect (IQHE) at odd integer filling factors at 100 mK and temperature dependence of the fractional quantum Hall effect (FQHE) around the filling facor ν=1/2 at temperatures between 100 mK and 1000 mK in magnetic fields up to 25 T are measured for the 2DES in two AlGaAs/GaAs heterostructures. The results in the IQHE measurements are compared with results at the even filling factors and derive the effective g-factor of about 10 in this system. The results in the FQHE measurements at ν=1/2 shows a logarithmic temperature dependence of the conductivity which is expected in a weakly localized Fermion system in zero magnetic fields

Metal-Insulator Transition and Spin Degree of Freedom in Silicon 2D Electron Systems

Magnetotransport in 2DES's formed in Si-MOSFET's and Si/SiGe quantum wells at low temperatures is reported. Metallic temperature dependence of resistivity is observed for the n-Si/SiGe sample even in a parallel magnetic field of 9T, where the spins of electrons are expected to be polarized completely. Correlation between the spin polarization and minima in the diagonal resistivity observed by rotating the samples for various total strength of the magnetic field is also investigated.Comment: 3 pages, RevTeX, 4 eps-figures, conference paper (EP2DS-13

Field-induced breakdown of the quantum Hall effect

A numerical analysis is made of the breakdown of the quantum Hall effect caused by the Hall electric field in competition with disorder. It turns out that in the regime of dense impurities, in particular, the number of localized states decreases exponentially with the Hall field, with its dependence on the magnetic and electric field summarized in a simple scaling law. The physical picture underlying the scaling law is clarified. This intra-subband process, the competition of the Hall field with disorder, leads to critical breakdown fields of magnitude of a few hundred V/cm, consistent with observations, and accounts for their magnetic-field dependence \propto B^{3/2} observed experimentally. Some testable consequences of the scaling law are discussed.Comment: 7 pages, Revtex, 3 figures, to appear in Phys. Rev.

An Augmented Lagrangian Based Compressed Sensing Reconstruction for Non-Cartesian Magnetic Resonance Imaging without Gridding and Regridding at Every Iteration

Background: Non-Cartesian trajectories are used in a variety of fast imaging applications, due to the incoherent image domain artifacts they create when undersampled. While the gridding technique is commonly utilized for reconstruction, the incoherent artifacts may be further removed using compressed sensing (CS). CS reconstruction is typically done using conjugate-gradient (CG) type algorithms, which require gridding and regridding to be performed at every iteration. This leads to a large computational overhead that hinders its applicability. Methods: We sought to develop an alternative method for CS reconstruction that only requires two gridding and one regridding operation in total, irrespective of the number of iterations. This proposed technique is evaluated on phantom images and whole-heart coronary MRI acquired using 3D radial trajectories, and compared to conventional CS reconstruction using CG algorithms in terms of quantitative vessel sharpness, vessel length, computation time, and convergence rate. Results: Both CS reconstructions result in similar vessel length (P = 0.30) and vessel sharpness (P = 0.62). The per-iteration complexity of the proposed technique is approximately 3-fold lower than the conventional CS reconstruction (17.55 vs. 52.48 seconds in C++). Furthermore, for in-vivo datasets, the convergence rate of the proposed technique is faster (60±13 vs. 455±320 iterations) leading to a ∼23-fold reduction in reconstruction time. Conclusions: The proposed reconstruction provides images of similar quality to the conventional CS technique in terms of removing artifacts, but at a much lower computational complexity

Dynamical Screening and Superconducting State in Intercalated Layered Metallochloronitrides

An essential property of layered systems is the dynamical nature of the screened Coulomb interaction. Low energy collective modes appear as a consequence of the layering and provide for a superconducting-pairing channel in addition to the electron-phonon induced attractive interaction. We show that taking into account this feature allows to explain the high critical temperatures (Tc~26K) observed in recently discovered intercalated metallochloronitrides. The exchange of acoustic plasmons between carriers leads to a significant enhancement of the superconducting critical temperature that is in agreement with the experimental observations

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation and to uncover novel components of the transcriptome employing a series of high-throughput experiments. The primary and unique technique is cap analysis of gene expression (CAGE), sequencing mRNA 5′-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP–chip for epigenetic marks and transcription factors. All the experiments are performed in a differentiation time course of the THP-1 human leukemic cell line. Furthermore, we performed a large-scale mammalian two-hybrid (M2H) assay between transcription factors and monitored their expression profile across human and mouse tissues with qRT-PCR to address combinatorial effects of regulation by transcription factors. These interdependent data have been analyzed individually and in combination with each other and are published in related but distinct papers. We provide all data together with systematic annotation in an integrated view as resource for the scientific community (http://fantom.gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial release

Magnetic von-Neumann lattice for two-dimensional electrons in the magnetic field

One-particle eigenstates and eigenvalues of two-dimensional electrons in the strong magnetic field with short range impurity and impurities, cosine potential, boundary potential, and periodic array of short range potentials are obtained by magnetic von-Neumann lattice in which Landau level wave functions have minimum spatial extensions. We find that there is a dual correspondence between cosine potential and lattice kinetic term and that the representation based on the von-Neumann lattice is quite useful for solving the system's dynamics.Comment: 21pages, figures not included, EPHOU-94-00