BackgroundMultiplex experimental assays coupled to computational predictions are being increasingly employed for the simultaneous analysis of many specimens at the genome scale, which quickly generates very large amounts of data. However, inferring valuable biological information from the comparisons of very large genomic datasets still represents an enormous challenge.ResultsAs a study model, we chose the NFI/CTF family of mammalian transcription factors and we compared the results obtained from a genome-wide study of its binding sites with chromatin structure assays, gene expression microarray data, and in silico binding site predictions. We found that NFI/CTF family members preferentially bind their DNA target sites when they are located around transcription start sites when compared to control datasets generated from the random subsampling of the complete set of NFI binding sites. NFI proteins preferably associate with the upstream regions of genes that are highly expressed and that are enriched in active chromatin modifications such as H3K4me3 and H3K36me3. We postulate that this is a causal association and that NFI proteins mainly act as activators of transcription. This was documented for one member of the family (NFI-C), which revealed as a more potent gene activator than repressor in global gene expression analysis. Interestingly, we also discovered the association of NFI with the tri-methylation of lysine 9 of histone H3, a chromatin marker previously associated with the protection against silencing of telomeric genes by NFI.ConclusionTaken together, we illustrate approaches that can be taken to analyze large genomic data, and provide evidence that NFI family members may act in conjunction with specific chromatin modifications to activate gene expression.
BackgroundThe Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequencing (ChIP-Seq), we performed a genome-wide mapping of NFI DNA binding sites in primary mouse embryonic fibroblasts.ResultsWe found that in vivo and in vitro NFI DNA binding specificities are indistinguishable, as in vivo ChIP-Seq NFI binding sites matched predictions based on previously established position weight matrix models of its in vitro binding specificity. Combining ChIP-Seq with mRNA profiling data, we found that NFI preferentially associates with highly expressed genes that it up-regulates, while binding sites were under-represented at expressed but unregulated genes. Genomic binding also correlated with markers of transcribed genes such as histone modifications H3K4me3 and H3K36me3, even outside of annotated transcribed loci, implying NFI in the control of the deposition of these modifications. Positional correlation between + and - strand ChIP-Seq tags revealed that, in contrast to other transcription factors, NFI associates with a nucleosomal length of cleavage-resistant DNA, suggesting an interaction with positioned nucleosomes. In addition, NFI binding prominently occurred at boundaries displaying discontinuities in histone modifications specific of expressed and silent chromatin, such as loci submitted to parental allele-specific imprinted expression.ConclusionsOur data thus suggest that NFI nucleosomal interaction may contribute to the partitioning of distinct chromatin domains and to epigenetic gene expression regulation.NFI ChIP-Seq and input control DNA data were deposited at Gene Expression Omnibus (GEO) repository under accession number GSE15844. Gene expression microarray data for mouse embryonic fibroblasts are on GEO accession number GSE15871.
We present a new approach for the reproduction of color images on a metallic substrate that look bright and colorful under specular reflection observation conditions and also look good under nonspecular reflection observation conditions. We fit amounts of both the white ink and the classical cyan, magenta and yellow inks according to a formula optimizing the reproduction of colors simultaneously under specular and non-specular observation conditions. In addition, we can hide patterns such as text or graphical symbols in one viewing mode, specular or non-specular, and reveal them in the other viewing mode. We rely on the tradeoff between amounts of white diffuse ink and amounts of cyan, magenta and yellow inks to control lightness in specular and in non-specular observation conditions. Further effects are grayscale images that alternate from a first image to a second independent image when tilting the print from specular to non-specular reflection observation conditions. Applications comprise art and entertainment, publicity, posters, as well as document security. IntroductionDirect prints on a pure metallic substrate provide bright and brilliant colors when seen under specular reflection, but they look dark and dull when viewed under non-specular reflection [Pjanic and Hersch 2013]. Such prints are becoming commercially available for advertisement purposes and for the decoration of private homes.In the present contribution, we aim at producing partly specular reflecting and partly diffusely reflecting prints that look bright and colorful under specular and also look nice under non-specular observation angles. We rely on the ability to print on top of the metallic substrate diffusely reflecting white ink halftones that reduce the specular reflection component and increase the diffuse reflection component of the print. In addition, we offer the possibility of hiding patterns within a grayscale or color image when seen under specular viewing angles and make them appear when viewed under non-specular viewing angles or vice versa. _______________________We rely on the fact that increasing the amount of white ink darkens the image in specular viewing mode but increases the lightness of the image in the non-specular viewing mode and that the increase of similar amounts of cyan, magenta and yellow inks darkens the image both in specular and non-specular viewing modes.Thanks to the trade-off between the amounts of the white and of the colored inks, the lightness can be kept constant in one viewing mode and can be varied in the second viewing node. This also enables us to produce a metallic print that shows a first grayscale image in one viewing mode, and then, by tilting it to the other viewing mode, shows a second independent grayscale image. We had to meet a number of challenges. The first challenge consisted in creating a color reproduction workflow that enables finding surface coverages of inks yielding colors similar to the original colors under both specular and non-specular observation conditions. This is...
We propose a color reproduction framework for creating specularly reflecting color images printed on a metallic substrate that change hue or chroma upon in-plane rotation by 90°. This framework is based on the anisotropic dot gain of line halftones when viewed under specular reflection. The proposed framework relies on a spectral prediction model specially conceived for predicting the color of non-rotated and of 90° in-plane rotated cross-halftones formed of superpositions of horizontal and vertical cyan, magenta and yellow line halftones. Desired non-rotated and rotated image colors are mapped onto the sub-gamut allowing for the desired hue or chroma shift and then, using a 6D correspondence table, converted to optimal cross-halftone ink surface coverages. The proposed recolorization and decolorization framework is especially effective for creating surprising effects such as image parts whose hues change, or gray regions that become colorful. It can be adapted to commercial printers capable of printing with cyan, magenta and yellow inks on substrates formed by an ink attracting polymer lying on top of a metallic film layer. Applications may include art, advertisement, exhibitions and document security.
We present a geometric calibration method to accurately register a galvanoscopic scanning laser projection system (GLP) based on 2D vector input data onto an arbitrarily complex 3D-shaped projection surface. This method allows for accurate merging of 3D vertex data displayed on the laser projector with geometrically calibrated standard rasterization-based video projectors that are registered to the same geometry. Because laser projectors send out a laser light beam via galvanoscopic mirrors, a standard pinhole model calibration procedure that is normally used for pixel raster displays projecting structured light patterns, such as Gray codes, cannot be carried out directly with sufficient accuracy as the rays do not converge into a single point. To overcome the complications of accurately registering the GLP while still enabling a treatment equivalent to a standard pinhole device, an adapted version is applied to enable straightforward content generation. Besides the geometrical calibration, we also present a photometric calibration to unify the color appearance of GLPs and standard video projectors maximizing the advantages of the large color gamut of the GLP and optimizing its color appearance to smoothly fade into the significantly smaller gamut of the video projector. The proposed algorithms were evaluated on a prototypical mixed video projector and GLP projection mapping setup.
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