Nuclear Factor I genomic binding associates with chromatin boundaries.

BACKGROUND: The 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. RESULTS: We 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. CONCLUSIONS: Our 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.

Nuclear factor I revealed as family of promoter binding transcription activators.

BACKGROUND: Multiplex 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. RESULTS: As 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. CONCLUSION: Taken 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.

Paxel: A Generic Framework to Superimpose High-Frequency Print Patterns using Projected Light.

In this paper, we propose Paxel, a generic framework for modeling the interaction between a projector and a high-frequency pattern surface. Using this framework, we present two different application setups (cf. Fig. 1a): a novel colorchanging effect, created with a single projected image and only when the projection surface is changed from a pattern surface to a uniform white surface. The observed effect relies on the spatially different reflectance properties of these two surfaces. Using this approach, one can alter color proprieties of the projected image such as hue or chroma. Furthermore, for a specific color range, defined by an full color-changing sub-gamut, one can embed two completely different images, within a single static projection, from which either one will be revealed depending on the surface. The second application allows the creation of color images using a single channel projector. For this application, we present a full color projection created using a 365 nm ultraviolet (UV) projector in combination with fluorescent pigments (cf. Fig. 1b), enabling new display possibilities, such as projection through participating media, e.g. fog, while hiding the scattering of the projection light outside of the visible spectrum. Both presented approaches create effects that might be striking to the observer, making this framework useful for art exhibitions, advertisements, entertainment and visual cryptography. Finally, in Sec. VI, we provide an in-depth analysis of the reproducible colors based on input parameters, used in the presented algorithm, such as: pattern layout, dot size of the pattern and the number of the clusters formed by k-means algorithm (IV-B).

Seamless Multi-Projection Revisited.

This paper introduces a novel photometric compensation technique for inter-projector luminance and chrominance variations. Although it sounds as a classical technical issue, to the best of our knowledge there is no existing solution to alleviate the spatial non-uniformity among strongly heterogeneous projectors at perceptually acceptable quality. Primary goal of our method is increasing the perceived seamlessness of the projection system by automatically generating an improved and consistent visual quality. It builds upon the existing research of multi-projection systems, but instead of working with perceptually non-uniform color spaces such as CIEXYZ, the overall computation is carried out using the RLab [10, pp. 243-254] color appearance model which models the color processing in an adaptive, perceptual manner. Besides, we propose an adaptive color gamut acquisition, spatially varying gamut mapping, and optimization framework for edge blending. The paper describes the overall workflow and detailed algorithm of each component, followed by an evaluation validating the proposed method. The experimental results both qualitatively and quantitatively show the proposed method significant improved the visual quality of projected results of a multi-projection display with projectors with severely heterogeneous color processing.

Geometric and Photometric Consistency in a Mixed Video and Galvanoscopic Scanning Laser Projection Mapping System.

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.