Comparative study of methyl-CpG-binding domain proteins

BACKGROUND: Methylation at CpG dinucleotides in genomic DNA is a fundamental epigenetic mechanism of gene expression control in vertebrates. Proteins with a methyl-CpG-binding domain (MBD) can bind to single methylated CpGs and most of them are involved in transcription control. So far, five vertebrate MBD proteins have been described as MBD family members: MBD1, MBD2, MBD3, MBD4 and MECP2. RESULTS: We performed database searches for new proteins containing an MBD and identified six amino acid sequences which are different from the previously described ones. Here we present a comparison of their MBD sequences, additional protein motifs and the expression of the encoding genes. A calculated unrooted dendrogram indicates the existence of at least four different groups of MBDs within these proteins. Two of these polypeptides, KIAA1461 and KIAA1887, were only present as predicted amino acid sequences based on a partial human cDNA. We investigated their expression by Northern blot analysis and found transcripts of ~8 kb and ~5 kb respectively, in all eight normal tissues studied. CONCLUSIONS: Eleven polypeptides with a MBD could be identified in mouse and man. The analysis of protein domains suggests a role in transcriptional regulation for most of them. The knowledge of additional existing MBD proteins and their expression pattern is important in the context of Rett syndrome

Randomized Comparison of 64-Slice Single- and Dual-Source Computed Tomography Coronary Angiography for the Detection of Coronary Artery Disease

ObjectivesThe purpose of this study was to analyze the influence of a systematic approach to lower heart rate for coronary computed tomography (CT) angiography on diagnostic accuracy of 64-slice single- and dual-source CT.BackgroundCoronary CT angiography is often impaired by motion artifacts, so that routine lowering of heart rate is usually recommended. This is often conceived as a major limitation of the technique. It is expected that higher temporal resolution, such as with dual-source 64-slice CT, would allow diagnostic imaging even without systematic pre-treatment for lowering the heart rate.MethodsTwo hundred patients with suspected coronary artery disease were first randomized to either 64-slice single-source CT (n = 100) or dual-source CT (n = 100) for contrast-enhanced coronary artery evaluation. In each group, patients were further randomized to either receive systematic heart rate control (oral and intravenous beta-blockade for a target heart rate ≤60 beats/min) or receive no premedication. Evaluability of datasets and diagnostic accuracy were compared between groups against the results obtained from invasive angiography.ResultsSystematic pre-treatment lowered heart rate during CT coronary angiography by 10 beats/min. Heart rate control significantly improved evaluability in single-source CT (93% vs. 69% on a per-patient basis, p = 0.005), whereas it did not in dual-source CT (96% vs. 98%). In evaluable patients, sensitivity to detect the presence of at least 1 coronary stenosis by single-source CT was 86% and 79%, respectively, with and without heart rate control (p = NS). For dual-source CT, it was 100% and 95%, respectively (p = NS). The rate of correctly classified patients, defined as evaluable and correct classification as to the presence or absence of at least 1 coronary artery stenosis, was significantly improved by heart rate control in single-source CT (78% vs. 57%, p = 0.04), whereas there was no such influence in dual-source CT (87% vs. 93%).ConclusionsSystematic heart rate control significantly improves image quality for coronary visualization by 64-slice single-source CT, whereas image quality and diagnostic accuracy remain unaffected in dual-source CT angiography. Improved temporal resolution obviates the need for heart rate control

Comparative study of methyl-CpG-binding domain proteins

Abstract Background Methylation at CpG dinucleotides in genomic DNA is a fundamental epigenetic mechanism of gene expression control in vertebrates. Proteins with a methyl-CpG-binding domain (MBD) can bind to single methylated CpGs and most of them are involved in transcription control. So far, five vertebrate MBD proteins have been described as MBD family members: MBD1, MBD2, MBD3, MBD4 and MECP2. Results We performed database searches for new proteins containing an MBD and identified six amino acid sequences which are different from the previously described ones. Here we present a comparison of their MBD sequences, additional protein motifs and the expression of the encoding genes. A calculated unrooted dendrogram indicates the existence of at least four different groups of MBDs within these proteins. Two of these polypeptides, KIAA1461 and KIAA1887, were only present as predicted amino acid sequences based on a partial human cDNA. We investigated their expression by Northern blot analysis and found transcripts of ~8 kb and ~5 kb respectively, in all eight normal tissues studied. Conclusions Eleven polypeptides with a MBD could be identified in mouse and man. The analysis of protein domains suggests a role in transcriptional regulation for most of them. The knowledge of additional existing MBD proteins and their expression pattern is important in the context of Rett syndrome.</p

Gene expression changes in the course of neural progenitor cell differentiation

The molecular changes underlying neural progenitor differentiation are essentially unknown. We applied cDNA microarrays with 13,627 clones to measure dynamic gene expression changes during the in vitro differentiation of neural progenitor cells that were isolated from the subventricular zone of postnatal day 7 mice and grown in vitro as neurospheres. In two experimental series in which we withdrew epidermal growth factor and added the neurotrophins Neurotrophin-4 or BDNF, four time points were investigated: undifferentiated cells grown as neurospheres, and cells 24, 48, and 96 hr after differentiation. Expression changes of selected genes were confirmed by semiquantitative RT-PCR. Ten different groups of gene expression dynamics obtained by cluster analysis are described. To correlate selected gene expression changes to the localization of respective proteins, we performed immunostainings of cultured neurospheres and of brain sections from adult mice. Our results provide new insights into the genetic program of neural progenitor differentiation and give strong hints to as yet unknown cellular communications within the adult subventricular zone stem cell niche

Global Gene Expression Analysis in a Mouse Model for Norrie Disease: Late Involvement of Photoreceptor Cells

PURPOSE. Mutations in the NDP gene give rise to a variety of eye diseases, including classic Norrie disease (ND), X-linked exudative vitreoretinopathy (EVRX), retinal telangiectasis (Coats disease), and advanced retinopathy of prematurity (ROP). The gene product is a cystine-knot–containing extracellular signaling molecule of unknown function. In the current study, gene expression was determined in a mouse model of ND, to unravel disease-associated mechanisms at the molecular level. METHODS. Gene transcription in the eyes of 2-year-old Ndp knockout mice was compared with that in the eyes of age-matched wild-type control animals, by means of cDNA subtraction and microarrays. Clones (n = 3072) from the cDNA subtraction libraries were spotted onto glass slides and hybridized with fluorescently labeled RNA-derived targets. More than 230 differentially expressed clones were sequenced, and their expression patterns were verified by virtual Northern blot analysis. RESULTS. Numerous gene transcripts that are absent or downregulated in the eye of Ndp knockout mice are photoreceptor cell specific. In younger Ndp knockout mice (up to 1 year old), however, all these transcripts were found to be expressed at normal levels. CONCLUSIONS. The identification of numerous photoreceptor cell–specific transcripts with a reduced expression in 2-year-old, but not in young, Ndp knockout mice indicates that normal gene expression in these light-sensitive cells of mutant mice is established and maintained over a long period and that rods and cones are affected relatively late in the mouse model of ND. Obviously, the absence of the Ndp gene product is not compatible with long-term survival of photoreceptor cells in the mouse

Gene expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis

Bone marrow stromal cells (BMSC) have gained increased attention because of their multipotency and adult stem cell character. They have been shown to differentiate into other cell types of the mesenchymal lineage and also into non-mesenchymal cells. The exact identity of the original cells, which are isolated from bone marrow by their selective adherence to plastic, remains unknown to date. We have established and characterized mouse BMSC cultures and analyzed three independent samples by cDNA microarrays. The expression profile was compared with two previous expression studies of human BMSC and revealed a high degree of concordance between different techniques and species. To gain clues about the positional context and biology of the isolated cells within the bone marrow stroma, we searched our data for genes that encode proteins of the extracellular matrix, cell adhesion proteins, cytoskeletal proteins and cytokines/cytokine receptors. This analysis revealed a close association of BMSC with vascular cells and indicated that BMSC resemble pericytes