胃食道逆流症における好酸球性食道炎の頻度とタイトジャンクション蛋白の変動に関する前向き研究

研究科: 千葉大学大学院医学薬学府学位:千大院医薬博甲第医1127号要約博士(医学)千葉大

A novel representation of RNA secondary structure based on element-contact graphs-0

Ions are illustrated. (A) Secondary structures of three typical RNAs (miRNA , SAM riboswitch, tRNA). (B) Stem-loop-contact graphs of the three typical RNAs. (C) Stem-contact graphs of the three typical RNAs. (D) Loop-contact graphs of the three typical RNAs.<p><b>Copyright information:</b></p><p>Taken from "A novel representation of RNA secondary structure based on element-contact graphs"</p><p>http://www.biomedcentral.com/1471-2105/9/188</p><p>BMC Bioinformatics 2008;9():188-188.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2373570.</p><p></p

A novel representation of RNA secondary structure based on element-contact graphs-1

Ions are illustrated. (A) Secondary structures of three typical RNAs (miRNA , SAM riboswitch, tRNA). (B) Stem-loop-contact graphs of the three typical RNAs. (C) Stem-contact graphs of the three typical RNAs. (D) Loop-contact graphs of the three typical RNAs.<p><b>Copyright information:</b></p><p>Taken from "A novel representation of RNA secondary structure based on element-contact graphs"</p><p>http://www.biomedcentral.com/1471-2105/9/188</p><p>BMC Bioinformatics 2008;9():188-188.</p><p>Published online 11 Apr 2008</p><p>PMCID:PMC2373570.</p><p></p

CTCF-cluster mapping and statistic estimation in K562 cells.

<p>The random probability of CTCF overlapping was calculated based on the more than 10,000 simulated numbers versus the observed numbers in each category of CTCF-clusters. Genomic DNA segments of the same number and size as the CTCF-defined loci were randomly extracted from the human genome assembly (hg19) as background.</p

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

<div><p>Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCF-binding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome.</p> </div

Additional file 2: Table S1. of Genome-wide identification and characterisation of HOT regions in the human genome

H1hESC TFBS Clusters info. Table S2. Comparison of motifless binding peaks and HOT regions. Table S3. Information of HOT regions in 154 files. Table S4. Key TF genes. Table S5. Developmental TF genes. Table S6. Repetitive elements in HOT regions. Table S7. 1046 Validated elements in HOT regions. Table S8. gene list of associated “gained” HOT regions. Table S9. Enriched TF gene list. Table S10. Enrichment of bivalent genes in HOT regions. Table S11 GO analysis of activated HOT regions in H1-derived cells. (XLSX 766 kb

Nucleosome positioning near the CTCF-binding sites in K562 cells.

<p>Nucleosome (blue lines) and CTCF-binding sites (red lines) profiles around cell type-specific (A), common (B), and ubiquitous (C) CTCF-binding sites are illustrated. Distances from the CTCF-binding sites are plotted along the <i>x</i>-axis. Left and right <i>y</i>-axes represent the normalized tag densities of the nucleosome and CTCF-binding sites, respectively. In (C), cyan ovals depict hypothetical nucleosome positions across the site with color intensities reflecting their positioning strength. The CTCF-binding site is indicated by the yellow rectangle. Left inset, linear fit to the positions of the phase peaks within 3 kb downstream of the CTCF-binding sites (slope  = 185.2 bp; 95% confidence interval (CI)  =  [184.6 bp, 185.7 bp]). Right inset, linear fit to the positions of the phase peaks within 3 kb upstream of CTCF-binding sites (slope  = 185.3 bp; 95% CI  =  [184.2 bp, 186.5 bp]).</p

Additional file 1: Table S1: of RevEcoR: an R package for the reverse ecology analysis of microbiomes

The seed sets of seven oral species. seed represents the exogenous required compound from its environment, and confidence represents the compounds probability of being a seed. Table S2A-D. The competition and complementarity index of seven oral species. (DOCX 23 kb

Chromatin features of CTCF-binding sites.

<p>(A) Open chromatin proximal to CTCF-binding sites in K562 cells. DNaseI HS, DNaseI DGF, and FAIRE profiles of cell type-specific (left), common (middle), and ubiquitous (right) CTCF-binding sites. The tag density for open chromatin is shown across the CTCF-binding sites and extending 3 kb upstream and downstream of the CTCF-binding sites. (B) Histone modifications proximal to the CTCF-binding sites in K562 cells. Histone modification profiles of cell type-specific (left), common (middle), and ubiquitous (right) CTCF-binding sites. The tag density for modifications is shown across the CTCF-binding sites and extending 3 kb upstream and downstream of the CTCF-binding sites. (C) The smoothed distributions of CpG methylation levels within different types of CTCF-binding sites in K562 cells (for CpGs with ≥10-fold coverage). The distributions of methylation levels (%) across all CpGs identified in all, unique, common, and ubiquitous CTCF-binding sites are illustrated as a smooth approximation of probability density, which was estimated based on a normal kernel function. The <i>x</i>-axis represents the density of the methylation levels. The median methylation levels of different types of CTCF sites are illustrated as vertical, dashed lines. (D, E) CTCF-binding sites colocalize with strong enhancers (D) and gene expression (E) in a cell type-specific manner. (D) Cell-type specific CTCF-binding sites (<i>x</i>-axis) are mapped relative to cell-specific enhancer binding regions (<i>y</i>-axis) in six different cell types. (E) Cell type-specific CTCF-binding sites (<i>x</i>-axis) are mapped relative to transcription start sites of genes with cell type-specific expression (<i>y</i>-axis). Bubble size represents the level of enrichment.</p

Additional file 2: of RevEcoR: an R package for the reverse ecology analysis of microbiomes

Additional information on 116 gut prevalent species, including species names, species interactions and co-occurrence scores. (XLSX 300 kb