Figure 6
PGBD5 chromatin structure confirms location of promoter and transcription start site. (Upper panel) Structure of the human PGBD5 gene (top), chromatin state segmentation data from 9 non-neuronal cell lines (middle), and CpG islands (bottom). (Lower panel) An expanded view of the PGBD5 promoter and presumptive enhancer region. Chromatin state segmentation data are from the same 9 human cell types: GM12878 (EBV-transformed B-lymphocytes), H1-hESC (embryonic stem cells), K562 (chronic myelogenous leukemia), HepG2 (hepatocellular carcinoma), HMEC (mammary epithelial cells), HSMM (skeletal muscle myoblasts), HUVEC (umbilical vein endothelial cells), NHEK (epidermal keratinocytes), and NHLF (lung fibroblasts). The DNase I hypersensitive sites are from H1-hESC and GM12878. The TF ChIP-seq data are a composite of 24 neural and non-neural cell lines including H1-hESC, A549 (adenocarcinomic alveolar basal epithelial cells), BE2_C (brain neuroblastoma), HEK293 (embryonic kidney), HeLa (cervical carcinoma), HUVEC, Jurkat (T-lymphocyte), K562, HepG2, NB4 (acute promyelocytic leukemia), PANC-1 (pancreatic carcinoma), PFSK-1, SK-N-MC (neuronal epithelioma), SK-N-SH_RA (neuroblastoma differentiated with retinoic acid), and U87 (primary glioblastoma), and 10 EBV-transformed B-lymphocytes from various ethnic backgrounds. For a color key to the chromatin state segmentation data, see inset (lower panel). For CpG islands, darker green indicates higher CpG density. For DNase I hypersensitive sites, stronger signals indicate higher sensitivity. For TF ChIP-seq data, darker gray reflects higher occupancy. All data is publicly available as UCSC Genome Browser tracks: Open Chromatin by DNase I HS (ENCODE/Duke University); TF ChIP-seq (ENCODE/Broad Institute/HudsonAlpha Institute/Stanford/Duke/University of Washington); and chromatin state segmentation using a Hidden Markov Model to identify genome-wide patterns in ChIP-seq data for histone methylations and acetylations, histone variant H2AZ, RNAP II, and CTCF (ChromHMM from ENCODE/Broad Institute). Only 8 of the 15 distinguishable chromatin states [48, 49] are seen in this particular genomic interval of the 9 cell lines. Figure adapted from visualizations of current ENCODE databases available on the UCSC Genome Browser for hg19.