Results: 4

1.
Figure 4

Figure 4. From: A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells.

PROM1 promoter activity using exon arrays. Transcript wide expression pattern of PROM1 measured by Affymetrix exon arrays with specific probes targeting exonic regions. Y-axis: normalized signal intensity (expression level). X-axis: genomic coordinates of the transcript. Expression of 5′ probes in CD133+ neural crest stem cells (blue), Ewing sarcoma (red), and CD133 neural crest stem cells (black), mesenchymal stem cells (gray), and Ewing sarcoma (green). Thick black bars: Probe regions overlapping CAGE defined TSS.

Ramakrishna Sompallae, et al. Front Genet. 2013;4:209.
2.
Figure 1

Figure 1. From: A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells.

Summary of PROM1 promoter architecture and cross-platform activity. Upper panel: CD133 promoter structure with known promoter regions P1–P5 (black rectangles), novel proximal promoter P6 (white rectangle), known exons A–E (gray rectangles), and CpG islands (~). Lower panel: Promoter activity (colored rectangles, number of studies expressing that category) in normal tissues, cancer, and developmental systems/stem cells as captured by different platforms. Orange: known promoter activities reported in the literature based on single gene studies. Blue: CAGE and RNA seq studies. Green: Affymetrix exon array exome expression. Promoters P1–P3 are widely expressed in the literature and using CAGE and RNA-seq assay. P6 is not yet reported in the literature.

Ramakrishna Sompallae, et al. Front Genet. 2013;4:209.
3.
Figure 3

Figure 3. From: A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells.

Validation of novel PROM1 TSS using 5′ RACE PCR. (A) Schema illustrating primer design for PROM1 TSS validation. PROM1 TSS is amplified using a pair of outer and inner primer sets targeted specifically to 5′ Rapid amplification of cDNA ends (RACE) adapter and PROM1 sequences. (B) The 5′ end regions of PROM1 mRNA were amplified from CD133+ and CD133 populations of LM-Mel-34 cell lines. Gel electrophoresis of amplified products shows difference in expression level in CD133+ and CD133 populations. Amplified 5′ends of PROM1 RNA were cloned in to plasmid pcDNA3.1 and then sequenced. (C) UCSC genome browser view of sequenced 5′ end region of PROM1 mapped to the promoter. The tracks shown here illustrates CAGE captured TSS regions from CD133+ melanoma cell lines and the RACE PCR identified 5′ end of the PROM1 transcript. The other tracks show outer and inner RACE PCR primers specific to PROM1.

Ramakrishna Sompallae, et al. Front Genet. 2013;4:209.
4.
Figure 2

Figure 2. From: A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells.

PROM1 regulatory landscape. (A) Previously described PROM1 TSS (Promoter 1–3, 4) supported by Capped Analysis of Gene Expression (CAGE) assays from the FANTOM3 collection 57 containing 72 experimental samples of which 13 from normal tissues, 25 from different cancers, and 34 are from developmental states (Table S3). Non-pathogenic tissue CAGE tags are distributed evenly whereas those obtained from tumors are biased toward promoter 1 and 2; transcription in embryonic tissues is biased toward promoter 2. Promoter 6 is supported by CAGE tags obtained from melanoma cell lines and normal colon, small intestine, and rectum. TSS for promoters 1–4 and promoter 6 are supported by predictive models from the SwitchGear and the oPOSSUM database. Exon array probes used to characterize differential exon usage (see Figure 4) are highlighted in red. (B) Epigenetic changes in PROM1 promoters. Data from ENCODE tier 1 human cell lines (H1-hESC: embryonic stem cell line, HepG2: liver carcinoma, GM12878: lymphoblastoid, HUVEC: umbilical vein endothelial cells, NHKE: kidney epithelium, K562: myelogenous leukemia). Promoters 1–3 are supported by active (weak) promoters in H1-hESC (HepG2) cells respectively, with stronger expression in H1-hESC as indicated by matching RNA-seq. PROM1 expression from all promoters is polycomb-repressed in GM12878, HUVEC, NHKE, and K562 resulting in no discernible expression. Expression in H1-hESC cells is enhanced at promoter 6, indicating an independent TSS unrelated to transcription driven by canonical promoters P1–3. The known CpG-island (REF) associated with the canonical promoters is unmethylated in both H1-hESC and HepG2 and methylated in GM12878 and K562, further repressing expression in those cells. (C) Regulatory potential. A strong regulatory potential is detected around the proximal promoter and promoter 1–3 (ESPERR, REF), with confirmed binding sites for transcription factors POUF2, STATS1, NFKB, and others in the ENCODE tier 1 samples (1: H1-hESC; G: GM12878; g: GM12891/GM12892/GM15510/GM18505/GM18526/GM18951/GM19099/GM19193; H: HeLa-S3; K:K562; L:HepG2). Binding sites for transcription factor found to be enriched in the proximal promoters (+300/−100 nucleotides) of 149 TSS found to be co-activated in CD133+-melanoma cells classify the PROM1 promoters into SP1-rich (promoters 1–3, in agreement with the CpG-island) or HMG-IY-rich (promoter 6, promoter 4).

Ramakrishna Sompallae, et al. Front Genet. 2013;4:209.

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Write to the Help Desk