Regulation of core-promoter elements by TFIID and TFIIB (adapted from Fig

<p><b>Copyright information:</b></p><p>Taken from "Computational analyses of eukaryotic promoters"</p><p>http://www.biomedcentral.com/1471-2105/8/S6/S3</p><p>BMC Bioinformatics 2007;8(Suppl 6):S3-S3.</p><p>Published online 27 Sep 2007</p><p>PMCID:PMC1995544.</p><p></p> 2 of Thomas & Chiang 2006 [3])

A thumbnail overview of the result of the two-way average-linkage hierarchical clustering of 38 arrays (columns) and 1532 isoforms (rows), as described in ref 30

<p><b>Copyright information:</b></p><p>Taken from "Profiling alternatively spliced mRNA isoforms for prostate cancer classification"</p><p>BMC Bioinformatics 2006;7():202-202.</p><p>Published online 11 Apr 2006</p><p>PMCID:PMC1458362.</p><p>Copyright © 2006 Zhang et al; licensee BioMed Central Ltd.</p> (Zoom-in view of the array clustering dendrogram. The two array clusters, C1 and C2, are enriched by normal samples and tumor samples, respectively. Cluster C2 is formed by two sub-clusters, reflecting differences in tumor percentage and stroma. (Isoform signatures up- or down-regulated in different array clusters. (The result of SVD. () The percentage of variation (y-axis) captured by each principal component (x-axis). (The low dimensional projection of arrays in the 3D space spanned by the first three principal components. SVD identified the same hierarchical structure as revealed by hierarchical clustering

A highly conserved regulatory element controls hematopoietic expression of in zebrafish-0

<p><b>Copyright information:</b></p><p>Taken from "A highly conserved regulatory element controls hematopoietic expression of in zebrafish"</p><p>http://www.biomedcentral.com/1471-213X/7/97</p><p>BMC Developmental Biology 2007;7():97-97.</p><p>Published online 20 Aug 2007</p><p>PMCID:PMC1988811.</p><p></p>ved between human, mouse, fugu and zebrafish showing that these regions are orthologous. By sequence comparison, three evolutionarily conserved elements were identified in the human, mouse, rat, fugu and zebrafish genomes, two upstream of , located at 12.9 kbp (Up1, open arrowhead) and 10 kbp (Up2, solid arrowhead), and one downstream of (Down1, black dot). (B) Zebrafish locus has 6 exons (blocks). An open arrowhead indicates the location of Up1; a solid arrowhead indicates the locations of Up2 in zebrafish genomic sequence flanking . Open blocks indicate the 5' UTR of zebrafish ; black blocks indicate zebrafish coding sequence. (C) Up1 stands for the genomic sequence lying 12892 bp to12811 bp upstream of the zebrafish start codon. The zebrafish Up1 sequence has an 81% sequence identity with the human Up1 sequence, an 80% sequence identity with both mouse and rat Up1sequences, and an 83% sequence identity with the fugu Up1 sequence. Up2 is the genomic sequence lying 10110 bp to 9887 bp upstream of the zebrafish start codon. Up2a is genomic sequence lying 10110 bp to 9999 bp upstream of start codon; Up2b is the genomic sequence lying 9998 bp to 9887 bp upstream of . The zebrafish Up2 sequence has a 74%, 72%, 72% and 94% sequence identity with Up2 sequences in the human, mouse, rat and fugu genomes, respectively

A highly conserved regulatory element controls hematopoietic expression of in zebrafish-3

<p><b>Copyright information:</b></p><p>Taken from "A highly conserved regulatory element controls hematopoietic expression of in zebrafish"</p><p>http://www.biomedcentral.com/1471-213X/7/97</p><p>BMC Developmental Biology 2007;7():97-97.</p><p>Published online 20 Aug 2007</p><p>PMCID:PMC1988811.</p><p></p>h wild type and mutant constructs identify HOXA3, LMO2 and E2F-1 as potential transcription factors. Also see Additional file , Supplementary Table S for more information about the results of hematopoietic transient expression assay. (B). Typical transient GFP expression patterns in injected embryos at 22 hpf. Left, GFP expression is detected in hematopoietic cells (arrow); Right, non-specific GFP expression was observed in muscle, heart and neuron tissue but not in hematopoietic cells (C). EMSA shows transcription factor E2F-1 (left) and HOXA3 (right) specifically bind to the probe corresponding to Up2 sequence, respectively. Probe containing HOXA3-A binding site was analyzed in EMSA. (D). Human myeloid leukemia cell lines, KG1 and K562, and mouse fibroblast cell line, NIH3T3 were transiently transfected with the mp/GFP, Up2-mp/GFP and Up2a-mp/GFP constructs. GFP expression was stronger in myeloid cells than in the fibroblast cell line. In the myeloid cell lines, enhancer activity of Up2 and Up2a was found to be statistically significant (*p < 0.002, ^p < 0.05, # p < 0.035, ** p < 0.032). The enhancer activity of Up2a/mp was less than that of Up2/mp. This figure represents the average of three independent experiments performed in duplicate

A highly conserved regulatory element controls hematopoietic expression of in zebrafish-1

<p><b>Copyright information:</b></p><p>Taken from "A highly conserved regulatory element controls hematopoietic expression of in zebrafish"</p><p>http://www.biomedcentral.com/1471-213X/7/97</p><p>BMC Developmental Biology 2007;7():97-97.</p><p>Published online 20 Aug 2007</p><p>PMCID:PMC1988811.</p><p></p>tely 14 kbp of the genomic region upstream of . (B) BAC/GFP: GFP modified BAC showing reporter GFP gene inserted before translational start codon. (C) GFP reporter gene construct contains a 7.3 kbp promoter. (D) BACΔUp1/GFP is a GFP modified zebrafish BAC having a deletion of the conserved non-coding sequence Up1. (E) BACΔUp2/GFP is a GFP modified BAC having a deletion of conserved non-coding sequence Up2. (F) BACΔUp1ΔUp2/GFP is a GFP modified BAC having deletions of conserved non-coding sequences Up1 and Up2. (G) mp/GFP is a plasmid vector containing GFP linked to a minimal promoter, (H) Up1Up2-mp/GFP is a plasmid vector containing Up1 and Up2 linked to mp/GFP, (I) Up1-mp/GFP is a plasmid vector containing Up1 linked to mp/GFP, (J) Up2-mp/GFP is a plasmid vector containing linked to mp/GFP, (K) Up2a-mp/GFP is a containing Up2a linked to mp/GFP, and (L) Up2b-mp/GFP is a plasmid vector containing Up2b linked to mp/GFP. In each plasmid vector, GFP reporter gene constructs were inserted between flanking sequences. Black block: Up1; Horizontal striped block: Up2; Open block: 5' UTR of zebrafish gene; Diagonal striped block: coding sequence of zebrafish gene

A highly conserved regulatory element controls hematopoietic expression of in zebrafish-4

<p><b>Copyright information:</b></p><p>Taken from "A highly conserved regulatory element controls hematopoietic expression of in zebrafish"</p><p>http://www.biomedcentral.com/1471-213X/7/97</p><p>BMC Developmental Biology 2007;7():97-97.</p><p>Published online 20 Aug 2007</p><p>PMCID:PMC1988811.</p><p></p>ved between human, mouse, fugu and zebrafish showing that these regions are orthologous. By sequence comparison, three evolutionarily conserved elements were identified in the human, mouse, rat, fugu and zebrafish genomes, two upstream of , located at 12.9 kbp (Up1, open arrowhead) and 10 kbp (Up2, solid arrowhead), and one downstream of (Down1, black dot). (B) Zebrafish locus has 6 exons (blocks). An open arrowhead indicates the location of Up1; a solid arrowhead indicates the locations of Up2 in zebrafish genomic sequence flanking . Open blocks indicate the 5' UTR of zebrafish ; black blocks indicate zebrafish coding sequence. (C) Up1 stands for the genomic sequence lying 12892 bp to12811 bp upstream of the zebrafish start codon. The zebrafish Up1 sequence has an 81% sequence identity with the human Up1 sequence, an 80% sequence identity with both mouse and rat Up1sequences, and an 83% sequence identity with the fugu Up1 sequence. Up2 is the genomic sequence lying 10110 bp to 9887 bp upstream of the zebrafish start codon. Up2a is genomic sequence lying 10110 bp to 9999 bp upstream of start codon; Up2b is the genomic sequence lying 9998 bp to 9887 bp upstream of . The zebrafish Up2 sequence has a 74%, 72%, 72% and 94% sequence identity with Up2 sequences in the human, mouse, rat and fugu genomes, respectively

A highly conserved regulatory element controls hematopoietic expression of in zebrafish-2

<p><b>Copyright information:</b></p><p>Taken from "A highly conserved regulatory element controls hematopoietic expression of in zebrafish"</p><p>http://www.biomedcentral.com/1471-213X/7/97</p><p>BMC Developmental Biology 2007;7():97-97.</p><p>Published online 20 Aug 2007</p><p>PMCID:PMC1988811.</p><p></p> cells, motor neurons and hematopoietic ICM region at 24 hpf stage. Arrows indicate the ICM. (B) Transgenic zebrafish carrying a modified BAC construct containing a 20 kb genomic sequence upstream of, and adjacent to the start codon show GFP expression in the ICM, brain and spinal cord at 24 hpf stage. (C) Transgenic zebrafish embryos carrying a GFP reporter gene construct linked to a 7.3 kb genomic sequence upstream of and adjacent to the start codon have strong GFP expression in neuronal cells, but not in the ICM at 24 hpf. (D) Transgenic zebrafish embryos carrying BACΔUp1/GFP have strong GFP expression in the ICM at 24 hpf stage. (E) Transgenic zebrafish embryos carrying BACΔUp2/GFP and (F) BACΔUp1ΔUp2/GFP have GFP expression in neuronal tissue but not in the ICM. (G) Transgenic zebrafish embryos carrying Up1-mp/GFP have strong GFP expression in the heart at 24 phf stage. (H) Stable transgenic zebrafish embryos containing the Up2 element linked with mp/GFP have strong GFP expression in the ICM and weak GFP expression in the spinal cord at 24 hpf stage. (I) Transgenic zebrafish embryos carrying Up2a-mp/GFP have GFP expression in ICM region at 24 hpf stage; non-specific GFP expression was observed the in notochord. (J-L) Transgenic zebrafish embryos carrying base change mutation in Up2 element derived from construct Up2-mp/GFP. (J) Mutation in the binding site of ARP1 shows no effect on the GFP hematopoietic expression. (K) Mutation in the binding site of E2F-1 results in weaker GFP expression in ICM and strong non-specific expression in muscle and notochord. (L) Mutation in HOXA3-A binding site shows significantly reduced GFP expression in ICM. Similar reduction of GFP in ICM was seen in LMO2 mutation (see Additional file , Supplementary Figure S2). White arrows indicate ICM expression of GFP