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The unusual sequence arrangement within the mouse Pecam-1 distal element prompted us to search if the microsatellite repeat motif is found in other species besides mouse. To this end, the sequence of the 1.5kb-fragment embracing the repeat motif was further analyzed with bioinformatics tools.

Using the Genomatix DiAlignTF software [220], an alignment of 20kb of the 5’- flanking sequence of the mouse Pecam-1 gene displays several areas of cross species homology with the corresponding human genomic sequence of Pecam-1. The area that contains the (TTTGT)n motif within the mouse genomic sequence only

aligns over a short distance with that of the human sequence (Fig. 19), indicating that a sequence block (-10,231 to -10,193) of the mouse (TTTGT)n microsatellite repeat

displays moderate cross-species homology to a TG-rich sequence around 16kb upstream of the human PECAM-1 gene (Fig 19). A second homology peak within the area of the microsatellite motif (-10,440 to -10,402) indicates a low cross-species homology stretch that is located between the major and minor block of ‘TTTGT’ repeats. However, the major parts of the two sequence blocks containing the (TTTGT)n repeat motif are not conserved between mouse and human, as seen by the

absence of a homology histogram (Fig. 19). In contrast, the proximal promoter areas located directly upstream of the transcriptional start site of Pecam-1 are strongly

conserved between the orthologue sequences (Fig. 19). In addition, various histograms indicating moderate to high homology can be found throughout the 20kb 5’-flanking sequence and - in addition to the proximal promoter areas - an area displaying very high cross-species homology to the human sequence is found around 19kb upstream of the mouse Pecam-1 transcription initiation site (Fig. 19).

Although we did not attempt to further analyze potential transcription factor binding sites, it is very well possible that these homology areas contain cis-regulatory motifs that may partake in the activation or repression of Pecam-1 expression.

0 2 4 6 8 10 12 ‘TTTGT’ repeat areas -20kb -18kb -16kb -14kb -12kb -10kb -8kb -6kb -4kb -2kb +1

*

*

Figure 19. Cross Species homology upstream of the Pecam-1 locus. Alignment of the respective Pecam-1 genomic sequence of mouse and human. Homology areas between the two species are

indicated by the histograms. The area containing the two blocks of ‘TTTGT’ repeats (-10,995 to -10,478 and -10,390 to -10,188) at the mouse 5’-flanking locus is indicated by the horizontal bar. A short stretch of low cross-species homology is seen in the area of the mouse ‘TTTGT’ microsatellite repeat (-10,231 to -10,193 - ‘TTTGT’ repeats in bold) as indicated by the vertical empty arrow. The neighbouring homology peak to the immediate left (-10,440 to -10,402) indicates a low cross-species homology area that is positioned between the major and minor block of ‘TTTGT’ repeats. The ‘TTTGT’ repeats are not conserved at the human Pecam-1 locus, but rather represented by a TG-rich sequence motif, as indicated by the alignment below the graphic (‘T’ and ‘G’ in italic and underlined). The asterix and the horizontal arrow indicate the start of transcription (+1) of the mouse Pecam-1 gene - strong cross- species sequence homology is found in the area surrounding the transcription initiation site, and various homology areas of different intensity are present throughout the 20kb 5’-flanking area. The alignment was performed by means of the genomatix “DiAlignTF” Tool (http://www.genomatix.de), using the

nucleotide sequences derived from the NCBI Entrez Gene MapViewer

(http://www.ncbi.nlm.nih.gov/sites/entrez).The relative degree of cross-species homology is indicated on the y-axis and is based on the output of the DiAlignTF sequence alignment, ranging from ‘0’ (no homology) to ‘10’ (very high homology). The overall nucleotide similarity of the two aligned sequences was calculated as 7% by the DiAlignTF program. All nucleotide numbering is relative to the transcription initiation site (+1) of the mouse Pecam-1 gene and is based on the NCBI Entrez Gene MapViewer sequence.

Using the MatInspector software [219], the 40kb 5’-flanking genomic sequence of the human PECAM-1 locus was screened for the presence of potential Foxc1 binding sites and/or ‘TTTGT’ repeat motifs, as found at the mouse Pecam-1 locus. As shown in Figure 20, the analysis picked several areas at the human locus that contain blocks of ‘TTTGT’ repeats, ranging from two up to six repeat units.

The MatInspector analysis identified those repeats as Forkhead binding site with ‘CAAA’ (reverse for ‘TTTG’) as core sequence. Likewise, the major block of ‘TTTGT’ repeats in the mouse sequence is identified by the software to contain numerous Forkhead binding sites with the same core sequence, thus allowing us to make the claim that the identified repeats in the human locus may serve as regulatory motifs and potential Foxc1 binding sites during human PECAM-1 expression.

The number of repeat units was lower at the human locus than at the mouse locus. Our analysis showed that the human PECAM-1 5’-flanking area contains an overall of nine short blocks of ‘TTTGT’ repeats identified by the software, indicating a total of 45 ‘TTTGT’ repeat units. However the repeat blocks were distributed over a range of 14kb (from around -33kb to -19kb) in the 5’-flanking area of the human PECAM-1 gene. All identified ‘TTTGT’ sequence repeats and their corresponding nucleotide positions in relation to the human PECAM-1 transcription initiation site are listed in Table 2.

+1

-35kb -30kb -25kb -20kb -15kb -10kb -5kb

-40kb

Human Pecam-1 5’-flanking area

6 5 6 6 6 4 2 ₂ 4 4 PECAM-1

+1 +1

-35kb -30kb -25kb -20kb -15kb -10kb -5kb

-40kb

Human Pecam-1 5’-flanking area

6 5 6 6 6 4 2 ₂ 4 4 PECAM-1

Figure 20. The human PECAM-1 locus contains various short (TTTGT)n repeat motifs. A) The 5’-

flanking sequence (40kb) of the human PECAM-1 gene was screened for putative Forkhead

Transcription Factor binding sites using the genomatix MatInspector Software

(http://www.genomatix.de). The schematic graphic depicts areas containing ‘TTTGT’ repeats (black boxes) that were identified by the software as Forkhead binding sites. The upstream area between - 33kb and -19kb contains several blocks of ‘TTTGT’ repeats. The number of single repeat units of each block is shown above the boxes, indicating a total of 45 identified repeat units. The width of the boxes reflects the total length of the sequence stretch embracing the repeats units.

To further verify the possibility that the (TTTGT)n repeat motifs serve as putative cis-

regulatory sites at the human PECAM-1 locus, an experimentally verified Foxc1 binding site at the mouse Tbx1 locus that was shown to be involved as cis-regulatory element in the expression of Tbx1 [195], was identified by the MatInspector software as Forkhead binding site with ‘CAAA’ as core binding site (data not shown), as seen for the (TTTGT)n repeat motifs at the mouse and human Pecam-1 locus. This

strengthened our assumption that, like in the mouse, transcriptional control of the human PECAM-1 gene may involve the randomly distributed (TTTGT)n repeat motifs

(Fig. 20).