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Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTPkappa, mu, rho and PCP-2).

Besco J, Popesco MC, Davuluri RV, Frostholm A, Rotter A - BMC Genomics (2004)

Bottom Line: The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction.Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length.Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA. besco.1@osu.edu

ABSTRACT

Background: Four genes designated as PTPRK (PTPkappa), PTPRL/U (PCP-2), PTPRM (PTPmu) and PTPRT (PTPrho) code for a subfamily (type R2B) of receptor protein tyrosine phosphatases (RPTPs) uniquely characterized by the presence of an N-terminal MAM domain. These transmembrane molecules have been implicated in homophilic cell adhesion. In the human, the PTPRK gene is located on chromosome 6, PTPRL/U on 1, PTPRM on 18 and PTPRT on 20. In the mouse, the four genes ptprk, ptprl, ptprm and ptprt are located in syntenic regions of chromosomes 10, 4, 17 and 2, respectively.

Results: The genomic organization of murine R2B RPTP genes is described. The four genes varied greatly in size ranging from approximately 64 kb to approximately 1 Mb, primarily due to proportional differences in intron lengths. Although there were also minor variations in exon length, the number of exons and the phases of exon/intron junctions were highly conserved. In situ hybridization with digoxigenin-labeled cRNA probes was used to localize each of the four R2B transcripts to specific cell types within the murine central nervous system. Phylogenetic analysis of complete sequences indicated that PTPrho and PTPmu were most closely related, followed by PTPkappa. The most distant family member was PCP-2. Alignment of RPTP polypeptide sequences predicted putative alternatively spliced exons. PCR experiments revealed that five of these exons were alternatively spliced, and that each of the four phosphatases incorporated them differently. The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction.

Conclusions: Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length. Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing.

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Alternative splicing of PTPκ mRNA. RT-PCR products were amplified using primers flanking exon 16 (panels A and B), exon 17a (panels C and D) and exon 20a (panels E and F). Left panels: bands in lanes 1, 2, and 3 are from human fetal brain, mouse P1 brain, and mouse P60 brain total RNA, respectively. Right panels: bands in lanes 4, 5, 6 and 7 contain total RNA from cerebellum, brain stem, basal forebrain and cortex (P23), respectively. Transcripts containing both splice forms of exons 16 and 20a were found in all lanes.
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Figure 13: Alternative splicing of PTPκ mRNA. RT-PCR products were amplified using primers flanking exon 16 (panels A and B), exon 17a (panels C and D) and exon 20a (panels E and F). Left panels: bands in lanes 1, 2, and 3 are from human fetal brain, mouse P1 brain, and mouse P60 brain total RNA, respectively. Right panels: bands in lanes 4, 5, 6 and 7 contain total RNA from cerebellum, brain stem, basal forebrain and cortex (P23), respectively. Transcripts containing both splice forms of exons 16 and 20a were found in all lanes.

Mentions: Each of the four R2B genes expressed in the brain used the five alternatively spliced exons in a different combination: In PTPρ transcripts, exon 17a and 20a were absent, and exons 14, 16, and 22a were alternatively spliced (Figure 11). In PTPμ transcripts, exons 14, 16, 20a and 22a were absent; exon 17a was present and not alternatively spliced. The alternative use of two 5' splice consensus sites resulted in the transcription of an additional 58 bp of the intron between exons 13 and 15 (Figure 12). In PTPκ mRNA, exons 14 and 22a were absent, and exons 16, 17a and 20a were alternatively spliced (Figure 13). In PCP-2 mRNA, exons 14 was absent, exon 16 was not transcribed in brain, and exons 17a, 20a, and 22a were alternatively spliced (Figure 14). These results are summarized in Table 2. Splicing was also examined in human R2B transcripts where the use of alternatively spliced exons was virtually identical to that observed in the mouse genes. No age-related or regional differences were observed in the CNS in any of the above studies.


Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTPkappa, mu, rho and PCP-2).

Besco J, Popesco MC, Davuluri RV, Frostholm A, Rotter A - BMC Genomics (2004)

Alternative splicing of PTPκ mRNA. RT-PCR products were amplified using primers flanking exon 16 (panels A and B), exon 17a (panels C and D) and exon 20a (panels E and F). Left panels: bands in lanes 1, 2, and 3 are from human fetal brain, mouse P1 brain, and mouse P60 brain total RNA, respectively. Right panels: bands in lanes 4, 5, 6 and 7 contain total RNA from cerebellum, brain stem, basal forebrain and cortex (P23), respectively. Transcripts containing both splice forms of exons 16 and 20a were found in all lanes.
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Related In: Results  -  Collection

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Figure 13: Alternative splicing of PTPκ mRNA. RT-PCR products were amplified using primers flanking exon 16 (panels A and B), exon 17a (panels C and D) and exon 20a (panels E and F). Left panels: bands in lanes 1, 2, and 3 are from human fetal brain, mouse P1 brain, and mouse P60 brain total RNA, respectively. Right panels: bands in lanes 4, 5, 6 and 7 contain total RNA from cerebellum, brain stem, basal forebrain and cortex (P23), respectively. Transcripts containing both splice forms of exons 16 and 20a were found in all lanes.
Mentions: Each of the four R2B genes expressed in the brain used the five alternatively spliced exons in a different combination: In PTPρ transcripts, exon 17a and 20a were absent, and exons 14, 16, and 22a were alternatively spliced (Figure 11). In PTPμ transcripts, exons 14, 16, 20a and 22a were absent; exon 17a was present and not alternatively spliced. The alternative use of two 5' splice consensus sites resulted in the transcription of an additional 58 bp of the intron between exons 13 and 15 (Figure 12). In PTPκ mRNA, exons 14 and 22a were absent, and exons 16, 17a and 20a were alternatively spliced (Figure 13). In PCP-2 mRNA, exons 14 was absent, exon 16 was not transcribed in brain, and exons 17a, 20a, and 22a were alternatively spliced (Figure 14). These results are summarized in Table 2. Splicing was also examined in human R2B transcripts where the use of alternatively spliced exons was virtually identical to that observed in the mouse genes. No age-related or regional differences were observed in the CNS in any of the above studies.

Bottom Line: The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction.Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length.Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA. besco.1@osu.edu

ABSTRACT

Background: Four genes designated as PTPRK (PTPkappa), PTPRL/U (PCP-2), PTPRM (PTPmu) and PTPRT (PTPrho) code for a subfamily (type R2B) of receptor protein tyrosine phosphatases (RPTPs) uniquely characterized by the presence of an N-terminal MAM domain. These transmembrane molecules have been implicated in homophilic cell adhesion. In the human, the PTPRK gene is located on chromosome 6, PTPRL/U on 1, PTPRM on 18 and PTPRT on 20. In the mouse, the four genes ptprk, ptprl, ptprm and ptprt are located in syntenic regions of chromosomes 10, 4, 17 and 2, respectively.

Results: The genomic organization of murine R2B RPTP genes is described. The four genes varied greatly in size ranging from approximately 64 kb to approximately 1 Mb, primarily due to proportional differences in intron lengths. Although there were also minor variations in exon length, the number of exons and the phases of exon/intron junctions were highly conserved. In situ hybridization with digoxigenin-labeled cRNA probes was used to localize each of the four R2B transcripts to specific cell types within the murine central nervous system. Phylogenetic analysis of complete sequences indicated that PTPrho and PTPmu were most closely related, followed by PTPkappa. The most distant family member was PCP-2. Alignment of RPTP polypeptide sequences predicted putative alternatively spliced exons. PCR experiments revealed that five of these exons were alternatively spliced, and that each of the four phosphatases incorporated them differently. The greatest variability in genomic organization and the majority of alternatively spliced exons were observed in the juxtamembrane domain, a region critical for the regulation of signal transduction.

Conclusions: Comparison of the four R2B RPTP genes revealed virtually identical principles of genomic organization, despite great disparities in gene size due to variations in intron length. Although subtle differences in exon length were also observed, it is likely that functional differences among these genes arise from the specific combinations of exons generated by alternative splicing.

Show MeSH
Related in: MedlinePlus