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Characterization of the transcripts and protein isoforms for cytoplasmic polyadenylation element binding protein-3 (CPEB3) in the mouse retina.

Wang XP, Cooper NG - BMC Mol. Biol. (2009)

Bottom Line: The relative abundance of the patterns in the retina is demonstrated.The level of CPEB3 was up-regulated in the retina during development.The presence of multiple CPEB3 isoforms indicates remarkable complexity in the regulation and function of CPEB3.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Anatomical Sciences and Neurobiology, Health Sciences Campus, 500 S, Preston Street, University of Louisville, Louisville, KY, USA. x0wang04@gwise.louisville.edu

ABSTRACT

Background: Cytoplasmic polyadenylation element binding proteins (CPEBs) regulate translation by binding to regulatory motifs of defined mRNA targets. This translational mechanism has been shown to play a critical role in oocyte maturation, early development, and memory formation in the hippocampus. Little is known about the presence or functions of CPEBs in the retina. The purpose of the current study is to investigate the alternative splicing isoforms of a particular CPEB, CPEB3, based on current databases, and to characterize the expression of CPEB3 in the retina.

Results: In this study, we have characterized CPEB3, whose putative role is to regulate the translation of GluR2 mRNA. We identify the presence of multiple alternative splicing isoforms of CPEB3 transcripts and proteins in the current databases. We report the presence of eight alternative splicing patterns of CPEB3, including a novel one, in the mouse retina. All but one of the patterns appear to be ubiquitous in 13 types of tissue examined. The relative abundance of the patterns in the retina is demonstrated. Experimentally, we show that CPEB3 expression is increased in a time-dependent manner during the course of postnatal development, and CPEB3 is localized mostly in the inner retina, including retinal ganglion cells.

Conclusion: The level of CPEB3 was up-regulated in the retina during development. The presence of multiple CPEB3 isoforms indicates remarkable complexity in the regulation and function of CPEB3.

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Related in: MedlinePlus

Known transcripts of CPEB3. Upper Panel: Representation of genomic DNA sequence. Boxes represented exons, and horizontal lines represented introns. Lower Panel: CPEB3 transcripts derived from alternative splicing. Ten transcripts were shown, with their accession numbers and types of tissue (if reported to the UniGene database) given to the right. The alternative splicings of exon 4, 5, 7 and 11 would generate different proteins products. The alternative splicings upstream of the start codon (exon 1-3) or downstream of the stop codon (exon 13) would give rise to different 5' and 3' UTRs, respectively. Dashed lines represented undetermined sequences. Partial sequence of transcript 2 (exon 5-7) was confirmed with the aid of PCR in a previous study [10], but its complete sequence was not documented in the UniGene database. Transcript 7 was a novel variant identified in the current study, of which the sequence upstream of exon 10 and downstream of exon 12 was not determined. Translational start codons and stop codons were annotated on top of the genomic DNA. Darkened boxed represented exons that could be alternatively spliced.
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Figure 1: Known transcripts of CPEB3. Upper Panel: Representation of genomic DNA sequence. Boxes represented exons, and horizontal lines represented introns. Lower Panel: CPEB3 transcripts derived from alternative splicing. Ten transcripts were shown, with their accession numbers and types of tissue (if reported to the UniGene database) given to the right. The alternative splicings of exon 4, 5, 7 and 11 would generate different proteins products. The alternative splicings upstream of the start codon (exon 1-3) or downstream of the stop codon (exon 13) would give rise to different 5' and 3' UTRs, respectively. Dashed lines represented undetermined sequences. Partial sequence of transcript 2 (exon 5-7) was confirmed with the aid of PCR in a previous study [10], but its complete sequence was not documented in the UniGene database. Transcript 7 was a novel variant identified in the current study, of which the sequence upstream of exon 10 and downstream of exon 12 was not determined. Translational start codons and stop codons were annotated on top of the genomic DNA. Darkened boxed represented exons that could be alternatively spliced.

Mentions: A previous study characterized four different alternative splicing variants of CPEB3 transcripts [9], in which two short motifs of 69 nucleotides (nt) and 24 nt (coding for 23 amino acids and 8 amino acids, respectively) are removed individually, or concurrently. However, the structure of CPEB3 seems to be more variable than previously reported. When investigating a nucleotide database (UniGene) for CPEB3 variants, we were able to identify eight transcripts labeled here as transcript variants 1a, 1b, 1c, 1d, 3, 4, 5 and 6 (figure 1). With the aid of sequence alignment tools (UCSC Genome Browser Blat), we mapped each cDNA to mouse genomic DNA, and acquired the information related to alternative splicing. In addition to the two previously reported short sequences (69 nt and 24 nt) whose presence or absence results in 4 variants [9], several other alternative splicing regions were discovered and elaborated here in diagrammatic form (figure 1). A similar search for the protein databases (UniProt and NCBI) identified six distinct CPEB3 protein isoforms labeled here as isoforms 1 through 6 (figure 2). With the bioinformatics tool Vector NTI, we inferred the matches between cDNA variants and protein isoforms, and designated the same numeric names to the matching transcripts and protein isoforms (figure 1, 2). Transcript 1a, 1b, 1c and 1d all give rise to protein isoform 1.


Characterization of the transcripts and protein isoforms for cytoplasmic polyadenylation element binding protein-3 (CPEB3) in the mouse retina.

Wang XP, Cooper NG - BMC Mol. Biol. (2009)

Known transcripts of CPEB3. Upper Panel: Representation of genomic DNA sequence. Boxes represented exons, and horizontal lines represented introns. Lower Panel: CPEB3 transcripts derived from alternative splicing. Ten transcripts were shown, with their accession numbers and types of tissue (if reported to the UniGene database) given to the right. The alternative splicings of exon 4, 5, 7 and 11 would generate different proteins products. The alternative splicings upstream of the start codon (exon 1-3) or downstream of the stop codon (exon 13) would give rise to different 5' and 3' UTRs, respectively. Dashed lines represented undetermined sequences. Partial sequence of transcript 2 (exon 5-7) was confirmed with the aid of PCR in a previous study [10], but its complete sequence was not documented in the UniGene database. Transcript 7 was a novel variant identified in the current study, of which the sequence upstream of exon 10 and downstream of exon 12 was not determined. Translational start codons and stop codons were annotated on top of the genomic DNA. Darkened boxed represented exons that could be alternatively spliced.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2807433&req=5

Figure 1: Known transcripts of CPEB3. Upper Panel: Representation of genomic DNA sequence. Boxes represented exons, and horizontal lines represented introns. Lower Panel: CPEB3 transcripts derived from alternative splicing. Ten transcripts were shown, with their accession numbers and types of tissue (if reported to the UniGene database) given to the right. The alternative splicings of exon 4, 5, 7 and 11 would generate different proteins products. The alternative splicings upstream of the start codon (exon 1-3) or downstream of the stop codon (exon 13) would give rise to different 5' and 3' UTRs, respectively. Dashed lines represented undetermined sequences. Partial sequence of transcript 2 (exon 5-7) was confirmed with the aid of PCR in a previous study [10], but its complete sequence was not documented in the UniGene database. Transcript 7 was a novel variant identified in the current study, of which the sequence upstream of exon 10 and downstream of exon 12 was not determined. Translational start codons and stop codons were annotated on top of the genomic DNA. Darkened boxed represented exons that could be alternatively spliced.
Mentions: A previous study characterized four different alternative splicing variants of CPEB3 transcripts [9], in which two short motifs of 69 nucleotides (nt) and 24 nt (coding for 23 amino acids and 8 amino acids, respectively) are removed individually, or concurrently. However, the structure of CPEB3 seems to be more variable than previously reported. When investigating a nucleotide database (UniGene) for CPEB3 variants, we were able to identify eight transcripts labeled here as transcript variants 1a, 1b, 1c, 1d, 3, 4, 5 and 6 (figure 1). With the aid of sequence alignment tools (UCSC Genome Browser Blat), we mapped each cDNA to mouse genomic DNA, and acquired the information related to alternative splicing. In addition to the two previously reported short sequences (69 nt and 24 nt) whose presence or absence results in 4 variants [9], several other alternative splicing regions were discovered and elaborated here in diagrammatic form (figure 1). A similar search for the protein databases (UniProt and NCBI) identified six distinct CPEB3 protein isoforms labeled here as isoforms 1 through 6 (figure 2). With the bioinformatics tool Vector NTI, we inferred the matches between cDNA variants and protein isoforms, and designated the same numeric names to the matching transcripts and protein isoforms (figure 1, 2). Transcript 1a, 1b, 1c and 1d all give rise to protein isoform 1.

Bottom Line: The relative abundance of the patterns in the retina is demonstrated.The level of CPEB3 was up-regulated in the retina during development.The presence of multiple CPEB3 isoforms indicates remarkable complexity in the regulation and function of CPEB3.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Anatomical Sciences and Neurobiology, Health Sciences Campus, 500 S, Preston Street, University of Louisville, Louisville, KY, USA. x0wang04@gwise.louisville.edu

ABSTRACT

Background: Cytoplasmic polyadenylation element binding proteins (CPEBs) regulate translation by binding to regulatory motifs of defined mRNA targets. This translational mechanism has been shown to play a critical role in oocyte maturation, early development, and memory formation in the hippocampus. Little is known about the presence or functions of CPEBs in the retina. The purpose of the current study is to investigate the alternative splicing isoforms of a particular CPEB, CPEB3, based on current databases, and to characterize the expression of CPEB3 in the retina.

Results: In this study, we have characterized CPEB3, whose putative role is to regulate the translation of GluR2 mRNA. We identify the presence of multiple alternative splicing isoforms of CPEB3 transcripts and proteins in the current databases. We report the presence of eight alternative splicing patterns of CPEB3, including a novel one, in the mouse retina. All but one of the patterns appear to be ubiquitous in 13 types of tissue examined. The relative abundance of the patterns in the retina is demonstrated. Experimentally, we show that CPEB3 expression is increased in a time-dependent manner during the course of postnatal development, and CPEB3 is localized mostly in the inner retina, including retinal ganglion cells.

Conclusion: The level of CPEB3 was up-regulated in the retina during development. The presence of multiple CPEB3 isoforms indicates remarkable complexity in the regulation and function of CPEB3.

Show MeSH
Related in: MedlinePlus