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Cloning and characterization of the mouse Mcoln1 gene reveals an alternatively spliced transcript not seen in humans.

Falardeau JL, Kennedy JC, Acierno JS, Sun M, Stahl S, Goldin E, Slaugenhaupt SA - BMC Genomics (2002)

Bottom Line: The transcript that results from murine specific alternative splicing encodes a 611 amino acid protein that differs at the c-terminus.Mcoln1 is highly similar to MCOLN1, especially in the transmembrane domains and ion pore region.To date, there are very few reports describing species-specific splice variants.

View Article: PubMed Central - HTML - PubMed

Affiliation: Harvard Institute of Human Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. falardea@helix.mgh.harvard.edu

ABSTRACT

Background: Mucolipidosis type IV (MLIV) is an autosomal recessive lysosomal storage disorder characterized by severe neurologic and ophthalmologic abnormalities. Recently the MLIV gene, MCOLN1, has been identified as a new member of the transient receptor potential (TRP) cation channel superfamily. Here we report the cloning and characterization of the mouse homologue, Mcoln1, and report a novel splice variant that is not seen in humans.

Results: The human and mouse genes display a high degree of synteny. Mcoln1 shows 91% amino acid and 86% nucleotide identity to MCOLN1. Also, Mcoln1 maps to chromosome 8 and contains an open reading frame of 580 amino acids, with a transcript length of approximately 2 kb encoded by 14 exons, similar to its human counterpart. The transcript that results from murine specific alternative splicing encodes a 611 amino acid protein that differs at the c-terminus.

Conclusions: Mcoln1 is highly similar to MCOLN1, especially in the transmembrane domains and ion pore region. Also, the late endosomal/lysosomal targeting signal is conserved, supporting the hypothesis that the protein is localized to these vesicle membranes. To date, there are very few reports describing species-specific splice variants. While identification of Mcoln1 is crucial to the development of mouse models for MLIV, the fact that there are two transcripts in mice suggests an additional or alternate function of the gene that may complicate phenotypic assessment.

No MeSH data available.


Related in: MedlinePlus

Physical and transcript map of the Mcoln1 gene region. (A) Physical map showing a 590 kb segment of mouse chromosome 8 syntenous to human chromosome 19, anchored by the genes Insr and Nte. The region is covered by three BACs: RPCI-23_334D24 (AC087153), RPCI-23_312B8 (AC087150), and RPCI-23_387H4 (AC079544). (B) The transcript map of Mcoln1 shows 14 exons, and the locations of the probes used in this study are illustrated. The map also shows the expanded exon 13 in the alternatively spliced transcript (hashed box). UniGene cluster Mm.39099 is the homologue of the human zinc finger gene (AC001252). It should be noted that the scale of the transcript map is in reference to the 201 kb scale of BAC RPCI-23_387H4.
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Figure 1: Physical and transcript map of the Mcoln1 gene region. (A) Physical map showing a 590 kb segment of mouse chromosome 8 syntenous to human chromosome 19, anchored by the genes Insr and Nte. The region is covered by three BACs: RPCI-23_334D24 (AC087153), RPCI-23_312B8 (AC087150), and RPCI-23_387H4 (AC079544). (B) The transcript map of Mcoln1 shows 14 exons, and the locations of the probes used in this study are illustrated. The map also shows the expanded exon 13 in the alternatively spliced transcript (hashed box). UniGene cluster Mm.39099 is the homologue of the human zinc finger gene (AC001252). It should be noted that the scale of the transcript map is in reference to the 201 kb scale of BAC RPCI-23_387H4.

Mentions: In order to clone the mouse homologue of MCOLN1, the human amino acid sequence was compared to the high throughput genomic sequence (HTGS) database using TBLASTN, which identified the mouse BAC clone RPCI-23_387H4 (GB No. AC079544.1). Correspondence with the Joint Genome Institute and the Lawrence Livermore National Laboratory (LLNL) Human Genome Center confirmed the location of this BAC to mouse chromosome 8 and allowed us to construct a physical map of this region [14] (Fig. 1A). The BAC sequence was then compared to the mouse EST database using BLASTN, and multiple ESTs and their corresponding I.M.A.G.E. clones were identified.


Cloning and characterization of the mouse Mcoln1 gene reveals an alternatively spliced transcript not seen in humans.

Falardeau JL, Kennedy JC, Acierno JS, Sun M, Stahl S, Goldin E, Slaugenhaupt SA - BMC Genomics (2002)

Physical and transcript map of the Mcoln1 gene region. (A) Physical map showing a 590 kb segment of mouse chromosome 8 syntenous to human chromosome 19, anchored by the genes Insr and Nte. The region is covered by three BACs: RPCI-23_334D24 (AC087153), RPCI-23_312B8 (AC087150), and RPCI-23_387H4 (AC079544). (B) The transcript map of Mcoln1 shows 14 exons, and the locations of the probes used in this study are illustrated. The map also shows the expanded exon 13 in the alternatively spliced transcript (hashed box). UniGene cluster Mm.39099 is the homologue of the human zinc finger gene (AC001252). It should be noted that the scale of the transcript map is in reference to the 201 kb scale of BAC RPCI-23_387H4.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC88885&req=5

Figure 1: Physical and transcript map of the Mcoln1 gene region. (A) Physical map showing a 590 kb segment of mouse chromosome 8 syntenous to human chromosome 19, anchored by the genes Insr and Nte. The region is covered by three BACs: RPCI-23_334D24 (AC087153), RPCI-23_312B8 (AC087150), and RPCI-23_387H4 (AC079544). (B) The transcript map of Mcoln1 shows 14 exons, and the locations of the probes used in this study are illustrated. The map also shows the expanded exon 13 in the alternatively spliced transcript (hashed box). UniGene cluster Mm.39099 is the homologue of the human zinc finger gene (AC001252). It should be noted that the scale of the transcript map is in reference to the 201 kb scale of BAC RPCI-23_387H4.
Mentions: In order to clone the mouse homologue of MCOLN1, the human amino acid sequence was compared to the high throughput genomic sequence (HTGS) database using TBLASTN, which identified the mouse BAC clone RPCI-23_387H4 (GB No. AC079544.1). Correspondence with the Joint Genome Institute and the Lawrence Livermore National Laboratory (LLNL) Human Genome Center confirmed the location of this BAC to mouse chromosome 8 and allowed us to construct a physical map of this region [14] (Fig. 1A). The BAC sequence was then compared to the mouse EST database using BLASTN, and multiple ESTs and their corresponding I.M.A.G.E. clones were identified.

Bottom Line: The transcript that results from murine specific alternative splicing encodes a 611 amino acid protein that differs at the c-terminus.Mcoln1 is highly similar to MCOLN1, especially in the transmembrane domains and ion pore region.To date, there are very few reports describing species-specific splice variants.

View Article: PubMed Central - HTML - PubMed

Affiliation: Harvard Institute of Human Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. falardea@helix.mgh.harvard.edu

ABSTRACT

Background: Mucolipidosis type IV (MLIV) is an autosomal recessive lysosomal storage disorder characterized by severe neurologic and ophthalmologic abnormalities. Recently the MLIV gene, MCOLN1, has been identified as a new member of the transient receptor potential (TRP) cation channel superfamily. Here we report the cloning and characterization of the mouse homologue, Mcoln1, and report a novel splice variant that is not seen in humans.

Results: The human and mouse genes display a high degree of synteny. Mcoln1 shows 91% amino acid and 86% nucleotide identity to MCOLN1. Also, Mcoln1 maps to chromosome 8 and contains an open reading frame of 580 amino acids, with a transcript length of approximately 2 kb encoded by 14 exons, similar to its human counterpart. The transcript that results from murine specific alternative splicing encodes a 611 amino acid protein that differs at the c-terminus.

Conclusions: Mcoln1 is highly similar to MCOLN1, especially in the transmembrane domains and ion pore region. Also, the late endosomal/lysosomal targeting signal is conserved, supporting the hypothesis that the protein is localized to these vesicle membranes. To date, there are very few reports describing species-specific splice variants. While identification of Mcoln1 is crucial to the development of mouse models for MLIV, the fact that there are two transcripts in mice suggests an additional or alternate function of the gene that may complicate phenotypic assessment.

No MeSH data available.


Related in: MedlinePlus