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Runx family genes in a cartilaginous fish, the elephant shark (Callorhinchus milii).

Nah GS, Lim ZW, Tay BH, Osato M, Venkatesh B - PLoS ONE (2014)

Bottom Line: Analysis of promoter regions revealed conservation of binding sites for transcription factors, including two tandem binding sites for Runx that are totally conserved in the distal promoter regions of elephant shark Runx1-3.Several conserved noncoding elements (CNEs), which are putative cis-regulatory elements, and miRNA binding sites were identified in the elephant shark and human Runx gene loci.Some of these CNEs and miRNA binding sites are absent in teleost fishes such as zebrafish and fugu.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.

ABSTRACT
The Runx family genes encode transcription factors that play key roles in hematopoiesis, skeletogenesis and neurogenesis and are often implicated in diseases. We describe here the cloning and characterization of Runx1, Runx2, Runx3 and Runxb genes in the elephant shark (Callorhinchus milii), a member of Chondrichthyes, the oldest living group of jawed vertebrates. Through the use of alternative promoters and/or alternative splicing, each of the elephant shark Runx genes expresses multiple isoforms similar to their orthologs in human and other bony vertebrates. The expression profiles of elephant shark Runx genes are similar to those of mammalian Runx genes. The syntenic blocks of genes at the elephant shark Runx gene loci are highly conserved in human, but represented by shorter conserved blocks in zebrafish indicating a higher degree of rearrangements in this teleost fish. Analysis of promoter regions revealed conservation of binding sites for transcription factors, including two tandem binding sites for Runx that are totally conserved in the distal promoter regions of elephant shark Runx1-3. Several conserved noncoding elements (CNEs), which are putative cis-regulatory elements, and miRNA binding sites were identified in the elephant shark and human Runx gene loci. Some of these CNEs and miRNA binding sites are absent in teleost fishes such as zebrafish and fugu. In summary, our analysis reveals that the genomic organization and expression profiles of Runx genes were already complex in the common ancestor of jawed vertebrates.

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Expression patterns of elephant shark Runx genes.Relative expression levels of (A) CmRunx1, (B) CmRunx2 and (C) CmRunx3 in various tissues of the elephant shark determined by qRT-PCR.
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pone-0093816-g005: Expression patterns of elephant shark Runx genes.Relative expression levels of (A) CmRunx1, (B) CmRunx2 and (C) CmRunx3 in various tissues of the elephant shark determined by qRT-PCR.

Mentions: We investigated the expression patterns of Runx genes in various tissues of adult elephant shark by quantitative RT-PCR. CmRunx1 is highly expressed in the gills, muscle, testis, skin and spleen (Fig. 5A). High CmRunx1 expression in the gill, a tissue enriched in blood cells, as well as the spleen, a lymphomyeloid tissue of the shark, is concordant with the integral function of Runx1 in hematopoiesis. In addition, high expression of CmRunx1 in the muscle reflects its known role in mammalian skeletal muscle development. Although Runx1 is not known to be expressed at high levels in testis of mammals, high expression of Runx1 has been reported in another cartilaginous fish, the dogfish. Thus, Runx1 might have a function in testis that is specific to cartilaginous fishes. However, this hypothesis remains to be verified. Furthermore, a significant level of Runx1 expression in the skin of the elephant shark is consistent with previous reports of Runx expression in placoid scales which are small conical structures in the skin of cartilaginous fishes [29].


Runx family genes in a cartilaginous fish, the elephant shark (Callorhinchus milii).

Nah GS, Lim ZW, Tay BH, Osato M, Venkatesh B - PLoS ONE (2014)

Expression patterns of elephant shark Runx genes.Relative expression levels of (A) CmRunx1, (B) CmRunx2 and (C) CmRunx3 in various tissues of the elephant shark determined by qRT-PCR.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3974841&req=5

pone-0093816-g005: Expression patterns of elephant shark Runx genes.Relative expression levels of (A) CmRunx1, (B) CmRunx2 and (C) CmRunx3 in various tissues of the elephant shark determined by qRT-PCR.
Mentions: We investigated the expression patterns of Runx genes in various tissues of adult elephant shark by quantitative RT-PCR. CmRunx1 is highly expressed in the gills, muscle, testis, skin and spleen (Fig. 5A). High CmRunx1 expression in the gill, a tissue enriched in blood cells, as well as the spleen, a lymphomyeloid tissue of the shark, is concordant with the integral function of Runx1 in hematopoiesis. In addition, high expression of CmRunx1 in the muscle reflects its known role in mammalian skeletal muscle development. Although Runx1 is not known to be expressed at high levels in testis of mammals, high expression of Runx1 has been reported in another cartilaginous fish, the dogfish. Thus, Runx1 might have a function in testis that is specific to cartilaginous fishes. However, this hypothesis remains to be verified. Furthermore, a significant level of Runx1 expression in the skin of the elephant shark is consistent with previous reports of Runx expression in placoid scales which are small conical structures in the skin of cartilaginous fishes [29].

Bottom Line: Analysis of promoter regions revealed conservation of binding sites for transcription factors, including two tandem binding sites for Runx that are totally conserved in the distal promoter regions of elephant shark Runx1-3.Several conserved noncoding elements (CNEs), which are putative cis-regulatory elements, and miRNA binding sites were identified in the elephant shark and human Runx gene loci.Some of these CNEs and miRNA binding sites are absent in teleost fishes such as zebrafish and fugu.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.

ABSTRACT
The Runx family genes encode transcription factors that play key roles in hematopoiesis, skeletogenesis and neurogenesis and are often implicated in diseases. We describe here the cloning and characterization of Runx1, Runx2, Runx3 and Runxb genes in the elephant shark (Callorhinchus milii), a member of Chondrichthyes, the oldest living group of jawed vertebrates. Through the use of alternative promoters and/or alternative splicing, each of the elephant shark Runx genes expresses multiple isoforms similar to their orthologs in human and other bony vertebrates. The expression profiles of elephant shark Runx genes are similar to those of mammalian Runx genes. The syntenic blocks of genes at the elephant shark Runx gene loci are highly conserved in human, but represented by shorter conserved blocks in zebrafish indicating a higher degree of rearrangements in this teleost fish. Analysis of promoter regions revealed conservation of binding sites for transcription factors, including two tandem binding sites for Runx that are totally conserved in the distal promoter regions of elephant shark Runx1-3. Several conserved noncoding elements (CNEs), which are putative cis-regulatory elements, and miRNA binding sites were identified in the elephant shark and human Runx gene loci. Some of these CNEs and miRNA binding sites are absent in teleost fishes such as zebrafish and fugu. In summary, our analysis reveals that the genomic organization and expression profiles of Runx genes were already complex in the common ancestor of jawed vertebrates.

Show MeSH