Whole transcriptome RNA sequencing detects multiple 1α 25- dihydroxyvitamin D3-sensitive metabolic pathways in developing zebrafish

Theodore A. Craig, Yuji Zhang, Melissa S. McNulty, Sumit Middha, Hemamalini Ketha, Ravinder Jit Singh, Andrew T. Magis, Cory Funk, Nathan D. Price, Stephen C Ekker, Rajiv Kumar

Research output: Contribution to journalArticle

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Abstract

The biological role of vitamin D receptors (VDR), which are abundantly expressed in developing zebrafish (Danio rerio) as early as 48 h after fertilization, and before the development of a mineralized skeleton and mature intestine and kidney, is unknown. We probed the role of VDR in developing zebrafish biology by examining changes in expression of RNA by whole transcriptome shotgun sequencing (RNA-seq) in fish treated with picomolar concentrations of the VDR ligand and hormonal form of vitamin D3, 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3)].We observed significant changes in RNAs of transcription factors, leptin, peptide hormones, and RNAs encoding proteins of fatty acid, amino acid, xenobiotic metabolism, receptor-activator of NFκB ligand (RANKL), and calcitonin-like ligand receptor pathways. Early highly restricted, and subsequent massive changes in more than 10% of expressed cellular RNA were observed. At days post fertilization (dpf) 2 [24 h 1α,25(OH)2D3-treatment], only four RNAs were differentially expressed (hormone vs. vehicle). On dpf 4 (72 h treatment), 77 RNAs; on dpf 6 (120 h treatment) 1039 RNAs; and on dpf 7 (144 h treatment), 2407 RNAs were differentially expressed in response to 1α,25(OH)2D3. Fewer RNAs (n = 481) were altered in dpf 7 larvae treated for 24 h with 1α,25(OH)2D3 vs. those treated with hormone for 144 h. At dpf 7, in 1α,25(OH)2D3-treated larvae, pharyngeal cartilage was larger and mineralization was greater. Changes in expression of RNAs for transcription factors, peptide hormones, and RNAs encoding proteins integral to fatty acid, amino acid, leptin, calcitonin-like ligand receptor, RANKL, and xenobiotic metabolism pathways, demonstrate heretofore unrecognized mechanisms by which 1α,25(OH)2D3 functions in vivo in developing eukaryotes.

Original languageEnglish (US)
Pages (from-to)1630-1642
Number of pages13
JournalMolecular Endocrinology
Volume26
Issue number9
DOIs
StatePublished - Sep 2012

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RNA Sequence Analysis
Calcitriol
Zebrafish
Metabolic Networks and Pathways
Transcriptome
RNA
Fertilization
Calcitriol Receptors
Ligands
Peptide Hormones
Calcitonin
Xenobiotics
Leptin
Larva
Transcription Factors
Fatty Acids
Hormones
Amino Acids
Cholecalciferol
Firearms

ASJC Scopus subject areas

  • Molecular Biology
  • Endocrinology
  • Medicine(all)

Cite this

Whole transcriptome RNA sequencing detects multiple 1α 25- dihydroxyvitamin D3-sensitive metabolic pathways in developing zebrafish. / Craig, Theodore A.; Zhang, Yuji; McNulty, Melissa S.; Middha, Sumit; Ketha, Hemamalini; Singh, Ravinder Jit; Magis, Andrew T.; Funk, Cory; Price, Nathan D.; Ekker, Stephen C; Kumar, Rajiv.

In: Molecular Endocrinology, Vol. 26, No. 9, 09.2012, p. 1630-1642.

Research output: Contribution to journalArticle

Craig, Theodore A. ; Zhang, Yuji ; McNulty, Melissa S. ; Middha, Sumit ; Ketha, Hemamalini ; Singh, Ravinder Jit ; Magis, Andrew T. ; Funk, Cory ; Price, Nathan D. ; Ekker, Stephen C ; Kumar, Rajiv. / Whole transcriptome RNA sequencing detects multiple 1α 25- dihydroxyvitamin D3-sensitive metabolic pathways in developing zebrafish. In: Molecular Endocrinology. 2012 ; Vol. 26, No. 9. pp. 1630-1642.
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