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Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis

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Abstract

Nuclear hormone receptors (NRs) form a large superfamily of ligand-activated transcription factors, which regulate genes underlying a wide range of (patho) physiological phenomena. Availability of the full genome sequence of Tetraodon nigroviridis facilitated a genome wide analysis of the NRs in fish genome. Seventy one NRs were found in Tetraodon and were compared with mammalian and fish NR family members. In general, there is a higher representation of NRs in fish genomes compared to mammalian ones. They showed high diversity across classes as observed by phylogenetic analysis. Nucleotide substitution rates show strong negative selection among fish NRs except for pregnane X receptor (PXR), estrogen receptor (ER) and liver X receptor (LXR). This may be attributed to crucial role played by them in metabolism and detoxification of xenobiotic and endobiotic compounds and might have resulted in slight positive selection. Chromosomal mapping and pairwise comparisons of NR distribution in Tetraodon and humans led to the identification of nine synthenic NR regions, of which three are common among fully sequenced vertebrate genomes. Gene structure analysis shows strong conservation of exon structures among orthologoues. Whereas paralogous members show different splicing patterns with intron gain or loss and addition or substitution of exons played a major role in evolution of NR superfamily.

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Abbreviations

DBA:

DNA binding domain

LBD:

ligand binding domain

LXR:

liver X receptors

NRs:

nuclear hormone receptors

PXR:

prephone X receptors

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Author notes

  1. Ramakrishnan Vigneshwar

    Present address: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore, 117576

Authors and Affiliations

  1. National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore, 560 065, India

    Raghu Prasad Rao Metpally, Ramakrishnan Vigneshwar & Ramanathan Sowdhamini

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  1. Raghu Prasad Rao Metpally
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  2. Ramakrishnan Vigneshwar
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  3. Ramanathan Sowdhamini
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Correspondence to Ramanathan Sowdhamini.

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Supplementary Data pertaining to this article is available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/jan2007/pp43-50-suppl.pdf

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Metpally, R.P.R., Vigneshwar, R. & Sowdhamini, R. Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis . J Biosci 32, 43–50 (2007). https://doi.org/10.1007/s12038-007-0005-4

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