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. 2014 Apr 29:5:100.
doi: 10.3389/fgene.2014.00100. eCollection 2014.

miRNA gene counts in chromosomes vary widely in a species and biogenesis of miRNA largely depends on transcription or post-transcriptional processing of coding genes

Atanu Ghorai  1 , Utpal Ghosh  1
Affiliations

miRNA gene counts in chromosomes vary widely in a species and biogenesis of miRNA largely depends on transcription or post-transcriptional processing of coding genes

Atanu Ghorai et al. Front Genet. .

Abstract

MicroRNAs target specific mRNA(s) to silence its expression and thereby regulate various cellular processes. We have investigated miRNA gene counts in chromosomes for 20 different species and observed wide variation. Certain chromosomes have extremely high number of miRNA gene compared with others in all the species. For example, high number of miRNA gene in X chromosome and the least or absence of miRNA gene in Y chromosome was observed in all species. To search the criteria governing such variation of miRNA gene counts in chromosomes, we have selected three parameters- length, number of non-coding and coding genes in a chromosome. We have calculated Pearson's correlation coefficient of miRNA gene counts with length, number of non-coding and coding genes in a chromosome for all 20 species. Major number of species showed that number of miRNA gene was not correlated with chromosome length. Eighty five percent of species under study showed strong positive correlation coefficient (r ≥ 0.5) between the numbers of miRNA gene vs. non-coding gene in chromosomes as expected because miRNA is a sub-set of non-coding genes. 55% species under study showed strong positive correlation coefficient (r ≥ 0.5) between numbers of miRNA gene vs. coding gene. We hypothesize biogenesis of miRNA largely depends on coding genes, an evolutionary conserved process. Chromosomes having higher number of miRNA genes will be most likely playing regulatory roles in several cellular processes including different disorders. In humans, cancer and cardiovascular disease associated miRNAs are mostly intergenic and located in Chromosome 19, X, 14, and 1.

Keywords: chromosome; coding genes; correlation coefficient; disease-association; intergenic; intronic; miRNA; non-coding gene.

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Figures

Figure 1
Figure 1
Species under Metazoa. The detail classification of 20 species (bold) which are chosen in this study.
Figure 2
Figure 2
The histogram represents the variation of miRNA precursors (from miRBase) in different chromosomes of species (A) S. mansoni, C. elegans, D. melanogaster, C. intestinalis; (B) A. carolinensis, G. gallus, T. guttata, D. rerio; (C) O. latipes, T. nigroviridis, S. scrofa, O. anatinus; (D) M. domestica, B. taurus, M. mulatta, P. troglodytes; (E) M. musculus, R. norvegicus, G. gorilla, H. sapiens.
Figure 3
Figure 3
Pattern of correlation coefficient of miRNAs and coding genes with chromosome length. The Pearson correlation coefficient of miRNAs count and coding genes count with chromosome length of a species is calculated using Microsoft Office Excel 2003 software and plotted.
Figure 4
Figure 4
Diversity of miRNA sub-types. The histogram depicts the variation of number of miRNA sub-types—intergenic, intronic, exonic, and others in each of the chromosomes of human genome.
Figure 5
Figure 5
Variation of number of miRNAs associated with cancer and cardiovascular disease in human chromosomes.
Figure 6
Figure 6
miRNA sub-types associated with diseases. Counts of intronic and intergenic miRNAs associated with cancer (A) and cardiovascular disease (B) in different human chromosomes.
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