Limits...
Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution.

He C, Li Z, Chen P, Huang H, Hurst LD, Chen J - Nucleic Acids Res. (2012)

Bottom Line: This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance.As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones.We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, University of Chicago, Chicago, IL 60637, USA.

ABSTRACT
MicroRNAs (miRNAs) have emerged as key regulators of gene expression. Intragenic miRNAs account for ∼50% of mammalian miRNAs. Classic studies reported that they are usually coexpressed with host genes. Here, using genome-wide miRNA and gene expression profiles from five sample sets, we show that evolutionarily conserved ('old') intragenic miRNAs tend to be coexpressed with host genes, but non-conserved ('young') ones rarely do so. This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance. As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones. For younger miRNAs, extrapolation of their expression profiles from those of their host genes should be treated with caution. We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms.

Show MeSH
The majority or most of the coexpressed intragenic miRNAs are conserved ones, which also exhibit coexpression with host genes in more data sets than non-conserved ones. (A) Conservational distribution of coexpressed intragenic miRNAs in individual sample sets based on the raw P-values. (B) Conservational distribution of the intragenic miRNAs that exhibit coexpression (based on raw P-values) with their host genes in more than one, more than two, more than three, more than four and all the five sample sets, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3351155&req=5

gkr1312-F2: The majority or most of the coexpressed intragenic miRNAs are conserved ones, which also exhibit coexpression with host genes in more data sets than non-conserved ones. (A) Conservational distribution of coexpressed intragenic miRNAs in individual sample sets based on the raw P-values. (B) Conservational distribution of the intragenic miRNAs that exhibit coexpression (based on raw P-values) with their host genes in more than one, more than two, more than three, more than four and all the five sample sets, respectively.

Mentions: As a result, the majority of the intragenic miRNAs that are likely coexpressed with their host genes are evolutionarily conserved ones in each data set (Table 2 and Figure 2A). The fact that we can recover high coexpression rates for conserved genes supports the view that our coexpression scoring method is adequately powerful to detect coexpression if it is present.Figure 2.


Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution.

He C, Li Z, Chen P, Huang H, Hurst LD, Chen J - Nucleic Acids Res. (2012)

The majority or most of the coexpressed intragenic miRNAs are conserved ones, which also exhibit coexpression with host genes in more data sets than non-conserved ones. (A) Conservational distribution of coexpressed intragenic miRNAs in individual sample sets based on the raw P-values. (B) Conservational distribution of the intragenic miRNAs that exhibit coexpression (based on raw P-values) with their host genes in more than one, more than two, more than three, more than four and all the five sample sets, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351155&req=5

gkr1312-F2: The majority or most of the coexpressed intragenic miRNAs are conserved ones, which also exhibit coexpression with host genes in more data sets than non-conserved ones. (A) Conservational distribution of coexpressed intragenic miRNAs in individual sample sets based on the raw P-values. (B) Conservational distribution of the intragenic miRNAs that exhibit coexpression (based on raw P-values) with their host genes in more than one, more than two, more than three, more than four and all the five sample sets, respectively.
Mentions: As a result, the majority of the intragenic miRNAs that are likely coexpressed with their host genes are evolutionarily conserved ones in each data set (Table 2 and Figure 2A). The fact that we can recover high coexpression rates for conserved genes supports the view that our coexpression scoring method is adequately powerful to detect coexpression if it is present.Figure 2.

Bottom Line: This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance.As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones.We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, University of Chicago, Chicago, IL 60637, USA.

ABSTRACT
MicroRNAs (miRNAs) have emerged as key regulators of gene expression. Intragenic miRNAs account for ∼50% of mammalian miRNAs. Classic studies reported that they are usually coexpressed with host genes. Here, using genome-wide miRNA and gene expression profiles from five sample sets, we show that evolutionarily conserved ('old') intragenic miRNAs tend to be coexpressed with host genes, but non-conserved ('young') ones rarely do so. This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance. As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones. For younger miRNAs, extrapolation of their expression profiles from those of their host genes should be treated with caution. We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms.

Show MeSH