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An evolutionary perspective of animal microRNAs and their targets.

Shomron N, Golan D, Hornstein E - J. Biomed. Biotechnol. (2009)

Bottom Line: MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to be the most abundant mode of posttranscriptional regulation affecting approximately 50% of the transcriptome. miRNA genes are often clustered and/or located in introns, and each targets a variable and often large number of mRNAs.Here we discuss the genomic architecture of animal miRNA genes and their evolving interaction with their target mRNAs.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. nshomron@post.tau.ac.il

ABSTRACT
MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to be the most abundant mode of posttranscriptional regulation affecting approximately 50% of the transcriptome. miRNA genes are often clustered and/or located in introns, and each targets a variable and often large number of mRNAs. Here we discuss the genomic architecture of animal miRNA genes and their evolving interaction with their target mRNAs.

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A possible scenario for acquiring a functional miRNA binding site.
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Related In: Results  -  Collection


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fig4: A possible scenario for acquiring a functional miRNA binding site.

Mentions: It would take several million years for a specific 7-mer binding site to evolve from a complete binding sequence [102]. However, miRNA binding sites evolve from existing sequences, and based on these partial binding sequences, (“almost-binding” sites or “pre-seed” sites), a corrected estimated time for a miRNA binding site to emerge is 0.2 million years (Durrett R., personal communications). For example, a 5 nt pre-seed site will appear every 1024 nt (4⋀5) or even 20 times more often since the position of the 5 nt within the 7 nt is not restricted and may also include inserts. Thus, a 1 kb 3′ UTR will contain several potential pre-seed sequences. A human specific miRNA that is absent even from the chimp genome should be roughly 6 million years old (last estimated split between human and chimp). Given 0.2 million years required for a 7-mer binding site to evolve, around 30 perfect 7-mer binding sites are expected. For an miRNA that is traced back to mouse (split more than 100 million years ago from human), about 500 conserved targets per miRNA are reasonable. This simplified calculation might indicate that, given a spontaneous mutation rate, there should be a direct correlation between the age of an miRNA and the number of targets it possesses and also to the number of duplicated events of the same miRNA site on one transcript. Eventually, it is not enough for the mutation to occur—it should also be maintained in the population after exhibiting a strong selective pressure towards a favorable regulation which can only take place when an miRNA and its targets are spatially and temporally coexpressed [83, 103]. This calculation allows us to set the general time line of events for miRNA formation. Nevertheless there are many outstanding exceptions of small and large miRNA target repertoires (also see Figure 4).


An evolutionary perspective of animal microRNAs and their targets.

Shomron N, Golan D, Hornstein E - J. Biomed. Biotechnol. (2009)

A possible scenario for acquiring a functional miRNA binding site.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2743850&req=5

fig4: A possible scenario for acquiring a functional miRNA binding site.
Mentions: It would take several million years for a specific 7-mer binding site to evolve from a complete binding sequence [102]. However, miRNA binding sites evolve from existing sequences, and based on these partial binding sequences, (“almost-binding” sites or “pre-seed” sites), a corrected estimated time for a miRNA binding site to emerge is 0.2 million years (Durrett R., personal communications). For example, a 5 nt pre-seed site will appear every 1024 nt (4⋀5) or even 20 times more often since the position of the 5 nt within the 7 nt is not restricted and may also include inserts. Thus, a 1 kb 3′ UTR will contain several potential pre-seed sequences. A human specific miRNA that is absent even from the chimp genome should be roughly 6 million years old (last estimated split between human and chimp). Given 0.2 million years required for a 7-mer binding site to evolve, around 30 perfect 7-mer binding sites are expected. For an miRNA that is traced back to mouse (split more than 100 million years ago from human), about 500 conserved targets per miRNA are reasonable. This simplified calculation might indicate that, given a spontaneous mutation rate, there should be a direct correlation between the age of an miRNA and the number of targets it possesses and also to the number of duplicated events of the same miRNA site on one transcript. Eventually, it is not enough for the mutation to occur—it should also be maintained in the population after exhibiting a strong selective pressure towards a favorable regulation which can only take place when an miRNA and its targets are spatially and temporally coexpressed [83, 103]. This calculation allows us to set the general time line of events for miRNA formation. Nevertheless there are many outstanding exceptions of small and large miRNA target repertoires (also see Figure 4).

Bottom Line: MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to be the most abundant mode of posttranscriptional regulation affecting approximately 50% of the transcriptome. miRNA genes are often clustered and/or located in introns, and each targets a variable and often large number of mRNAs.Here we discuss the genomic architecture of animal miRNA genes and their evolving interaction with their target mRNAs.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. nshomron@post.tau.ac.il

ABSTRACT
MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to be the most abundant mode of posttranscriptional regulation affecting approximately 50% of the transcriptome. miRNA genes are often clustered and/or located in introns, and each targets a variable and often large number of mRNAs. Here we discuss the genomic architecture of animal miRNA genes and their evolving interaction with their target mRNAs.

Show MeSH