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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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Related in: MedlinePlus

Genomic organization of miRNA genes and their expression. The number of miRNA genes correlates with chromosome length (a) and the number of protein-coding genes (b). Outliers chromosomes 14, 19, and X are indicated. When removing these three chromosomes the number of miRNA genes aligns well on the regression line (R2 indicated). (c) Proportion of miRNA genes hosted in Introns—Intronic (based on Refseq genes), Clustered on the same genomic strand, or Stand-alone miRNAs. Overlapping intronic and clustered miRNAs are also indicated. Each row refers to 50 kb, 10 kb, and 1 kb distance between paired genes on the same strand. It was shown that clusters of size 3 kb give a large proportion of clusters (27%) with little change when increasing pairwise distance to 10 kb [54]. Diagrams are based on data from Refseq. (d) Human miRNA copy number was plotted against the average miRNA expression level of 40 Human tissues [60]. A similar plot of another dataset [55] gave comparable results (data not shown).
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fig2: Genomic organization of miRNA genes and their expression. The number of miRNA genes correlates with chromosome length (a) and the number of protein-coding genes (b). Outliers chromosomes 14, 19, and X are indicated. When removing these three chromosomes the number of miRNA genes aligns well on the regression line (R2 indicated). (c) Proportion of miRNA genes hosted in Introns—Intronic (based on Refseq genes), Clustered on the same genomic strand, or Stand-alone miRNAs. Overlapping intronic and clustered miRNAs are also indicated. Each row refers to 50 kb, 10 kb, and 1 kb distance between paired genes on the same strand. It was shown that clusters of size 3 kb give a large proportion of clusters (27%) with little change when increasing pairwise distance to 10 kb [54]. Diagrams are based on data from Refseq. (d) Human miRNA copy number was plotted against the average miRNA expression level of 40 Human tissues [60]. A similar plot of another dataset [55] gave comparable results (data not shown).

Mentions: In accordance with genomic duplication events that accompany evolution of species, we see a correlation between the number of miRNA genes and chromosome length. miRNA gene number per chromosome also correlates with the protein-coding gene density (Figure 2(a) and 2(b)). This indicates that integration and/or maintenance of miRNA genes roughly follows protein-coding genes.


An evolutionary perspective of animal microRNAs and their targets.

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

Genomic organization of miRNA genes and their expression. The number of miRNA genes correlates with chromosome length (a) and the number of protein-coding genes (b). Outliers chromosomes 14, 19, and X are indicated. When removing these three chromosomes the number of miRNA genes aligns well on the regression line (R2 indicated). (c) Proportion of miRNA genes hosted in Introns—Intronic (based on Refseq genes), Clustered on the same genomic strand, or Stand-alone miRNAs. Overlapping intronic and clustered miRNAs are also indicated. Each row refers to 50 kb, 10 kb, and 1 kb distance between paired genes on the same strand. It was shown that clusters of size 3 kb give a large proportion of clusters (27%) with little change when increasing pairwise distance to 10 kb [54]. Diagrams are based on data from Refseq. (d) Human miRNA copy number was plotted against the average miRNA expression level of 40 Human tissues [60]. A similar plot of another dataset [55] gave comparable results (data not shown).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Genomic organization of miRNA genes and their expression. The number of miRNA genes correlates with chromosome length (a) and the number of protein-coding genes (b). Outliers chromosomes 14, 19, and X are indicated. When removing these three chromosomes the number of miRNA genes aligns well on the regression line (R2 indicated). (c) Proportion of miRNA genes hosted in Introns—Intronic (based on Refseq genes), Clustered on the same genomic strand, or Stand-alone miRNAs. Overlapping intronic and clustered miRNAs are also indicated. Each row refers to 50 kb, 10 kb, and 1 kb distance between paired genes on the same strand. It was shown that clusters of size 3 kb give a large proportion of clusters (27%) with little change when increasing pairwise distance to 10 kb [54]. Diagrams are based on data from Refseq. (d) Human miRNA copy number was plotted against the average miRNA expression level of 40 Human tissues [60]. A similar plot of another dataset [55] gave comparable results (data not shown).
Mentions: In accordance with genomic duplication events that accompany evolution of species, we see a correlation between the number of miRNA genes and chromosome length. miRNA gene number per chromosome also correlates with the protein-coding gene density (Figure 2(a) and 2(b)). This indicates that integration and/or maintenance of miRNA genes roughly follows protein-coding genes.

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
Related in: MedlinePlus