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Small RNA expression and strain specificity in the rat.

Linsen SE, de Wit E, de Bruijn E, Cuppen E - BMC Genomics (2010)

Bottom Line: We confirmed the expression of 588 known miRNAs (54 in antisense orientation) and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs.Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome.Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.

View Article: PubMed Central - HTML - PubMed

Affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Cancer Genomics Center, Utrecht, The Netherlands.

ABSTRACT

Background: Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs.

Results: We confirmed the expression of 588 known miRNAs (54 in antisense orientation) and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters.

Conclusions: Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.

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miRNA tissue expression profiles. A-C) Heatmaps show the expression (normalized, log10) of miRNAs. Each arm is represented separately, as are miRNAs in the reverse orientation (if applicable). In (A), the first 10% of the heatmap is shown. miRNAs derived from loci that are homologous to miRBase human or mouse miRNA loci are shown in (B). Completely novel miRNAs are shown in (C). The legend is valid for the 3 heatmaps. D) Each tissue expresses a distinct set of miRNAs (tissue specific miRNAs). Also, some miRNAs are specifically not expressed in certain tissues (tissue avoidant miRNAs). miRNAs are specific in both replicates and the arbitrary, but strict, cutoff of 5-fold difference in expression was applied to determine specificity and avoidance.
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Figure 1: miRNA tissue expression profiles. A-C) Heatmaps show the expression (normalized, log10) of miRNAs. Each arm is represented separately, as are miRNAs in the reverse orientation (if applicable). In (A), the first 10% of the heatmap is shown. miRNAs derived from loci that are homologous to miRBase human or mouse miRNA loci are shown in (B). Completely novel miRNAs are shown in (C). The legend is valid for the 3 heatmaps. D) Each tissue expresses a distinct set of miRNAs (tissue specific miRNAs). Also, some miRNAs are specifically not expressed in certain tissues (tissue avoidant miRNAs). miRNAs are specific in both replicates and the arbitrary, but strict, cutoff of 5-fold difference in expression was applied to determine specificity and avoidance.

Mentions: miRNAs may act redundantly [42] or in concert [43,44]. In order to understand the function of miRNAs in specific tissues, it may therefore be helpful to identify global miRNA profiles. To be able to compare miRNA profiles, we normalized the miRNA reads per tissue and determined the relative expression of miRNAs among the six tissues. Comparisons between strains showed highly similar expression profiles, with the Spearman's ρ ranging from 0.88 (testis) to 0.95 (brain). The ρ among different tissue profiles was considerably lower, as expected [45], ranging from 0.62 (brain vs. Testis) to 0.87 (e.g. liver vs. spleen) (Additional file 8, Figure S2). We determined the number of reads that covered individual known miRNAs (Figure 1A, B, C and Additional file 9, Figure S3) and observed that 38% of the known miRNAs are ubiquitously expressed among all tissues that were assayed, whereas only 14% of the homologous and 2% of the novel miRNAs were identified in all examined tissues.


Small RNA expression and strain specificity in the rat.

Linsen SE, de Wit E, de Bruijn E, Cuppen E - BMC Genomics (2010)

miRNA tissue expression profiles. A-C) Heatmaps show the expression (normalized, log10) of miRNAs. Each arm is represented separately, as are miRNAs in the reverse orientation (if applicable). In (A), the first 10% of the heatmap is shown. miRNAs derived from loci that are homologous to miRBase human or mouse miRNA loci are shown in (B). Completely novel miRNAs are shown in (C). The legend is valid for the 3 heatmaps. D) Each tissue expresses a distinct set of miRNAs (tissue specific miRNAs). Also, some miRNAs are specifically not expressed in certain tissues (tissue avoidant miRNAs). miRNAs are specific in both replicates and the arbitrary, but strict, cutoff of 5-fold difference in expression was applied to determine specificity and avoidance.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864251&req=5

Figure 1: miRNA tissue expression profiles. A-C) Heatmaps show the expression (normalized, log10) of miRNAs. Each arm is represented separately, as are miRNAs in the reverse orientation (if applicable). In (A), the first 10% of the heatmap is shown. miRNAs derived from loci that are homologous to miRBase human or mouse miRNA loci are shown in (B). Completely novel miRNAs are shown in (C). The legend is valid for the 3 heatmaps. D) Each tissue expresses a distinct set of miRNAs (tissue specific miRNAs). Also, some miRNAs are specifically not expressed in certain tissues (tissue avoidant miRNAs). miRNAs are specific in both replicates and the arbitrary, but strict, cutoff of 5-fold difference in expression was applied to determine specificity and avoidance.
Mentions: miRNAs may act redundantly [42] or in concert [43,44]. In order to understand the function of miRNAs in specific tissues, it may therefore be helpful to identify global miRNA profiles. To be able to compare miRNA profiles, we normalized the miRNA reads per tissue and determined the relative expression of miRNAs among the six tissues. Comparisons between strains showed highly similar expression profiles, with the Spearman's ρ ranging from 0.88 (testis) to 0.95 (brain). The ρ among different tissue profiles was considerably lower, as expected [45], ranging from 0.62 (brain vs. Testis) to 0.87 (e.g. liver vs. spleen) (Additional file 8, Figure S2). We determined the number of reads that covered individual known miRNAs (Figure 1A, B, C and Additional file 9, Figure S3) and observed that 38% of the known miRNAs are ubiquitously expressed among all tissues that were assayed, whereas only 14% of the homologous and 2% of the novel miRNAs were identified in all examined tissues.

Bottom Line: We confirmed the expression of 588 known miRNAs (54 in antisense orientation) and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs.Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome.Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.

View Article: PubMed Central - HTML - PubMed

Affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Cancer Genomics Center, Utrecht, The Netherlands.

ABSTRACT

Background: Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs.

Results: We confirmed the expression of 588 known miRNAs (54 in antisense orientation) and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters.

Conclusions: Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.

Show MeSH
Related in: MedlinePlus