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Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis.

Luo QJ, Samanta MP, Köksal F, Janda J, Galbraith DW, Richardson CR, Ou-Yang F, Rock CD - PLoS Genet. (2009)

Bottom Line: Antisense smRNAs were also found associated with MIRNA genes.Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants.Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA.

ABSTRACT
Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA cleavage site. Antisense smRNAs were also found associated with MIRNA genes. This suggests that miRNA-associated "transitivity" (production of small interfering RNAs through antisense transcription) is more common than previously reported. High-resolution (3 nt) custom tiling microarray transcriptome analysis was performed with probes 400 bp 5' upstream and 3' downstream of the miRNA cleavage sites (direction relative to the mRNA) for 22 select miRNA target genes. We hybridized RNAs labeled from the smRNA pathway mutants, including hen1-1, dcl1-7, hyl1-2, rdr6-15, and sgs3-14. Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants. This was corroborated by semi-quantitative reverse transcription PCR; however, a direct correlation of antisense transcript abundance in MIR164 gene knockouts was not observed. Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation. HEN1 and SGS3 may be links for miRNA target entry into different RNA processing pathways.

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Normalized delta signals for antisense transcripts of selected validated miRNA targets showing differences between rdr6-15 versus wild type Col-0.Refer to Figure 2 for details of legend.
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pgen-1000457-g006: Normalized delta signals for antisense transcripts of selected validated miRNA targets showing differences between rdr6-15 versus wild type Col-0.Refer to Figure 2 for details of legend.

Mentions: (A) APS1/AT3G22890; (B) MYB12/AT2G47460; (C) SCR6(IV)/AT4G00150; (D) TOE2/AT5G60120; (E) AP2/AT4G36920; (F) GRF8/AT4G24150. Each data point is the average signal of at least 3 technical samples and is represented by the difference between the signals from hen1-1 versus Ler-0 divided by that from Ler-0 [normalized “delta” Δ signal, (mutant signal-wild type signal)/wild type signal]. The normalized delta signal is plotted as a function of probe position relative to the miRNA cleavage site (coordinate 0 on x-axis). Black arrow pinpoints the signals in the plot which were identified by probe sets containing at least 3 contiguous probes showing at least 20% differences (up or down, not both) for the normalized delta signals. The precise same region with changed signals, if any, is indicated by black arrows for other smRNA mutants in Figures 3–6.


Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis.

Luo QJ, Samanta MP, Köksal F, Janda J, Galbraith DW, Richardson CR, Ou-Yang F, Rock CD - PLoS Genet. (2009)

Normalized delta signals for antisense transcripts of selected validated miRNA targets showing differences between rdr6-15 versus wild type Col-0.Refer to Figure 2 for details of legend.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2664332&req=5

pgen-1000457-g006: Normalized delta signals for antisense transcripts of selected validated miRNA targets showing differences between rdr6-15 versus wild type Col-0.Refer to Figure 2 for details of legend.
Mentions: (A) APS1/AT3G22890; (B) MYB12/AT2G47460; (C) SCR6(IV)/AT4G00150; (D) TOE2/AT5G60120; (E) AP2/AT4G36920; (F) GRF8/AT4G24150. Each data point is the average signal of at least 3 technical samples and is represented by the difference between the signals from hen1-1 versus Ler-0 divided by that from Ler-0 [normalized “delta” Δ signal, (mutant signal-wild type signal)/wild type signal]. The normalized delta signal is plotted as a function of probe position relative to the miRNA cleavage site (coordinate 0 on x-axis). Black arrow pinpoints the signals in the plot which were identified by probe sets containing at least 3 contiguous probes showing at least 20% differences (up or down, not both) for the normalized delta signals. The precise same region with changed signals, if any, is indicated by black arrows for other smRNA mutants in Figures 3–6.

Bottom Line: Antisense smRNAs were also found associated with MIRNA genes.Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants.Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA.

ABSTRACT
Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA cleavage site. Antisense smRNAs were also found associated with MIRNA genes. This suggests that miRNA-associated "transitivity" (production of small interfering RNAs through antisense transcription) is more common than previously reported. High-resolution (3 nt) custom tiling microarray transcriptome analysis was performed with probes 400 bp 5' upstream and 3' downstream of the miRNA cleavage sites (direction relative to the mRNA) for 22 select miRNA target genes. We hybridized RNAs labeled from the smRNA pathway mutants, including hen1-1, dcl1-7, hyl1-2, rdr6-15, and sgs3-14. Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants. This was corroborated by semi-quantitative reverse transcription PCR; however, a direct correlation of antisense transcript abundance in MIR164 gene knockouts was not observed. Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation. HEN1 and SGS3 may be links for miRNA target entry into different RNA processing pathways.

Show MeSH