Evidence for antisense transcription associated with microRNA target mRNAs in arabidopsis

Qing Jun Luo, Manoj P. Samanta, Fatih Köksal, Jaroslav Janda, David W Galbraith, Casey R. Richardson, Fangqian Ou-Yang, Christopher D. Rock

Research output: Contribution to journalArticle

25 Citations (Scopus)

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.

Original languageEnglish (US)
JournalPLoS Genetics
Volume5
Issue number4
DOIs
StatePublished - Apr 2009

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MicroRNAs
microRNA
Arabidopsis
RNA
transcription (genetics)
Messenger RNA
gene
cleavage
transcriptomics
Genes
genes
genome
probe
High-Throughput Nucleotide Sequencing
mutants
Gene Knockout Techniques
Gene Expression Profiling
gene targeting
Microarray Analysis
small interfering RNA

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Evidence for antisense transcription associated with microRNA target mRNAs in arabidopsis. / Luo, Qing Jun; Samanta, Manoj P.; Köksal, Fatih; Janda, Jaroslav; Galbraith, David W; Richardson, Casey R.; Ou-Yang, Fangqian; Rock, Christopher D.

In: PLoS Genetics, Vol. 5, No. 4, 04.2009.

Research output: Contribution to journalArticle

Luo, QJ, Samanta, MP, Köksal, F, Janda, J, Galbraith, DW, Richardson, CR, Ou-Yang, F & Rock, CD 2009, 'Evidence for antisense transcription associated with microRNA target mRNAs in arabidopsis', PLoS Genetics, vol. 5, no. 4. https://doi.org/10.1371/journal.pgen.1000457
Luo, Qing Jun ; Samanta, Manoj P. ; Köksal, Fatih ; Janda, Jaroslav ; Galbraith, David W ; Richardson, Casey R. ; Ou-Yang, Fangqian ; Rock, Christopher D. / Evidence for antisense transcription associated with microRNA target mRNAs in arabidopsis. In: PLoS Genetics. 2009 ; Vol. 5, No. 4.
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