A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data
- 382 Downloads
The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional “omics” (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts. Here, we used the model plant Arabidopsis thaliana to improve the ability to identify candidate promoter locations in intergenic miRNAs and to determine rules for identifying primary transcription start sites of miRNAs by integrating high-throughput omics data, such as the DNase I hypersensitive sites, chromatin immunoprecipitation-sequencing of polymerase II and H3K4me3, as well as high throughput transcriptomic data. As a result, 93% of refined primary transcripts could be confirmed by the primer pairs from a previous study. Cis-element and secondary structure analyses also supported the feasibility of our results. This work will contribute to the primary transcriptional regulatory analysis of miRNAs, and the conserved regulatory pattern may be a suitable miRNA characteristic in other plant species.
KeywordsPrimary transcription start site Epigenomics Intergenic miRNA Arabidopsis Cis-element
This work was supported by grants from the National Natural Science Foundation of China (31371291).
Conflict of interest
The authors declare that they have no conflict of interest.
- Akpinar BA, Kantar M, Budak H (2015) Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress Functional & integrative genomics 15:587–598 doi: 10.1007/s10142-015-0453-0
- Brion P, Westhof E (1997) Hierarchy and dynamics of RNA folding Annual review of biophysics and biomolecular structure 26:113–137 doi: 10.1146/annurev.biophys.26.1.113
- Duncan CD, Weeks KM (2010) Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding Biochemistry 49:5418–5425 doi: 10.1021/bi100267g
- Mejia-Guerra MK, Li W, Galeano NF, Vidal M, Gray J, Doseff AI, Grotewold E (2015) Core promoter plasticity between maize tissues and genotypes contrasts with predominance of sharp transcription initiation sites. Plant Cell 27:3309–3320. doi: 10.1105/tpc.15.00630 CrossRefPubMedPubMedCentralGoogle Scholar
- Ng DW, Zhang C, Miller M, Palmer G, Whiteley M, Tholl D, Chen ZJ (2011) Cis- and trans-Regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids. Plant Cell 23:1729–1740. doi: 10.1105/tpc.111.083915 CrossRefPubMedPubMedCentralGoogle Scholar
- Shiraki T et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage Proceedings of the National Academy of Sciences of the United States of America 100:15776–15781 doi: 10.1073/pnas.2136655100
- Sims RJ, 3rd, Mandal SS, Reinberg D (2004) Recent highlights of RNA-polymerase-II-mediated transcription Current opinion in cell biology 16:263–271 doi: 10.1016/j.ceb.2004.04.004
- Wang H, Chung PJ, Liu J, Jang IC, Kean MJ, Xu J, Chua NH (2014) Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis Genome research 24:444–453 doi: 10.1101/gr.165555.113
- LYi X, Zhang Z, Ling Y, Xu W, Su Z (2015) PNRD: a plant non-coding RNA database Nucleic acids research 43:D982–989 doi: 10.1093/nar/gku1162
- Zhang S, Liu Y, Yu B (2015) New insights into pri-miRNA processing and accumulation in plants Wiley Interdisciplinary Reviews: RNA 6:533–545 doi: 10.1002/wrna.1292