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Background: The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for the triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, compare to other plant species, relative fewer phasiRNA biogenesis pathways have been discovered in rice, which limits the comprehensive understanding of the mechanism of phasiRNA biogenesis and the miRNA derived regulatory network.
Results: In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further exploration of the regulatory function of phasiRNAs revealed eleven novel phasiRNAs with 21-nt length targeting forty-one genes, most of which involving in the growth and development of rice. In addition, five novel phasiRNAs with 24-nt length were found targeting the promoter of an OsCKI1 gene and causing higher methylation status in panicle, implying their regulatory function of the transcription of OsCKI1, and subsequently affect the development of rice.
Conclusions: These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.
Keywords
Oryza sativa, phased small interfering RNAs, precursor, degradome sequencing, regulatory network
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This is a list of supplementary files associated with this preprint. Click to download.
- TableS1revised.xlsx
Additional file 1: Table S1. Identification of 21-nt PHAS loci in Rice
- TableS2revised.xlsx
Additional file 2:Table S2. Identification of 24-nt PHAS loci in Rice
- figureS1.pdf
Additional file 3: Figure S1. 21-nt phasiRNAs generated from the novel PHAS lociin wild-type and DCL4 mutant. 21-nt phasiRNAs generated from transcripts of LOC_Os01g57968.1 (A) and LOC_Os05g43650.1 (D) in seedling, LOC_Os02g18750.1 (B), LOC_Os04g25740.1 (C) and LOC_Os06g30680.1(E) in wild-type and osdcl4-1 mutant, respectively. The black arrows indicate the sRNA trigger cleavage sites, the x-axis represent the phasiRNA position mapped within the PHAS loci, the y-axis represent the read abundance (in RMP, reads per million)of the small RNAs mapped to the sense and antisense strands of PHAS loci.
- figureS2.pdf
Additional file 4: Figure S2. 24-nt phasiRNAs generated from the novel PHAS lociin wild-type and DCL3 mutant. 21-nt phasiRNAs generated from transcripts of LOC_Os01g37325.1 (A) in root, LOC_Os02g20200.1 (B), LOC_Os02g55550.1 (C), LOC_Os04g45834.2 (D) and LOC_Os09g14490.1 (E) in wild-type and osdcl3-1 mutant, respectively. The black arrows indicate the sRNA trigger cleavage sites, the x-axis represent the phasiRNA position mapped within the PHAS loci, the y-axis represent the read abundance (in RMP, reads per million)of the small RNAs mapped to the sense and antisense strands of PHAS loci.
- figureS3.pdf
Additional file 5: Figure S3.Degradome sequencing-based validation of the phasiRNA-target interactions. Four libraries of degradome sequencing data libraries (GSM434596, GSM455938, GSM455939 and GSM476257) were recruited for T-plot profiling. The IDs of the target transcripts and the corresponding phasiRNAs generated from the transcripts of LOC_Os02g18750.1, LOC_Os05g43650.1, LOC_Os06g30680.1 and LOC_Os12g42380.1 are listed on the top. The y axis measure the normalized reads (in RMP, reads per million) of the degradome signals, and the x axis represent the position of the cleavage signals on the target transcripts. The binding sites of the phasiRNA on their target transcripts were denoted by gray horizontal lines, and the dominant cleavage signals were marked by black arrows.
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See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 3
Posted 05 Jan, 2021
No community comments so far
Editorial decision: Minor revision
On 17 Jan, 2021
Review #2 received
Received 10 Jan, 2021
Reviewer #2 agreed
On 21 Dec, 2020
Editor assigned
On 20 Dec, 2020
Reviewers invited
Invitations sent on 20 Dec, 2020
Reviewer #1 agreed
On 20 Dec, 2020
Review #1 received
Received 20 Dec, 2020
Submission checks complete
On 20 Dec, 2020
Editor invited
On 20 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 02 Dec, 2020
Review #2 received
Received 19 Nov, 2020
Review #1 received
Received 19 Nov, 2020
Reviewer #2 agreed
On 01 Nov, 2020
Editor assigned
On 01 Nov, 2020
Reviewers invited
Invitations sent on 01 Nov, 2020
Reviewer #1 agreed
On 01 Nov, 2020
Submission checks complete
On 01 Nov, 2020
Editor invited
On 01 Nov, 2020
No comments provided
Editorial decision: Major revision
On 02 Oct, 2020
Review #1 received
Received 05 Sep, 2020
Review #2 received
Received 05 Sep, 2020
Reviewers invited
Invitations sent on 19 Aug, 2020
Reviewer #1 agreed
On 19 Aug, 2020
Reviewer #2 agreed
On 19 Aug, 2020
Editor assigned
On 04 Aug, 2020
Submission checks complete
On 03 Aug, 2020
Editor invited
On 03 Aug, 2020
First submitted
On 31 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for the triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, compare to other plant species, relative fewer phasiRNA biogenesis pathways have been discovered in rice, which limits the comprehensive understanding of the mechanism of phasiRNA biogenesis and the miRNA derived regulatory network.
Results: In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further exploration of the regulatory function of phasiRNAs revealed eleven novel phasiRNAs with 21-nt length targeting forty-one genes, most of which involving in the growth and development of rice. In addition, five novel phasiRNAs with 24-nt length were found targeting the promoter of an OsCKI1 gene and causing higher methylation status in panicle, implying their regulatory function of the transcription of OsCKI1, and subsequently affect the development of rice.
Conclusions: These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
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