Preprint Concept Paper Version 1 This version is not peer-reviewed

Cooperation of Alternative Splicing and microRNA Targeting in the Gene Regulation Network of Arabidopsis thaliana

Version 1 : Received: 13 April 2020 / Approved: 16 April 2020 / Online: 16 April 2020 (07:37:32 CEST)

How to cite: Li, Y.; Feng, H. Cooperation of Alternative Splicing and microRNA Targeting in the Gene Regulation Network of Arabidopsis thaliana. Preprints 2020, 2020040259 (doi: 10.20944/preprints202004.0259.v1). Li, Y.; Feng, H. Cooperation of Alternative Splicing and microRNA Targeting in the Gene Regulation Network of Arabidopsis thaliana. Preprints 2020, 2020040259 (doi: 10.20944/preprints202004.0259.v1).

Abstract

MicroRNA (miRNA) is a typical class of small RNAs that could modulate gene expression in trans at the post-transcriptional level. miRNAs bind to the miRNA binding sites (MBSs) in target mRNAs by sequence complementarity. Alternative splicing (AS) is another commonly occurred process in pre-mRNAs that changes the isoforms of a gene. It is hypothesized that there should be an interaction for gene regulation that involves both AS and miRNA targeting. Studies have verified this hypothesis in the model organism Arabidopsis thaliana. High-throughput sequencing data suggested that in Arabidopsis a considerably large fraction of MBSs are affected by AS events. The overlapping between MBS and AS exceeds the randomly simulated number. Functional experiments have indicated that the AS events are required for the gene expression changes of miRNA targets. Therefore, AS and MBS are mutually favored. The observed expression changes caused by miRNAs could also be contributed by AS events. In the present perspective article, we propose that the AS analysis should be incorporated in the differential-expression analysis of miRNA studies. When defining a differentially-expressed gene, it should be clarified whether the change in gene expression is caused by AS events or solely by miRNA targeting.

Subject Areas

alternative splicing; microRNA; gene expression; Arabidopsis

Comments (3)

Comment 1
Received: 16 April 2020
Commenter: Hongwei Guo
The commenter has declared there is no conflict of interests.
Comment: Why not directly quantify the amount of each transcript?
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Response 1 to Comment 1
Received: 17 April 2020
Commenter: Huizhi
The commenter has declared there is no conflict of interests.
Comment: Many transcripts share common exons. It is difficult to quantify the amount of each transcript from the reads. The estimation is usually not accurate.
Comment 2
Received: 19 April 2020
Commenter: Can Xie
The commenter has declared there is no conflict of interests.
Comment: The previous commenter is reasonable. Some software could quantify the amount of each transcript using the unique exons of each transcript.
The author's response is also reasonable. It is only possible to estimate the amount of some transcripts if they have many overlapping regions.
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