In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue

Yanxiao Jia, Chao Qin, Milton Brian Traw, Xiaonan Chen, Ying He, Jing Kai, Sihai Yang, Long Wang, Laurence D. Hurst

Research output: Contribution to journalArticlepeer-review

2 Citations (SciVal)

Abstract

The introduction of frameshifting non-3n indels enables the identification of gene-trait associations. However, it has been hypothesised that recovery of the original reading frame owing to usage of non-canonical splice forms could cause rescue. To date there is very little evidence for organism-level rescue by such a mechanism and it is unknown how commonly indels induce, or are otherwise associated with, frame-restoring splice forms. We perform CRISPR/Cas9 editing of randomly selected loci in rice to investigate these issues. We find that the majority of loci have a frame-restoring isoform. Importantly, three quarters of these isoforms are not seen in the absence of the indels, consistent with indels commonly inducing novel isoforms. This is supported by analysis in the context of NMD knockdowns. We consider in detail the two top rescue candidates, in wax deficient anther 1 (wda1) and brittle culm (bc10), finding that organismal-level rescue in both cases is strong but owing to different splice modification routes. More generally, however, as frame-restoring isoforms are low abundance and possibly too disruptive, such rescue we suggest to be the rare exception, not the rule. Nonetheless, assuming that indels commonly induce frame-restoring isoforms, these results emphasize the need to examine RNA level effects of non-3n indels and suggest that multiple non-3n indels in any given gene are advisable to probe a gene’s trait associations.

Original languageEnglish
Article numbere1010071
JournalPlos Genetics
Volume18
Issue number2
DOIs
Publication statusPublished - 18 Feb 2022

Bibliographical note

Funding Information:
National Natural Science Foundation of China (Grant NO. 31900203, 31970236 and 31671322) to SY (http://www.nsfc.gov.cn/english/ site_1/index.html). European Research Council Grant EvoGenMed ERC-2014-ADG 669207 to LDH (https://erc.europa.eu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Funding

National Natural Science Foundation of China (Grant NO. 31900203, 31970236 and 31671322) to SY (http://www.nsfc.gov.cn/english/ site_1/index.html). European Research Council Grant EvoGenMed ERC-2014-ADG 669207 to LDH (https://erc.europa.eu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

ASJC Scopus subject areas

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

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