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Review
. 2018 Dec 17:7:F1000 Faculty Rev-1940.
doi: 10.12688/f1000research.16203.1. eCollection 2018.

Beyond transcription factors: roles of mRNA decay in regulating gene expression in plants

Leslie E Sieburth  1 , Jessica N Vincent  1
Affiliations
Review

Beyond transcription factors: roles of mRNA decay in regulating gene expression in plants

Leslie E Sieburth et al. F1000Res. .

Abstract

Gene expression is typically quantified as RNA abundance, which is influenced by both synthesis (transcription) and decay. Cytoplasmic decay typically initiates by deadenylation, after which decay can occur through any of three cytoplasmic decay pathways. Recent advances reveal several mechanisms by which RNA decay is regulated to control RNA abundance. mRNA can be post-transcriptionally modified, either indirectly through secondary structure or through direct modifications to the transcript itself, sometimes resulting in subsequent changes in mRNA decay rates. mRNA abundances can also be modified by tapping into pathways normally used for RNA quality control. Regulated mRNA decay can also come about through post-translational modification of decapping complex subunits. Likewise, mRNAs can undergo changes in subcellular localization (for example, the deposition of specific mRNAs into processing bodies, or P-bodies, where stabilization and destabilization occur in a transcript- and context-dependent manner). Additionally, specialized functions of mRNA decay pathways were implicated in a genome-wide mRNA decay analysis in Arabidopsis. Advances made using plants are emphasized in this review, but relevant studies from other model systems that highlight RNA decay mechanisms that may also be conserved in plants are discussed.

Keywords: DIS3L2; P-bodies; SOV; VCS; decapping; gene expression; mRNA decay.

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Conflict of interest statement

No competing interests were disclosed.No competing interests were disclosed.No competing interests were disclosed.No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Schematic of the major cytoplasmic mRNA decay pathways.
Mature mRNAs are first deadenylated by removal of the poly(A) tail. Deadenylated transcripts can be degraded in either the 3′→5′ or 5′→3′ direction. 3′→5′ degradation can occur by activity of the RNA exosome or by SUPPRESSOR OF VARICOSE (SOV). For degradation to occur in the 5′→3′ direction, transcripts must first be stripped of their 5′ m 7G cap by the RNA decapping complex, and further decay occurs by XRN4. VCS, VARICOSE.
Figure 2.
Figure 2.. Loss of SUPPRESSOR OF VARICOSE (SOV) induces RNA decay feedback in Arabidopsis.
( A) Heat map depicts RNA decay rates, relative to the wild type, and histogram indicates the degree to which each pattern was represented. Bar with two asterisks indicates RNAs with VARICOSE (VCS)-dependent faster decay rates in sov mutants. ( B) Diagram of VCS and SOV decay in wild type. Yellow circles represent the 5′ m 7G cap, blue RNAs decay by mRNA decapping, orange RNAs by SOV, and blue-orange gradient colored RNAs are substrates of both pathways. ( C) In sov mutants, some RNAs that are normally substrates of SOV instead decay by mRNA decapping, and they decay faster. ( D) In sov mutants, faster-decay RNAs maintain a normal abundance, indicating transcriptional feedback, which is also called RNA buffering.
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This work was supported by National Science Foundation grant MCB-1616779 to LES.

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