Epitranscriptomics and Flowering: mRNA Methylation/Demethylation Regulates Flowering Time

Corresponding author: Robert M. Stupar

DNA modifications such as methylation serve as epigenetic markers (表观遗传标记) that influence gene expression and function. The importance of similar modifications in RNA is gaining appreciation, leading to the emergence of epitranscriptomic analyses (表观转录组分析). RNA modifications appear to be a general feature of eukaryotes, and is best understood in mammals, where reversible mRNA methylation is now known to regulate processes ranging from cell fate transition (细胞命运转变) to stress responses (reviewed in Zhao et al., 2017). Methylation of mRNA—and other types of RNA—is also present in plants. In a recent epitranscriptomics study, David et al. (2017) catalogued (记载) over 1000 sites of cytosine methylation (m5C; 胞嘧啶甲基化) in the Arabidopsis thaliana transcriptome. In mammals, N6-methyladenosine (m6A; N6-甲基腺苷) is the most common modification of mRNA (see Figure). The m6A mark is reversible: it can be placed (or ‘written’) by a methylation complex made of several subunits, and ‘erased’ by demethylases. So-called ‘readers’ interpret the marks and transduce them into downstream effects via alterations in RNA splicing, maturation, translation, and degradation.

The first plant homolog of an m6A eraser was recently reported: Arabidopsis ALKBH9B,a homolog of the human m6A demethylase ALKBH5, has m6A demethylase activity and is involved in defense against viral infection (病毒感染) (Martínez-Pérez et al., 2017). Now, Duan et al.(2017) report that another m6A demethylase functions in the regulation of flowering time.

Among five orthologues of human ALKBH5 in Arabidopsis, Duan and coworkers found that ALKBH10B had the most abundant transcripts in flowers and was expressed in most tissues tested. When ALKBH10B was expressed in Nicotiana benthamiana, the purified protein showed m6A demethylation activity that was dependent on the presence two conserved iron(II)-binding residues. Similar to human ALKBH5, ALKBH10B had greater activity with a non-structured RNA (or single stranded RNA) substrate than with a stem-loop structured substrate in vitro.

The authors found that the alkbh10b-1 mutant had higher levels of m6A-modified mRNA in both reproductive and vegetative organs and that overexpression of ALKBH10B in wild type plants decreased m6A levels, establishing that ALKBH10B indeed functions as an RNA demethylase in vivo. The authors further showed that this activity was specific for m6A in mRNA.

Notably, the alkbh10b-1 mutant exhibited late flowering, while the overexpression line flowered early (see Figure). The authors found that ALKBH10B activity enhanced the transcript accumulation of the flowering promoter FT and that FT mRNA had a higher level of m6A in the mutant than in the wild type. The FT-regulators SPL3 and SPL9 also had lower transcript levels and higher m6A levels in the alkbh10b-1 mutant. Further, Duan et al. showed that ALKBH10B directly interacted with FT, SPL3, and SPL9 transcripts. Demethylation decreased the degradation of these transcripts, again similar to its effects on human mRNA.

Finally, Duan et al. examined global ALKBH10B-mediated demethylation, identifying 1276 sites in 1190 genes with greater m6A levels in the mutant compared towild type. Their work thus provides a solid foundation for understanding the roles of m6A-type methylation and demethylation in plants, which appears to share fundamental characteristics with that in mammals. In addition, it is clear that models for the regulation of flowering time must be updated to include post-transcriptional control of multiple transcripts via m6A marks.

最终，Duan et al.揭示了整个ALKBH10B介导的去甲基化作用，并鉴定了1190基因上1276个位点相比于野生型在突变体中具有更高水平的m6A。他们的工作为理解m6A类型的甲基化及去甲基化在植物中的作用奠定了基础，显示其具有与哺乳动物类似的基础特性。另外，显然开花时间的调控应该包括通过对多个转录本进行m6A修饰的转录后调控。

个人简介：1996年，获斯沃斯莫尔学院生物学学士；2005年，获加州大学戴维斯分校细胞生物学与分子生物学博士，论文题目为“Protein Targeting in Chloroplasts”。

个人简历：

Plant Editors联合创始人和主编. (2009-present). Edit manuscripts, grant proposals, and scientific documents in the field of Plant Biology.

The Plant Cell杂志科学编辑. (2008-present). Edit manuscripts with respect to presentation of scientific content, compliance with journal policies, and presentation for a broad readership. Write press releases and In Brief articles highlighting selected papers.

加州大学戴维斯分校博士后研究员. (2005). Continued studies begun as dissertation research on chloroplast protein targeting in Dr. Steven Theg’s laboratory.

费城宾夕法尼亚大学助理研究员. (1996-1998). Research technician in the laboratories of Dr. Stuart Moss and Dr. Gregory Kopf, in the Center for Research on Reproduction and Women’s Health. Studied the expression and localization of hexokinase in mouse sperm cells.

doi: 10.1105/tpc.17.00929

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