Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.
Plant Biology Graduate Field, Cornell University, Ithaca, NY 14853, USA.
Plant Cell. 2023 May 29;35(6):1762-1786. doi: 10.1093/plcell/koad027.
Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.
长非编码 RNA（lncRNA）是真核基因组中一大类多样化的基因，参与多种调控过程。功能表征的 lncRNA 在植物中发挥着关键作用，从调节开花到控制侧根形成。然而，过去十年的研究结果表明，植物转录组中存在数千种 lncRNA，而对它们的鉴定远远落后于其功能表征。在这种情况下，区分功能和噪声是具有挑战性的。然而，植物界一直在 lncRNA 生物学的发现前沿，提供了许多功能和机制上的见解，增加了我们对这一类基因的理解。在这篇综述中，我们考察了过去二十五年中植物 lncRNA 生物学的关键发现和见解。我们描述了在基因组学时代之前的发现如何为随后几十年识别和功能表征 lncRNA 提供信息。我们概述了已鉴定的植物 lncRNA 所适合的功能原型，并推测了可能揭示更多原型的新研究途径。最后，本文讨论了该领域面临的挑战以及一些令人兴奋的新的分子和计算方法，这些方法可能有助于 lncRNA 的比较和功能分析。
