Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration

第一作者：Yu-Chan Zhang

第一单位：中山大学

第一通讯：Yue-Qin Chen

 Abstarct 

背景回顾：Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration. Global chromatin remodeling is required for this cell fate transition, but how the process is regulated is not fully understood. Chromatin-enriched noncoding RNAs (cheRNAs) are thought to play important roles in maintaining chromatin state. 

植物能够形成一个具有多能性的细胞团，即愈伤组织，该类细胞具有组织再生的能力。这种细胞命运的转变需要全基因组范围上的染色质重塑，但是该过程是如何被调控的尚不清楚。染色质富集的非编码RNAs，即cheRNAs被认为在维持染色质状态过程中发挥重要作用。

提出问题：However, whether cheRNAs participate in somatic cell regeneration in plants has not yet been clarified. 

但是，cheRNAs是否参与到植物的体细胞再生过程尚存悬念。

主要研究：To uncover the characteristics and functions of cheRNAs during somatic cell reprogramming in plants, we systematically investigate cheRNAs during callus induction, proliferation and regeneration in rice. 

为了揭示cheRNAs在植物体细胞重编程中的特征和功能，作者系统地研究了cheRNAs在水稻愈伤诱导、增殖和再生过程中的作用。

结果1-总体鉴定：We identify 2284 cheRNAs, most of which are novel long non-coding RNAs or small nucleolar RNAs. These cheRNAs, which are highly conserved across plant species, shuttle between chromatin and the nucleoplasm during somatic cell regeneration.

作者一共鉴定到了2284个cheRNAs，其中大多数是新的长链非编码RNAs或者小分子核仁RNAs。这些cheRNAs在不同植物物种之间十分保守，在植物体细胞再生过程中在染色质与核质之间穿梭。

结果2-cheRNAs的功能鉴定：They positively regulate the expression of neighboring genes via specific RNA motifs, which may interact with DNA motifs around cheRNA loci. Large-scale mutant analysis shows that cheRNAs are associated with plant size and seed morphology. 

这些cheRNAs通过特异性的RNA基序，正向调控邻近基因的表达，可能会与cheRNA位点附近的DNA基序互作。大范围的突变分析显示cheRNAs主要与植物的大小和种子的形态有关。

结果3-两个che-lncRNAs的功能鉴定：Further detailed functional investigation of two che-lncRNAs demonstrates that their loss of function impairs cell dedifferentiation and plant regeneration, highlighting the functions of cheRNAs in regulating the expression of neighboring genes via specific motifs. 

进一步对两个che-lncRNAs的功能验证显示，这些che-lncRNAs的功能缺失会导致细胞分化和植物再生出现缺陷，表明cheRNAs能够通过特异的基序调控邻近基因的表达这一功能。

结论：These findings support cis-regulatory roles of cheRNAs in influencing a variety of rice traits. cheRNAs are a distinct subclass of regulatory non-coding RNAs that are required for somatic cell regeneration and regulate rice traits. Targeting cheRNAs has great potential for crop trait improvement and breeding in future.

这些发现显示cheRNAs作用于水稻多种性状的顺式调控作用。cheRNAs是调控非编码RNAs的一个独特亚类，是水稻体细胞再生所必需的，此外还调控水稻的多种性状。cheRNAs是未来作物性状改良和育种的潜在靶标。

doi: https://doi.org/10.1186/s13059-022-02608-y

Journal: Genome Biology

Published date: January 19, 2022