综合分析与杨树木质部发育相关的 lncRNA-mRNA 调控网络。

Comprehensive analysis of lncRNA-mRNA regulatory network in Populus associated with xylem development.

机构信息

State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.

The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.

出版信息

J Plant Physiol. 2023 Aug;287:154055. doi: 10.1016/j.jplph.2023.154055. Epub 2023 Jul 18.

DOI:10.1016/j.jplph.2023.154055

PMID:37506405

Abstract

Long noncoding RNAs (lncRNAs) play essential roles in numerous biological processes in plants, such as regulating the gene expression. However, only a few studies have looked into their potential functions in xylem development. High-throughput sequencing of P. euramericana 'Zhonglin46' developing and mature xylem was performed in this study. Through sequencing analysis, 14,028 putative lncRNA transcripts were identified, including 4525 differentially expressed lncRNAs (DELs). Additional research revealed that in mature xylem, a total of 2320 DELs were upregulated and 2205 were downregulated compared to developing xylem. Meanwhile, there were a total of 8122 differentially expressed mRNAs (DEMs) that were upregulated and 16,424 that were downregulated in mature xylem compared with developing xylem. The cis- and trans-target genes of DELs were analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, which indicated that these DELs participate in controlling the phenylpropanoid and lignin biosynthesis pathway as well as the starch and sucrose metabolism pathway. Among the cis-regulated DELs, LNC_006291, LNC_006292, and LNC_006532 all participate in regulating multiple HCT gene family membranes. As targets, POPTR_001G045900v3 (CCR2) and POPTR_018G063500v3 (SUS) both have only one cis-regulatory lncRNA, referred to as LNC_000057 and LNC_006212, respectively. Moreover, LNC_004484 and two DELs named LNC_008014 and LNC_010781 were revealed to be important nodes in the co-expression network of trans-lncRNAs and mRNAs associated to the lignin biosynthesis pathway and cellulose and xylan biosynthetic pathways, respectively. Finally, quantitative real-time PCR (qRT-PCR) was used to confirme 34 pairs of lncRNA-mRNA. Taken together, these findings may help to clarify the regulatory role that lncRNAs play in xylem development and wood formation.

摘要

长链非编码 RNA（lncRNA）在植物的许多生物学过程中发挥着重要作用，例如调节基因表达。然而，只有少数研究探讨了它们在木质部发育中的潜在功能。本研究对欧洲山杨‘中林 46’发育和成熟木质部进行了高通量测序。通过测序分析，鉴定出 14028 个潜在的 lncRNA 转录本，包括 4525 个差异表达的 lncRNA（DEL）。进一步研究表明，在成熟木质部中，与发育中的木质部相比，共有 2320 个 DEL 上调，2205 个 DEL 下调。同时，与发育中的木质部相比，成熟木质部中共有 8122 个差异表达的 mRNAs（DEMs）上调，16424 个 DEMs 下调。对 DEL 的顺式和反式靶基因进行了基因本体（GO）和京都基因与基因组百科全书（KEGG）通路富集分析，表明这些 DEL 参与了苯丙烷和木质素生物合成途径以及淀粉和蔗糖代谢途径的调控。在顺式调控的 DEL 中，LNC_006291、LNC_006292 和 LNC_006532 都参与了多个 HCT 基因家族膜的调控。作为靶基因，POPTR_001G045900v3（CCR2）和 POPTR_018G063500v3（SUS）都只有一个顺式调控 lncRNA，分别称为 LNC_000057 和 LNC_006212。此外，LNC_004484 和两个名为 LNC_008014 和 LNC_010781 的 DEL 被揭示为与木质素生物合成途径和纤维素及木聚糖生物合成途径相关的转 lncRNA 和 mRNAs 的共表达网络中的重要节点。最后，采用实时荧光定量 PCR（qRT-PCR）对 34 对 lncRNA-mRNA 进行了验证。综上所述，这些发现可能有助于阐明 lncRNA 在木质部发育和木材形成中的调控作用。