Abstract
Long noncoding RNAs (lncRNAs) are essential regulators of gene expression in eukaryotes. Despite increasing knowledge on the function of lncRNAs, little is known about their effects on crop yield. Here, we identify a lncRNA transcribed from the antisense strand of neighbouring gene LRK (leucine-rich repeat receptor kinase) cluster named LAIR (LRK Antisense Intergenic RNA). LAIR overexpression increases rice grain yield and upregulates the expression of several LRK genes. Additionally, chromatin immunoprecipitation assay results indicate H3K4me3 and H4K16ac are significantly enriched at the activated LRK1 genomic region. LAIR binds histone modification proteins OsMOF and OsWDR5 in rice cells, which are enriched in LRK1 gene region. Moreover, LAIR is demonstrated to bind 5′ and 3′ untranslated regions of LRK1 gene. Overall, this study reveals the role of lncRNA LAIR in regulating rice grain yield and lncRNAs may be useful targets for crop breeding.
Highlights
Long noncoding RNAs are essential regulators of gene expression in eukaryotes
The LRK1 gene was located in the first intron of LAIR, and there was no overlap between the two antisense transcripts (Fig. 1a)
The LAIR sequence is encoded in the antisense strand of the 5′ terminal region of the leucine-rich repeat receptor kinase (LRK) gene cluster
Summary
Long noncoding RNAs (lncRNAs) are essential regulators of gene expression in eukaryotes. This study reveals the role of lncRNA LAIR in regulating rice grain yield and lncRNAs may be useful targets for crop breeding. Long noncoding RNAs (lncRNAs), which lack any obvious open reading frames (ORFs)[5,6,7], function as key regulators of diverse mechanisms in a range of biological processes[6,8,9] They may regulate the expression of neighbouring genes with cis-acting (close to the transcription site) or transacting (multiple loci throughout the genome) mechanisms[10]. ChIRP assays reveal that LAIR binds 5′ and 3′ UTR genomic regions of the LRK1 gene These results imply that LAIR overexpression increases rice yield and regulates the expression of neighbouring LRK gene cluster
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