Abstract
Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels when both were present. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. B. rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and identified a suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus.
Highlights
The Brassica genus comprises vegetable and oil seed crops
In order to investigate the relationship between Long noncoding RNAs (lncRNAs) and epigenetic modifications or the species specificity of lncRNAs, we analyzed in more detail the RNA-seq data of the 14-day first and second leaves without cold treatment
We identified the lncRNAs having perfect sequence identity to genomic regions encoding 24-nt small interfering RNAs (siRNAs). 219 of 1,173 (18.7%) lincRNAs, 74 of 529 (14.0%) natural antisense transcripts (NATs), and 16 of 92 (17.4%) intronic noncoding RNAs (incRNAs) in A01-A10 overlapped with unique-mapped genomic regions encoding 24-nt siRNAs, and more than 80% of the lncRNAs overlapping with genomic regions encoding 24-nt siRNAs were from regions that harbored inverted repeat regions (IRRs) (Fig 2). 24-nt siRNAs were mapped in a similar way to lncRNA and its 5’ and 3’ flanking regions; this mapping pattern is different from those of genic regions or IRRs (Fig 3)
Summary
The Brassica genus comprises vegetable and oil seed crops. The “Triangle of U” proposed the genomic relationship among six major species of the Brassica genus. Each of which contains two complete diploid genomes derived from two different parental species, Brassica juncea L. (BBCC, 2n = 4x = 34) are derived from the natural hybridization of the diploid species, B. rapa L. Some species in the Brassica genus show morphological divergence (termed morphotype). B. rapa includes leafy vegetables such as Chinese cabbage The first whole genome sequence determined in the genus Brassica was that of B. rapa [3]. Whole genome sequences of B. oleracea, B. nigra, B. napus, and B. juncea were determined [4,5,6,7]
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