Transcriptional Association between mRNAs and Their Paired Natural Antisense Transcripts Following Fusarium oxysporum Inoculation in Brassica rapa L.

Mst Arjina Akter,Takeshi Takasaki-Yasuda,Motoaki Seki,Satoshi Takahashi,Kenji Osabe,Ryo Fujimoto,Elizabeth S Dennis,Naomi Miyaji,Hasan Mehraj

doi:10.3390/horticulturae8010017

Abstract

Long noncoding RNAs (lncRNAs) play important roles in abiotic and biotic stress responses; however, studies on the mechanism of regulation of lncRNA expression are limited in plants. The present study examined the relationship between lncRNA expression level and two active histone modifications (H3K4me3 and H3K36me3) in Brassica rapa. Both histone marks were enriched in the chromatin regions encoding lncRNAs, especially around the transcription start site. The transcription level of long intergenic noncoding RNAs was positively associated with the level of H3K4me3 and H3K36me3, while this association was not observed in natural antisense RNAs (NATs) and intronic noncoding RNAs. As coordinate expression of mRNAs and paired NATs under biotic stress treatment has been identified, the transcriptional relationship between mRNAs and their paired NATs following Fusarium oxysporum f. sp. conglutinans (Foc) inoculation was examined. A positive association of expression levels between mRNAs and their paired NATs following Foc inoculation was observed. This association held for several defense-response-related genes and their NAT pairs. These results suggest that coordinate expression of mRNAs and paired NATs plays a role in the defense response against Foc.

Highlights

LncRNAs are not just transcriptional noise, and thousands of Long noncoding RNAs (lncRNAs) have been identified in plants [27,30,32,34,48,49]
We have examined H3K27me3 distribution in the genomic regions encoding lncRNAs in B. rapa [41], and unlike mRNAs, there was no negative association between the presence of H3K27me3 marks and lncRNA expression levels [39,41]. intronic noncoding RNAs (incRNAs) with encoding regions having H3K27me3 marks showed higher expression levels than those without H3K27me3 marks; this trend is the opposite of mRNA [41]
We identified lncRNAs with active histone modification (H3K4me3- and H3K36me3-marks) in their encoding regions and examined the relationship of histone marks to expression level

Summary

Introduction

Brassica rapa L. includes leafy vegetables such as Chinese cabbage Perviridis), as well as root vegetables such as turnip These vegetables provide nutrition, vitamins, minerals, dietary fiber, and health-promoting substances. Most of the modern cultivars of these vegetables are F1 hybrids [2]. Disease resistance is an important trait in a breeding program of F1 hybrid cultivars [3], and a major disease problem is Fusarium yellows. Fusarium yellows is caused by infection with a soil-borne fungus, Fusarium oxysporum f. Fusarium yellows is caused by infection with a soil-borne fungus, Fusarium oxysporum f. sp. conglutinans (Foc) or

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Conclusion