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Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Shin, Sang-Yoon | - |
dc.contributor.author | Jeong, Jin Seo | - |
dc.contributor.author | Lim, Jae Yun | - |
dc.contributor.author | Kim, Taewook | - |
dc.contributor.author | Park, June Hyun | - |
dc.contributor.author | Kim, Ju-Kon | - |
dc.contributor.author | Shin, Chanseok | - |
dc.date.accessioned | 2018-10-25T04:57:54Z | - |
dc.date.available | 2018-10-25T14:09:42Z | - |
dc.date.issued | 2018-07-13 | - |
dc.identifier.citation | BMC Genomics, 19(1):532 | ko_KR |
dc.identifier.issn | 1471-2164 | - |
dc.identifier.uri | https://hdl.handle.net/10371/142938 | - |
dc.description.abstract | Background
Nitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism. Results Here, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches. Analysis of rice genes involved in N metabolism and/or transport using strand-specific RNA-Seq identified 2588 novel putative lncRNA encoding loci. Analysis of previously published RNA-Seq datasets revealed a group of N starvation-responsive lncRNAs showing differential expression under other abiotic stress conditions. Poly A-primed sequencing (2P-Seq) revealed alternatively polyadenylated isoforms of N starvation-responsive lncRNAs and provided precise 3′ end information on the transcript models of these lncRNAs. Analysis of small RNA-Seq data identified N starvation-responsive miRNAs and down-regulation of miR169 family members, causing de-repression of NF-YA, as confirmed by strand-specific RNA-Seq and qRT-PCR. Moreover, we profiled the N starvation-responsive down-regulation of root-specific miRNA, osa-miR444a.4-3p, and Degradome sequencing confirmed MADS25 as a novel target gene. Conclusions In this study, we used a combination of multiple RNA-Seq analyses to extensively profile the expression of genes, newly identified lncRNAs, and microRNAs in N-starved rice roots and shoots. Data generated in this study provide an in-depth understanding of the regulatory pathways modulated by N starvation-responsive miRNAs. The results of comprehensive, large-scale data analysis provide valuable information on multiple aspects of the rice transcriptome, which may be useful in understanding the responses of rice plants to changes in the N supply status of soil. | ko_KR |
dc.description.sponsorship | This work was supported by the Next-Generation BioGreen 21 Program (No. PJ01332501), Rural Development Administration, Republic of Korea | ko_KR |
dc.language.iso | en | ko_KR |
dc.publisher | BioMed Central | ko_KR |
dc.subject | Longnon-codingRNA | ko_KR |
dc.subject | microRNA | ko_KR |
dc.subject | NGS | ko_KR |
dc.subject | Nitrogenstarvation | ko_KR |
dc.subject | Oryzasativa | ko_KR |
dc.subject | Transcriptome | ko_KR |
dc.subject | PolyA-primedsequencing | ko_KR |
dc.title | Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies | ko_KR |
dc.type | Article | ko_KR |
dc.contributor.AlternativeAuthor | 신상윤 | - |
dc.contributor.AlternativeAuthor | 정진서 | - |
dc.contributor.AlternativeAuthor | 임재윤 | - |
dc.contributor.AlternativeAuthor | 김태욱 | - |
dc.contributor.AlternativeAuthor | 박준현 | - |
dc.contributor.AlternativeAuthor | 김주곤 | - |
dc.contributor.AlternativeAuthor | 신찬석 | - |
dc.identifier.doi | 10.1186/s12864-018-4897-1 | - |
dc.language.rfc3066 | en | - |
dc.rights.holder | The Author(s). | - |
dc.date.updated | 2018-07-15T03:28:42Z | - |
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