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Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance

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Authors
Chung, Pil Joong; Jung, Harin; Choi, Yang Do; Kim, Ju-Kon
Issue Date
2018-01-12
Publisher
BioMed Central
Citation
BMC Genomics, 19(1):40
Keywords
Drought toleranceGenome-wide analysisNAC transcription factorsOryza sativaRNA-SeqChIP-Seq
Abstract
Background
Plant stress responses and mechanisms determining tolerance are controlled by diverse sets of genes. Transcription factors (TFs) have been implicated in conferring drought tolerance under drought stress conditions, and the identification of their target genes can elucidate molecular regulatory networks that orchestrate tolerance mechanisms.

Results
We generated transgenic rice plants overexpressing the 4 rice TFs, OsNAC5, 6, 9, and 10, under the control of the root-specific RCc3 promoter. We showed that they were tolerant to drought stress with reduced loss of grain yield under drought conditions compared with wild type plants. To understand the molecular mechanisms underlying this tolerance, we here performed chromatin immunoprecipitation (ChIP)-Seq and RNA-Seq analyses to identify the direct target genes of the OsNAC proteins using the RCc3:6MYC-OsNAC expressing roots. A total of 475 binding loci for the 4 OsNAC proteins were identified by cross-referencing their binding to promoter regions and the expression levels of the corresponding genes. The binding loci were distributed among the promoter regions of 391 target genes that were directly up-regulated by one of the OsNAC proteins in four RCc3:6MYC-OsNAC transgenic lines. Based on gene ontology (GO) analysis, the direct target genes were related to transmembrane/transporter activity, vesicle, plant hormones, carbohydrate metabolism, and TFs. The direct targets of each OsNAC range from 4.0–8.7% of the total number of up-regulated genes found in the RNA-Seq data sets. Thus, each OsNAC up-regulates a set of direct target genes that alter root system architecture in the RCc3:OsNAC plants to confer drought tolerance. Our results provide a valuable resource for functional dissection of the molecular mechanisms of drought tolerance.

Conclusions
Many of the target genes, including transmembrane/transporter, vesicle related, auxin/hormone related, carbohydrate metabolic processes, and transcription factor genes, that are up-regulated by OsNACs act as the cellular components which would alter the root architectures of RCc3:OsNACs for drought tolerance.
ISSN
1471-2164
Language
English
URI
http://hdl.handle.net/10371/138486
DOI
https://doi.org/10.1186/s12864-017-4367-1
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Graduate School of International Agricultural Technology (국제농업기술대학원)Dept. of International Agricultural Technology (국제농업기술학과)Journal Papers (저널논문_국제농업기술학과)
College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Agricultural Biotechnology (농생명공학부)Journal Papers (저널논문_농생명공학부)
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