GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE136373 Query DataSets for GSE136373
Status Public on Jun 04, 2020
Title A lamin-like protein OsNMCP1 regulates drought resistance and root growth partially through chromatin accessibility modulation by interacting with a chromatin remodeler OsSWI3C in rice
Organism Oryza sativa Japonica Group
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Lamin proteins in animals are implicated in many nuclear functions, including chromatin organization, signaling transduction, gene regulation, and cell differentiation. Nuclear Matrix Constituent Proteins (NMCPs) are lamin analogues in plants, but their regulatory functions remain largely unknown. In this work, we report that OsNMCP1 positively regulates root growth and drought resistance through modulating chromatin state and expression levels of many genes functioning in root growth and stress resistance. OsNMCP1 is localized at the nuclear periphery and induced by drought stress. Overexpression of OsNMCP1 resulted in a deeper and thicker root system and enhanced drought resistance compared to the wild-type control. Assay for transposase accessible chromatin with sequencing (ATAC-seq) analysis revealed that OsNMCP1-overexpression altered chromatin accessibility in many genes related to drought resistance and root growth, including OsNAC10, OsERF48, OsSGL, and OsMSR15. Interestingly, OsNMCP1 can interact with SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complex OsSWI3C. The reported drought resistance or root growth related genes that were positively regulated by OsNMCP1 were negatively regulated by OsSWI3C, and OsSWI3C overexpression led to decreased drought resistance. We propose that the interaction between OsNMCP1 and OsSWI3C may lead to release of OsSWI3C from the gene silencing complexes SWI/SNF under drought condition thus changing the chromatin accessibility in genes related to root growth and drought resistance.
Overall design ATAC-seq for root tissue from OsNMCP1-OE, OsSWI3C-RNAi, and ZH11 seedlings under normal and drought conditions. RNA-seq for root tissue from OsNMCP1-OE and ZH11 under normal and drought conditions. Three biological replicates were involved for each experiment (two for the OsNMCP1-OE RNA-Seq under normal condition).
Contributor(s) Yang J, Chang Y, Qin Y, Chen D, Zhu T, Peng K, Wang H, Tang N, Li X, Wang Y, Liu Y, Li X, Xie W, Xiong L
Citation(s) 32129897
Submission date Aug 26, 2019
Last update date Jun 04, 2020
Contact name Yu Chang
Organization name Huazhong Agricultural University
Department National Key Laboratory of Crop Genetic Improvement
Street address No.1, Shizishan Street, Hongshan District
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
Platforms (1)
GPL23876 HiSeq X Ten (Oryza sativa Japonica Group)
Samples (29)
GSM4047570 NMCP1OE_RNAseq_1
GSM4047571 NMCP1OE_RNAseq_2
GSM4047572 ZH11-WT_RNAseq_1
BioProject PRJNA562309
SRA SRP219889

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 367.8 Mb (ftp)(http) BW 763.1 Mb (ftp)(http) BW
GSE136373_RAW.tar 11.7 Mb (http)(custom) TAR (of TAB) 306.8 Mb (ftp)(http) BW 803.3 Mb (ftp)(http) BW 369.4 Mb (ftp)(http) BW 825.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap