PRJNA562309: 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
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).
Seedling (25-day-old) roots from hydroponic culture were harvested for genomic DNA or total RNA extraction.
Treatment Protocol:
Seedlings were grown in normal condition (28°C during day light, 22°C at night). For drought stress treatment, the seedlings were deprived from water supply for three hours before sampling.
Extract Protocol:
Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596018) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596019) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596020) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596021) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596022) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596023) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596024) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596025) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596026) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596027) /chloroform extraction according to the manufacturer’s instructions.; Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596028) /chloroform extraction according to the manufacturer’s instructions.
Library Construction Protocol:
Library construction was performed by Novogene Inc (Tianjin, China) accroding to the standard protocol of Illumina.
