N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression,Plant Development, and Stress Responses

N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive.Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars,Nipponbare (Nip;Japonica)and 93-11 (Indica).Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis.We found that 6mA levels are positively correlated with the expression of key stressrelated genes,which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover,we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.

Nuclear translocation of OsMFT1 that is impeded by OsFTIP1 promotes drought toleranee in rice

Drought is the leading environmental threat affecting crop productivity,and plants have evolved a series of mechanisms to adapt to drought stress.The FT-interacting proteins(FTIPs)and phosphatidylethanola mine.binding proteins(PEBPs)play key roles in developmental processes,whereas their roles in the regulation of stress response are still largely unknown.Here,we report that OsFTIP1 negatively regulates drought response in rice.We showed that OsFTIP1 interacts with rice MOTHER OF FT AND TFL1(OsMFT1),a PEBP that promotes rice tolerance to drought treatment.Further studies discovered that OsMFT1 interacts with two key drought-related transcription factors,OsbZIP66 and OsMYB26,regulating their binding capacity on drought-related genes and thereby enhancing drought toleranee in rice.Interestingly,we found that OsFTIP1 impedes the nucleocytoplasmic translocation of OsMFT1,implying that dynamic modulation of drought-responsive genes by the OsMFT1-OsMYB26 and OsMFT1-OsbZIP66 complexes is integral to OsFTIP1-modulated nuclear accumulation of OsMFT1.Our findings also suggest that OsMFT1 might act as a hitherto unknown nucleocytoplasmic trafficking signal that regulates drought tolerance in rice in response to environmental signals.

5-Methylcytosine RNA Methylation in Arabidopsis Thaliana

5-Methylcytosine （m^5C） is a well-characterized DNA modification, and is also predominantly reported in abundant non-coding RNAs in both prokaryotes and eukaryotes. However, the distribution and biological functions of m^5C in plant mRNAs remain largely unknown. Here, we report transcriptome-wide profiling of RNA m^5C in Arabidopsis thaliana by applying m^5C RNA immunoprecipitation followed by a deep- sequencing approach （m^5C-RIP-seq）. LC-MS/MS and dot blot analyses reveal a dynamic pattern of m^5C mRNA modification in various tissues and at different developmental stages, m^5C-RIP-seq analysis identified 6045 m^5C peaks in 4465 expressed genes in young seedlings. We found that m^5C is enriched in coding sequences with two peaks located immediately after start codons and before stop codons, and is associated with mRNAs with low translation activity. We further demonstrated that an RNA （cytosine-5）-methyl- transferase, tRNA-specific methyltransferase 4B （TRM4B）, exhibits m^5C RNA methyltransferase activity. Mutations in TRM4B display defects in root development and decreased m^5C peaks. TRM4B affects the transcript levels of the genes involved in root development, which is positively correlated with their mRNA stability and m^5C levels. Our results suggest that m^5C in mRNA is a new epitranscriptome marker inArabidopsis, and that regulation of this modification is an integral part of gene regulatory networks underlying plant development.

The OsFTIP6-OsHB22-OsMYBR57 module regulates drought response in rice

Plants have evolved a sophisticated set of mechanisms to adapt to drought stress.Transcription factors play crucial roles in plant responses to various environmental stimuli by modulating the expression of numerous stress-responsive genes.However,how the crosstalk between different transcription factor families orchestrates initiation of the key transcriptional network and the role of posttranscriptional modification of transcription factors,especially in cellular localization/trafficking in response to stress in rice,remain still largely unknown.In this study,we isolated an Osmybr57 mutant that displays a drought-sensitive phenotype through a genetic screen for drought stress sensitivity.We found that OsMYBR57,an MYB-related protein,directly regulates the expression of several key drought-related OsbZ/Ps in response to drought treatment.Further studies revealed that OsMYBR57 interacts with a homeodomain transcription factor,OsHB22,which also plays a positive role in drought signaling.We further demonstrate that OsFTIP6 interacts with OsHB22 and promotes the nucleocytoplasmic translocation of OsHB22 into the nucleus,where OsHB22 cooperates with OsMYBR57 to regulate the expression of drought-responsive genes.Our findings have revealed a mechanistic framework underlying the OsFTIP6-0sHB22-0sMYBR57 module-mediated regulation of drought response in rice.The OsFTIP6-mediated OsHB22 nucleocytoplasmic shuttling and OsMYBR57-0sHB22 regulation of OsbZIP transcription ensure precise control of expression of OsLEA3 and Rab21,and thereby regulate the response to water deficiency in rice.