The OsSRO1c-OsDREB2B complex undergoes protein phase transition to enhance cold tolerance in rice

Cold stress is one of the major abiotic stress factors affecting rice growth and development,leading to significant yield loss in the context of global climate change.Exploring natural variants that confer cold resistance and the underlying molecular mechanism responsible for this is the major strategy to breed cold-tolerant rice varieties.Here,we show that natural variations of a SIMILAR to RCD ONE(SRO)gene,OsSRO1c,confer cold tolerance in rice at both seedling and booting stages.Our in vivo and in vitro experiments demonstrated that OsSRO1c possesses intrinsic liquid–liquid phase-separation ability and recruits OsDREB2B,an AP2/ERF transcription factor that functions as a positive regulator of cold stress,into its biomolecular condensates in the nucleus,resulting in elevated transcriptional activity of OsDREB2B.We found that the OsSRO1c-OsDREB2B complex directly responds to low temperature through dynamic phase transitions and regulates key cold-response genes,including COLD1.Furthermore,we showed that introgression of an elite haplotype of OsSRO1c into a cold-susceptible indica rice could significantly increase its cold resistance.Collectively,our work reveals a novel cold-tolerance regulatory module in rice and provides promising genetic targets for molecular breeding of cold-tolerant rice varieties.

Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants

Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.

The LEAFY floral regulator displays pioneer transcription factor properties

Pioneer transcription factors(TFs)are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and may be highly methylated.Subsequently,pioneer TFs are able to modify the chromatin state to initiate gene expression.In plants,LEAFY(LFY)is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis.Here,we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genomewide binding experiments and structural modeling.Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that a subset of LFY bound regions is occupied by nucleosomes.We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes.Finally,we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes APETALA1 and AGAMOUS.Taken together,our study suggests that LFY possesses key pioneer TF features that contribute to launching the floral gene expression program.

Getting in phase: DNA damage repair mechanisms and liquid-liquid phase separation of the plant-specific histone methyltransferase MtSUVR2

Liquid-liquid phase separation(LLPS)has become a widely accepted mechanism forthedynamic compartmentalization of different cellular components into membraneless organelles or other cellular bodies.LLPS occurs when the concentration of a protein,nucleic acid,or other molecule reaches a saturation concentration and its partition into high-and low-concentration phases is energetically favorable.