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2. Ultrafast ion sieving in two dimensional graphene oxide membranes

Author

Liu, Junfan, Gu, Zonglin, Duan, Mengru, Li, Pei, Li, Lu, Jiang, Jianjun, Yang, Rujie, Chen, Junlang, Wang, Zhikun, Zhao, Liang, Tu, Yusong, and Chen, Liang

Subjects
Physics - Fluid Dynamics
Abstract

Ultrahigh water permeance, together with a high rejection rate through nanofiltration and separation membranes1,2, is crucial but still challenging for multivalent ion sieving in water treatment processes of desalination, separation, and purification3,4. To date, no theory or equation has ever been quantitatively clarified the mechanism of water permeance in two-dimensional (2D) membranes, despite intensive and prolonged searches. Here, we established a new general equation of permeation through 2D membranes, and experimentally achieved unprecedented advances in water permeance one to two orders of magnitude higher than state-of-the-art membranes while simultaneously maintaining high ion rejection rates for multivalent metal ions, by staking nano-sized reduced graphene oxide (nano-rGO) flakes into nanofiltration membranes. The equation is simply based on a fundamental steady-state flow assumption and provides an essential description of water permeance through 2D membranes, demonstrating that the ultrahigh water permeance is attributed to the high effective channel area and shortened channel length elicited from the nano-sized-flake stacking effects in nano-rGO membranes, consistent with our theoretical simulations and previous experiments. These results pave the way for fabrication of advanced 2D nanofiltration membranes to realize a breakthrough in water permeance with exceptional ion sieving performance., Comment: 12 pages, 3 figures, 1 table

Published
2022

19. Mechanistic basis for maintenance of CHG DNA methylation in plants

Author

Fang, Jian, Jiang, Jianjun, Leichter, Sarah M, Liu, Jie, Biswal, Mahamaya, Khudaverdyan, Nelli, Zhong, Xuehua, and Song, Jikui

Subjects
Biological Sciences, Genetics, Human Genome, DNA Methylation, Epigenesis, Genetic, Zea mays
Abstract

DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, DNA methylation widely occurs in the CG, CHG, and CHH (H = A, C, or T) contexts, with the maintenance of CHG methylation mediated by CMT3 chromomethylase. However, how CMT3 interacts with the chromatin environment for faithful maintenance of CHG methylation is unclear. Here we report structure-function characterization of the H3K9me2-directed maintenance of CHG methylation by CMT3 and its Zea mays ortholog ZMET2. Base-specific interactions and DNA deformation coordinately underpin the substrate specificity of CMT3 and ZMET2, while a bivalent readout of H3K9me2 and H3K18 allosterically stimulates substrate binding. Disruption of the interaction with DNA or H3K9me2/H3K18 led to loss of CMT3/ZMET2 activity in vitro and impairment of genome-wide CHG methylation in vivo. Together, our study uncovers how the intricate interplay of CMT3, repressive histone marks, and DNA sequence mediates heterochromatic CHG methylation.

Published
2022

25. Substrate deformation regulates DRM2-mediated DNA methylation in plants

Author

Fang, Jian, Leichter, Sarah M, Jiang, Jianjun, Biswal, Mahamaya, Lu, Jiuwei, Zhang, Zhi-Min, Ren, Wendan, Zhai, Jixian, Cui, Qiang, Zhong, Xuehua, and Song, Jikui

Subjects
Biochemistry and Cell Biology, Genetics, Biological Sciences, Generic health relevance, Animals, Arabidopsis, Arabidopsis Proteins, Archaeal Proteins, DNA, DNA Methylation, Gene Expression Regulation, Plant, Mammals, Methyltransferases
Abstract

DNA methylation is a major epigenetic mechanism critical for gene expression and genome stability. In plants, domains rearranged methyltransferase 2 (DRM2) preferentially mediates CHH (H = C, T, or A) methylation, a substrate specificity distinct from that of mammalian DNA methyltransferases. However, the underlying mechanism is unknown. Here, we report structure-function characterization of DRM2-mediated methylation. An arginine finger from the catalytic loop intercalates into the nontarget strand of DNA through the minor groove, inducing large DNA deformation that affects the substrate preference of DRM2. The target recognition domain stabilizes the enlarged major groove via shape complementarity rather than base-specific interactions, permitting substrate diversity. The engineered DRM2 C397R mutation introduces base-specific contacts with the +2-flanking guanine, thereby shifting the substrate specificity of DRM2 toward CHG DNA. Together, this study uncovers DNA deformation as a mechanism in regulating the specificity of DRM2 toward diverse CHH substrates and illustrates methylome complexity in plants.

Published
2021

33. UVR8 interacts with de novo DNA methyltransferase and suppresses DNA methylation in Arabidopsis

Author

Jiang, Jianjun, Liu, Jie, Sanders, Dean, Qian, Shuiming, Ren, Wendan, Song, Jikui, Liu, Fengquan, and Zhong, Xuehua

Subjects
Biochemistry and Cell Biology, Genetics, Biological Sciences, Climate-Related Exposures and Conditions, Human Genome, Prevention, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Arabidopsis, DNA Methylation, Gene Expression Regulation, Plant, Genes, Plant, Genetic Variation, Genotype, Methyltransferases, Mutation, Signal Transduction, Ultraviolet Rays, Plant Biology, Crop and Pasture Production, Ecology, Plant biology
Abstract

DNA methylation is an important epigenetic gene regulatory mechanism conserved in eukaryotes. Emerging evidence shows DNA methylation alterations in response to environmental cues. However, the mechanism of how cells sense these signals and reprogramme the methylation landscape is poorly understood. Here, we uncovered a connection between ultraviolet B (UVB) signalling and DNA methylation involving UVB photoreceptor (UV RESISTANCE LOCUS 8 (UVR8)) and a de novo DNA methyltransferase (DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2)) in Arabidopsis. We demonstrated that UVB acts through UVR8 to inhibit DRM2-mediated DNA methylation and transcriptional de-repression. Interestingly, DNA transposons with high DNA methylation are more sensitive to UVB irradiation. Mechanistically, UVR8 interacts with and negatively regulates DRM2 by preventing its chromatin association and inhibiting the methyltransferase activity. Collectively, this study identifies UVB as a potent inhibitor of DNA methylation and provides mechanistic insights into how signalling transduction cascades intertwine with chromatin to guide genome functions.

Published
2021

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