Biology subjects

Ren, W.

Publications and source records attributed to Ren, W..

62 records · Page 4Linked to original sources

bioRxiv2020

Substrate deformation regulates DRM2-mediated DNA methylation in plants

DNA methylation is an important epigenetic mechanism that critically regulates gene expression and genomic stability. In plants, Domains Rearranged Methyltransferase 2 (DRM2) preferentially mediates CHH methylation (H=C, T, A), a substrate specificity distinct from that of mammalian DNA methyltransferases. However, the underlying mechanism is unknown. Here, we report structure-function characterizations of DRM2-mediated methylation. An arginine finger from the catalytic loop intercalates into DNA minor groove, inducing large DNA deformation that impacts the substrate specificity of DRM2. To accommodate the substrate deformation, the target recognition domain of DRM2 embraces the enlarged DNA major groove via shape complementarity, disruption of which via C397R mutation shifts the substrate specificity of DRM2 toward CHG DNA. This study uncovers DNA deformation as a mechanism in regulating the substrate specificity of DRM2, implicative of transposon-specific repression in plants.

biochemistry↗

bioRxiv2020

Functions of olfactory receptors are decoded from their sequence

G protein-coupled receptors (GPCRs) conserve common structural folds and activation mechanisms, yet their ligand spectra and functions are highly diversified. This work investigated how the functional variations in olfactory GPCRs (ORs)-the largest GPCR family-are encoded in the primary sequence. With the aid of site-directed mutagenesis and molecular simulations, we built machine learning models to predict OR-ligand pairs as well as basal activity of ORs. In vitro functional assay confirmed 20 new OR-odorant pairs, including 9 orphan ORs. Residues around the odorant-binding pocket dictate the odorant selectivity/specificity of the ORs. Residues that encode the varied basal activities of the ORs were found to mostly surround the conserved motifs as well as the binding pocket. The machine learning approach, which is readily applicable to mammalian OR families, will accelerate OR-odorant mapping and the decoding of combinatorial OR codes for odors.

bioinformatics↗

bioRxiv2019

Admistration of Exogenous Melatonin Improves the Diurnal Rhythms of Gut Microbiota in High Fat Diet-Fed Mice

Melatonin, a circadian hormone, has been reported to improve host lipid metabolism by reprogramming gut microbiota, which also exhibits rhythmicity in a light/dark cycle. However, the effect of admistartion of exogenous melatonin on the diurnal variation in gut microbiota in high fat diet (HFD)-fed mice is obscure. Here, we further confirmed the anti-obesogenic effect of melatonin on in mice feed with HFD for two weeks. Samples were collected every 4 h within a 24-h period and diurnal rhythms of clock genes expression (Clock, Cry1, Cry2, Per1, and Per2) and serum lipid indexes varied with diurnal time. Notably, Clock and triglycerides (TG) showed a marked rhythm only in the control and melatonin treated mice, but not in the HFD-fed mice. Rhythmicity of these parameters were similar between control and melatonin treated HFD mice compared with the HFD group, indicating an improvement of melatonin in the diurnal clock of host metabolism in HFD-fed mice. 16S rDNA sequencing showed that most microbiota exhibited a daily rhythmicity and the trends differentiated at different groups and different time points. We also identified several specific microbiota correlating with the circadian clock genes and serum lipid indexes, which might contribute the potential mechanism of melatonin in HFD-fed mice. Interestingly, administration of exogenous melatonin only at daytime exhibited higher resistance to HFD-induced lipid dysmetabolism than nighttime treatment companying with altered gut microbiota (Lactobacillus, Intestinimonas, and Oscillibacter). Importantly, the responses of microbiota transplanted mice to HFD feeding also varied at different transplanting times (8:00 and 16:00) and different microbiota donors. In summary, daily oscillations in the expression of circadian clock genes, serum lipid indexes, and gut microbiota, appears to be driven by a short-time feeding of an HFD. Administration of exogenous melatonin improved the compositions and diurnal rhythmicity of gut microbiota, which might be linked to host diurnal rhythm and metabolism.\n\nImportancePrevious studies show that a circadian hormone, melatonin, involves in host lipid metabolism by reprogramming gut microbiota, which also exhibits rhythmicity in a light/dark cycle. However, the effect of melatonin drinking on the diurnal variation in gut microbiota in high fat diet-fed mice is obscure. Here, we found that 24-h oscillations were widely occurred in circadian clock genes, serum lipid indexes, and gut microbiota. Melatonin drinking improved the compositions and circadian rhythmicity of gut microbiota, which might be linked to host circadian rhythm and metabolism.

microbiology↗

bioRxiv2019

Essentiality of CREBBP in EP300 truncated B-cell lymphoma revealed by genome-wide CRISPR-Cas9 screen

Histone acetyltransferases (HATs), including CREBBP and EP300, are frequently mutated in B-cell malignancies and usually play a tumor-suppressive role. In this study, we performed whole genome and transcriptome sequencing and a genome-wide CRISPR-Cas9 knockout screen to study a germinal center B-cell like diffuse large B-cell lymphoma (DLBCL) cell line (RC-K8). Using a summarizing method that is optimized to address the complexity introduced by the time-course design, we identified a distinct pattern of genetic essentialities in RC-K8, including a dependency on CREBBP and MDM2, shown already at early time points and a gradually increased dependency on oxidative phosphorylation related genes. The dependency on CREBBP is associated with the corresponding genetic alterations identified in this cell line, i.e. a balanced translocation involves EP300, which resulted in a truncated form of protein that lacks the critical bromodomain and HAT domain. We further evaluated the previously published CRISPR-Cas9 screens and identified a genetic essentiality of CREBBP or EP300 gene in a small set of cancer cell lines, including several DLBCL cell lines that are highly sensitive for EP300 knockout and with CREBBP mutations or copy number loss. The dependency of the remaining HAT function in CREBBP and/or EP300-deficient genotype was validated by testing the HAT-domain inhibitor A-485. Our study suggests that integration of the unbiased, time-course-based functional screen results with the genomic and transcriptomic data can identify druggable vulnerability in individual or subgroups of cell lines/patients, which may help to develop more effective therapeutic strategies for cancers that are genetically highly heterogeneous, like DLBCL.

cancer biology↗

bioRxiv2019

Contraction of the ROS scavenging enzyme glutathione S-transferase gene family in cetaceans

Cetaceans are a group of marine mammals whose ancestors were adaptated for life on land. Life in an aquatic environment poses many challenges for air-breathing mammals. Diving marine mammals have adapted to rapid reoxygenation and reactive oxygen species (ROS)-mediated reperfusion injury. Here, we considered the evolution of the glutathione transferase (GST) gene family which has important roles in the detoxification of endogenously-derived ROS and environmental pollutants. We characterized the cytosolic GST gene family in 21 mammalian species; cetaceans, sirenians, pinnipeds, and their terrestrial relatives. All seven GST classes were identified, showing that GSTs are ubiquitous in mammals. Some GST genes are the product of lineage-specific duplications and losses, in line with a birth-and-death evolutionary model. We detected sites with signatures of positive selection that possibly influence GST structure and function, suggesting that adaptive evolution of GST genes is important for defending mammals from various types of noxious environmental compounds. We also found evidence for loss of alpha and mu GST subclass genes in cetacean lineages. Notably, cetaceans have retained a homolog of at least one of the genes GSTA1, GSTA4, and GSTM1; GSTs that are present in both the cytosol and mitochondria. The observed variation in number and selection pressure on GST genes suggest that the gene family structure is dynamic within cetaceans. Taken together, our results indicate that the cytosolic GST family in cetaceans reflects unique evolutionary dynamics related to oxygen-poor aquatic environments.

evolutionary biology↗

bioRxiv2018

Comparative genomics reveals contraction in cytosolic glutathione transferase genes in cetaceans: implications for oxidative stress adaptation

Cetaceans, a highly specialized group of aquatic mammals, experience oxidative stress induced by reactive oxygen species (ROS) production associated with the apnea/reoxygenation. The glutathione transferases (GST) family possesses multiple functions in detoxification and antioxidant defenses. However, the molecular evolution of GST family in cetaceans is still poorly investigated. Here, we characterized the GST gene family across 21 mammalian genomes including cetaceans and terrestrial relatives. Overall, 7 GST classes were identified, showing GSTs are ubiquitous and conservative to all mammals. Some of GSTs are lineage-specific duplication and loss, in line with a birth-and-death evolutionary model. We detected positive selection sites that possibly influence GST structure and function, suggesting adaptive evolution of GSTs is important for defending mammals from various types of noxious environmental compounds. There is evidence for loss of alpha and mu GST class in cetacean lineages when compared to their terrestrial relatives, consisting with the lower GST activities observed in cetaceans. Notably, we find that retained GSTA1, GSTA4 and GSTM1 in cetaceans, indicating a vital role in against lipid peroxidation and superoxide. Besides, variation in gene number, enzyme activity and selection pressure of GSTs between marine mammals suggests there is a divergent evolution of GSTs in aquatic species that might be associated to diving ability and oxidative status with different habitats. Summarily, our findings demonstrate that the GST family in cetaceans has been subject to evolutionary dynamics as response for their adaptations to oxidative stress, and highlighted the differential selection associated with different life history traits among mammals.

evolutionary biology↗

bioRxiv2018

Variation and diversification of the microbiome of Schlechtendalia chinensis on two alternate host plants

Schlechtendalia chinensis, a gall-inducing aphid, has two host plants in its life cycle. Its wintering host is a moss (typically Plagiomnium maximoviczii) and its main host is Rhus chinensis (Sumac), on which it forms galls during the summer.. This study investigated bacteria associated with S. chinensis living on the two different host plants by sequencing 16S rRNAs. A total of 183 Operational Taxonomic Units (OTUs) from 50 genera were identified from aphids living on moss, whereas 182 OTUs from 49 genera were found from aphids living in Sumac galls. The most abundant bacterial genus among identified OTUs from aphids feeding on both hosts was Buchnera. Despite similar numbers of OTUs, the composition of bacterial taxa showed significant differences between aphids living on moss and those living on R. chinensis. Specifically, there were 12 OTUs from 5 genera (family) unique to aphids living on moss, and 11 OTUs from 4 genera (family) unique to aphids feeding in galls on R. Chinensis. Principal Coordinate Analysis (PCoA) also revealed that bacteria from moss-residing aphids clustered differently from aphids collected from galls. Our results provid a foundation for future analyses on the roles of symbiotic bacteria in plant - aphid interactions in general, and how gall-specific symbionts differ in this respect.

microbiology↗

bioRxiv2018

Dorsal Hippocampal Activation Suppresses Neuropathic Pain Behaviors: Chronic pain as extinction-resistant pain-related memory traces

Accumulating evidence suggests the hippocampus being involved in, and modified with, chronic neuropathic pain. However, it is still not clear whether hippocampal activity has direct control over neuropathic behaviors. Here we show that activation of the dorsal, but not ventral, hippocampus, by glutamate microinjection or by chemogenetically increasing excitability (PSAM/PSEM), completely or partially reversed neuropathic behaviors: tactile allodynia and thermal hyperalgesia in the models of spared nerve injury and lumbar spinal nerve ligation. Using a new methodology (chemo-fMRI), where we combine awake resting state brain imaging with viral vector mediated chemogenetic activation (PSAM/PSEM), we could demonstrate that increased excitability of dorsal hippocampus neurons altered resting state functional connectivity within circuitry specifically related to the extent of diminution of neuropathic behavior (tactile allodynia). The identified circuitry most reliably (survived a validation procedure) identified dorsal hippocampal connections to the somatosensory cortex and the thalamus. Moreover, anterograde tracing indicated non-overlapping projections from dorsal and ventral hippocampus. Thus, the present study exhibits a novel causal role for the dorsal hippocampus, and mediating circuitry, controlling neuropathic pain-related behaviors. Altogether, these results imply downregulation of dorsal hippocampus circuitry in chronic neuropathic pain; the activation of which reverses pain behaviors either through disruption of accumulated memories and/or by enhancing extinction circuitry.

neuroscience↗