A5035354986- Plant Molecular Biology Research
- Soybean genetics and cultivation
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Legume Nitrogen Fixing Symbiosis
- Plant Reproductive Biology
- Plant tissue culture and regeneration
- Genomics and Phylogenetic Studies
- Plant nutrient uptake and metabolism
- Cancer, Stress, Anesthesia, and Immune Response
- RNA modifications and cancer
- Insect-Plant Interactions and Control
- Plant Gene Expression Analysis
- Immune cells in cancer
- Genomics and Chromatin Dynamics
- Genetic diversity and population structure
- Protist diversity and phylogeny
- Genetic Mapping and Diversity in Plants and Animals
- Bioenergy crop production and management
- Neuropeptides and Animal Physiology
- Plant Stress Responses and Tolerance
- Adipokines, Inflammation, and Metabolic Diseases
- 3D Printing in Biomedical Research
- Plant Disease Resistance and Genetics
- Cell Image Analysis Techniques
Novartis (United States)
2025
University of Georgia
2014-2024
Cygnal Therapeutics (United States)
2021-2022
Beijing Forestry University
2012-2021
Shandong Academy of Forestry
2021
DNA methylation is an important feature of plant epigenomes, involved in the formation heterochromatin and affecting gene expression. Extensive variation patterns within a species has been uncovered from studies natural variation. However, extent to which varies between flowering still unclear. To understand genomic patterning across species, we compared single base resolution methylomes 34 diverse angiosperm species.By analyzing whole-genome bisulfite sequencing data phylogenetic context,...
Significance DNA methylation in plants is found at CG, CHG, and CHH sequence contexts. In plants, CG enriched the transcribed regions of many constitutively expressed genes (gene body methylation; gbM) shows correlations with several chromatin modifications. Contrary to other types methylation, evolution function gbM are largely unknown. Here we show two independent concomitant losses methyltransferase CHROMOMETHYLASE 3 (CMT3) without predicted disruption transcription modifications...
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained genes and being highly expressed, a phenomenon termed subgenome dominance. The genomic features determine how quickly which dominates within newly formed polyploid remain poorly understood. To investigate rate emergence dominance, we examined gene expression, methylation, transposable element (TE) methylation natural, <140-year-old allopolyploid (Mimulus...
Abstract Solid tumours are innervated by nerve fibres that arise from the autonomic and sensory peripheral nervous systems 1–5 . Whether neo-innervation of pain-initiating neurons affects cancer immunosurveillance remains unclear. Here we show melanoma cells interact with nociceptor neurons, leading to increases in their neurite outgrowth, responsiveness noxious ligands neuropeptide release. Calcitonin gene-related peptide (CGRP)—one such nociceptor-produced neuropeptide—directly exhaustion...
DNA methylation and dimethylation of lysine 9 histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape interspersed genes transposons. genome-wide distribution H3K9me2 were investigated in seedling tissue for the inbred B73 compared to patterns these observed Arabidopsis thaliana. Most transposons highly enriched CG CHG contexts H3K9me2. In contrast findings Arabidopsis, CHH levels...
The evolution of gene body methylation (gbM), its origins, and functional consequences are poorly understood. By pairing the largest collection transcriptomes (>1000) methylomes (77) across Viridiplantae, we provide novel insights into gbM relationship to CHROMOMETHYLASE (CMT) proteins.CMTs evolutionary conserved DNA methyltransferases in Viridiplantae. Duplication events gave rise what now referred as CMT1, 2 3. Independent losses 2, 3 eudicots, CMT2 ZMET monocots monocots/commelinids,...
Significance In plants, 12-oxo-phytodienoic acid (12-OPDA) and jasmonic are key 13-lipoxygenase-derived linolenate oxidation products termed jasmonates that regulate diverse processes in development innate immunity. A less-studied metabolic pathway branch is generated by 9-lipoxygenase activity on linoleic acid, enabling the production of 10-oxo-11-phytoenoic (10-OPEA). maize, fungal infection southern leaf blight ( Cochliobolus heterostrophus ) results localized 10-OPEA, a series related...
Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed (RdDM). In plants, canonical RdDM functions through RNA polymerase IV reinforce pre-existing element silencing. Recent investigations have identified "non-canonical" form of dependent on II expression initiate and re-establish silencing active elements. This expression-dependent mechanism RNAi degradation mRNAs into guided the RNA-dependent 6 (RDR6) protein is...
Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all which are Hymenoptera. If genomic influences on sociality do exist, we need data from wider range taxa that also vary their levels sociality. Here, present the assembled annotated genome subsocial beetle...
Significance Regulators of chromatin structure play critical roles in DNA-based processes. Lysine (K) Methyltransferase 1 (KMT1) homologs perform methylation H3 lysine-9 and are best known for their essential role heterochromatin formation transcriptional silencing. Heterochromatin is also important maintenance genome stability, although the mechanisms not well understood. We report that altered activity Polycomb repressive complex-2 (PRC2), a histone lysine-27 methyltransferase complex,...
The development of whole-genome bisulfite sequencing (WGBS) has led to a number exciting discoveries about the role DNA methylation leading plethora novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently advanced point that bottleneck experiments use WGBS shifted data analysis interpretation. Here we present empirical evidence an over-representation reads from methylated in WGBS. This enrichment is exacerbated by higher cycles PCR...
In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM unclear, yet flowering species naturally without lack the methyltransferase, CMT3, which maintains CHG (H = A, C, or T) and not CG at constitutive heterochromatin. Here, we identify mechanistic basis for establishment expressing CMT3 in lacking CMT3. expression reconstituted through progression de novo on...
Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging 6 weeks 13 years continuous culture. We identified genome-wide increases in DNA methylation cultured samples, especially CHH sites. The hypermethylation almost exclusively...
DNA methylation and epigenetic silencing play important roles in the regulation of transposable elements (TEs) many eukaryotic genomes. A majority maize genome is derived from TEs that can be classified into different orders families based on their mechanism transposition sequence similarity, respectively. themselves are highly methylated it tempting to view them as a single uniform group. However, analysis profiles flanking regions provides evidence for distinct groups chromatin properties...
In plants and mammals, DNA methylation plays a critical role in transcriptional silencing by delineating heterochromatin from transcriptionally active euchromatin. A homeostatic balance between euchromatin is essential to genomic stability. This evident many diseases mutants for maintenance, which are characterized global losses of coupled with localized ectopic gains that alter transcription. Furthermore, we have shown genome-wide patterns Arabidopsis thaliana highly stable over...
DNA methylation in the promoters of plant genes sometimes leads to transcriptional repression, and loss methyltransferase mutants results altered gene expression severe developmental defects. However, many cases naturally occurring variations have been reported, whereby differentially methylated is responsible for agronomically important traits. The ability manipulate methylomes generate epigenetically distinct individuals could be invaluable breeding research purposes. Here, we describe...
Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. tomentosa Carr. is widely distributed cultivated in eastern region of Asia, where it plays multiple important roles forestry, agriculture, conservation, urban horticulture. Reference genomes available for several species, however, our goals were to produce very high quality de novo chromosome-level genome assembly P. that could serve as reference evolutionary ecological studies...
Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification methylation in R-M systems, including N(6)-methyladenine (6mA), 5-methylcytosine (5mC) N(4)-methylcytosine (4mC), will enable strategies make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable detecting 4mC directly for any regardless whether an assembled genome exists or not, it...
Abstract To understand the variation in genomic patterning of DNA methylation we compared methylomes 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data a phylogenetic context it becomes clear that there is extensive throughout angiosperms gene body methylation, euchromatic silencing transposons and repeats, as well heterochromatic transposons. The Brassicaceae have reduced CHG levels also or loss CG methylation. Poaceae are characterized by lack reduction CHH...