A5063006064- Plant Molecular Biology Research
- Plant nutrient uptake and metabolism
- Chromosomal and Genetic Variations
- Genetic Syndromes and Imprinting
- Legume Nitrogen Fixing Symbiosis
- Epigenetics and DNA Methylation
- Plant tissue culture and regeneration
- Plant Gene Expression Analysis
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Nuclear Materials and Properties
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Plant Reproductive Biology
- Soybean genetics and cultivation
- Nuclear reactor physics and engineering
- Insect symbiosis and bacterial influences
- Plant Genetic and Mutation Studies
- Flame retardant materials and properties
- Phytoplasmas and Hemiptera pathogens
- Plant Virus Research Studies
- Seed Germination and Physiology
- Laser Design and Applications
- Gas Dynamics and Kinetic Theory
- Spectroscopy and Laser Applications
North Carolina State University
2015-2024
David H. Murdock Research Institute
2017-2023
University of California, Berkeley
2003-2017
Texas A&M University
1998-2002
Caterpillar (United States)
1999
Argonne National Laboratory
1981-1982
Materials Science & Engineering
1982
Northwestern University
1982
Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated DNA glycosylase DEMETER, but extent methylation changes not known. Here, we show that virtually entire demethylated, coupled with extensive local non-CG hypermethylation small interfering RNA-targeted sequences. Mutation DEMETER partially restores CG to levels found other tissues, indicating specific Endosperm accompanied CHH embryo...
The relative ease, speed, and biological scope of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated Protein9 (Cas9)-based reagents for genomic manipulations are revolutionizing virtually all areas molecular biosciences, including functional genomics, genetics, applied biomedical research, agricultural biotechnology. In plant systems, however, a number hurdles currently exist that limit this technology from reaching its full potential. For example,...
Intergenerational Transposable Shutdown elements (TEs) are a potential threat, especially to the germline genome. In many eukaryotes, TEs shut down by DNA methylation and/or small-RNA–mediated silencing. Therefore, it seems counterintuitive that results obtained Ibarra et al. (p. 1360 ) on Arabidopsis showed in cells of this plant's sexual apparatus, small demethylated DEMETER (DME) glycosylase and become activated. But turns out activation triggers formation small-interfering RNAs, which...
Imprinted genes are expressed primarily or exclusively from either the maternal paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described endosperm, terminal nutritive tissue consumed by embryo during seed development after germination. Arabidopsis thaliana endosperm is orchestrated differences cytosine DNA methylation between genomes as well Polycomb group proteins. Currently, only 11 A. known. Here, we use...
LEAFY COTYLEDON2 (LEC2) is a central regulator of embryogenesis sufficient to induce somatic cells form embryos when expressed ectopically. Here, we analyze the cellular processes induced by LEC2, B3 domain transcription factor, that may underlie its ability promote embryogenesis. We show auxin-responsive genes are after LEC2 activation in seedlings. Genes encoding enzymes involved auxin biosynthesis, YUC2 and YUC4, activated within 1 h induction activity, YUC4 appears be direct...
Significance We describe the spatial and temporal profiles of soybean Arabidopsis seed methylomes during development. CHH methylation increases globally from fertilization through dormancy in all parts, decreases following germination, targets primarily transposons. By contrast, CG- CHG-context remains constant throughout Mutant seeds lacking non-CG develop normally, but have a set up-regulated transposon RNAs suggesting that increase may be failsafe mechanism to reinforce silencing. Major...
Hexaploid oat ( Avena sativa L., 2 n = 6 x 42) is a member of the Poaceae family and has large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered development linkage maps in this species. The objective work was to develop single high‐density consensus map that representative majority commonly grown varieties. Data cDNA‐derived single‐nucleotide polymorphism (SNP) array genotyping‐by‐sequencing (GBS) were...
Significance Centromeres are the fundamental unit required for segregation of chromosomes during mitosis and meiosis, they defined by centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). In contrast to relatively well-known process de novo assembly CenH3 at centromeres, little is known how actively removed, leading centromere disassembly, an essential biological life a cell. This study describes demonstrating that it occurs via active, proteolytic mechanism, which...
Abstract Motivation: MethylCoder is a software program that generates per-base methylation data given set of bisulfite-treated reads. It provides the option to use either two existing short-read aligners, each with different strengths. accounts for soft-masked alignments and overlapping paired-end outputs in text binary formats addition final alignment SAM format, so common high-throughput sequencing tools can be used on resulting output. more flexible than competitive terms speed memory...
How do epigenetic modifications change across species and how these affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human chimpanzee brain methylomes, but it was limited by lack outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains humans, chimpanzees also rhesus macaques (outgroup) to elucidate changes during...
4-Hydroxyphenylpyruvate dioxygenase (4HPPD) catalyzes the formation of homogentisate (2,5-dihydroxyphenylacetate) from p-hydroxyphenylpyruvate and molecular oxygen. In plants this enzyme activity is involved in two distinct metabolic processes, biosynthesis prenylquinones catabolism tyrosine. We report here biochemical characterization an Arabidopsis 4HPPD compartmentation recombinant protein chlorophyllous tissues. isolated a 1508-bp cDNA with one large open reading frame 1338 bp. Southern...
Phenotypic variation within organisms is driven primarily by genetic diversity. However, there a growing appreciation that epigenetic variation, resulting from multitude of diverse chemical modifications to the DNA and chromatin, can have profound effects on phenotype. Heritable marks persist through meiosis be stably transmitted next generation, in transgenerational inheritance. Importantly, when changes occur near coding genes, affecting their transcriptional state, heritable result...
Leaf senescence is a genetically regulated, highly complex and ordered process. Although it has been extensively studied, the mechanism of leaf not well understood. In this study, we isolated rice mutant, designated as premature (psl), which exhibits early spontaneous lesion mimic phenotype after flowering. The psl mutant displays programmed cell death with elevated accumulation reactive oxygen species (ROS). Molecular genetic analyses revealed that phenotypes were caused by phenylalanine...
Epigenetic variants broaden phenotypic diversity in eukaryotes. Epialleles may also provide a new genetic source for crop breeding, but very few epialleles related to agricultural traits have been identified rice. Here, we Epi-sp, gain-of-function epiallele of the rice ESP (Epigenetic Short Panicle, Os01g0356951), which encodes putative long noncoding RNA. The Epi-sp plants show dense and short panicle phenotype, an agronomically important phenotypes that is inherited semidominant manner. We...