A5056282469- Plant Molecular Biology Research
- Plant nutrient uptake and metabolism
- Chromosomal and Genetic Variations
- Genetic Syndromes and Imprinting
- Epigenetics and DNA Methylation
- Legume Nitrogen Fixing Symbiosis
- Plant Reproductive Biology
- Soybean genetics and cultivation
- Plant responses to water stress
- Plant tissue culture and regeneration
- Genomics and Chromatin Dynamics
- Plant Disease Resistance and Genetics
- Genetic Mapping and Diversity in Plants and Animals
- RNA modifications and cancer
- Plant Diversity and Evolution
- Cancer-related gene regulation
- Photosynthetic Processes and Mechanisms
- Bioenergy crop production and management
- Gene Regulatory Network Analysis
- Genetics and Neurodevelopmental Disorders
- Plant Genetic and Mutation Studies
- Interprofessional Education and Collaboration
- Coastal wetland ecosystem dynamics
- Studies on Chitinases and Chitosanases
- Global Health Workforce Issues
Massachusetts Institute of Technology
2015-2024
Whitehead Institute for Biomedical Research
2015-2024
Howard Hughes Medical Institute
2006-2024
Fred Hutch Cancer Center
2006-2011
University of California, Berkeley
2002-2009
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2007
Williams College
2002
DNA methylation is an epigenetic mark associated with transposable element silencing and gene imprinting in flowering plants mammals. In plants, occurs the endosperm, which nourishes embryo during seed development. We have profiled Arabidopsis genome-wide endosperm found that large-scale changes accompany development endosperm-specific expression. Transposable fragments are extensively demethylated endosperm. discovered new imprinted genes by identification of candidates regions reduced...
Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on development. We investigated intraspecific variation imprinting, coupled analysis small RNAs, among three Arabidopsis strains diverse phenotypes. The majority imprinted genes were parentally biased the same manner all...
Genomes must balance active suppression of transposable elements (TEs) with the need to maintain gene expression. In Arabidopsis, euchromatic TEs are targeted by RNA-directed DNA methylation (RdDM). Conversely, demethylation prevents accumulation at genes proximal these TEs. It is unknown how a cellular between and activities achieved. Here we show that both RdDM highly TE major demethylase ROS1. Unexpectedly, in contrast most other genomic targets, expression ROS1 promoted antagonized...
Abstract Imprinting describes the differential expression of alleles based on their parent origin. Deep sequencing RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set ~12,000 that were expressed contained sequence polymorphisms between B73 Mo17 genotypes. The analysis parent-of-origin patterns resulted in identification 100 putative endosperm, including 54 maternally (MEGs) 46 paternally (PEGs). Three these have been...
Differential expression of maternally and paternally inherited alleles a gene is referred to as imprinting, form epigenetic regulation common flowering plants mammals. In plants, imprinting primarily occurs in the endosperm, seed tissue that supports embryo during its growth development. Previously, we demonstrated widespread DNA demethylation at remnants transposable elements accompanies endosperm development subset these methylation changes are associated with imprinting. Here assay...
Significance In many eukaryotes, reproduction involves contributions of genetic material from two parents. At some genes there are parent-of-origin differences in the expression maternal and paternal alleles a gene this is referred to as imprinting. The analysis allele-specific several maize hybrids allowed comprehensive detection imprinted genes. By comparing allelic patterns multiple crosses, it was possible observe variation for imprinting maize. comparison subject plant species reveals...
Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here, we find that transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana lyrata, 24-nt small RNAs reduced transposable elements enriched compared with embryo. We an inverse relationship parent origin sRNAs mRNAs, more likely to be associated maternally...
The contribution of epigenetic variation to phenotypic is unclear. Imprinted genes, because their strong association with modifications, represent an opportunity for the discovery such phenomena. In mammals and flowering plants, a subset genes are expressed from only one parental allele in process called gene imprinting. Imprinting associated differential DNA methylation chromatin modifications between alleles. plants imprinting occurs seed tissue - endosperm. Proper endosperm development...
Abstract Epigenetic states are stably propagated in eukaryotes. In plants, DNA methylation patterns faithfully inherited over many generations but it is unknown how the dynamic activities of cytosine methyltransferases and 5-methylcytosine glycosylases interact to maintain epigenetic homeostasis. Here we show that a methylation-sensing gene regulatory circuit centered on glycosylase required for long-term fidelity Arabidopsis . Disrupting this causes widespread losses abnormal phenotypes...
Seed development is sensitive to parental dosage, with excess maternal or paternal genomes creating reciprocal phenotypes. Paternal genomic frequently results in extensive endosperm proliferation without cellularization and seed abortion. We previously showed that loss of the RNA polymerase IV gene
Application of a low-input chromatin profiling method, CUT&RUN, to FACS-purified Arabidopsis endosperm nuclei generates parental-specific genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility. Endosperm is an essential seed tissue unique epigenetic landscape. During development, differential regulation the maternal paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. In Arabidopsis, landscape on scale...