Works (57)
Updated: April 3rd, 2024 19:46
2023 journal article
Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughout Arabidopsis embryogenesis
FRONTIERS IN PLANT SCIENCE, 14.
author keywords: DNA methylation; CHH methylation; transposable elements; CMT2; RdDM; embryogenesis
TL;DR:
DNA methylome profiling at five stages of Arabidopsis embryogenesis revealed that the gradual increase in mCHH in embryos coincided with the expansion of small RNA expression and regional m CHH spreading to nearby sites at numerous loci, and highlighted the interplay between the length, location, and cytosine frequency of transposons and themCHH machinery in modulating mCHh dynamics during embryogenesis.
(via Semantic Scholar)
www.frontiersin.org (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 3, 2023
2023 article
Embryo-specific epigenetic mechanisms reconstitute the CHH methylation landscape during Arabidopsis embryogenesis
Hsieh, P.-H., Frost, J. M., Choi, Y., Hsieh, T.-F., Zilberman, D., & Fischer, R. L. (2023, April 8).
TL;DR:
It is revealed that embryos are more methylated than leaves at shared CMT2 and RdDM targeting loci, accounting for most embryonic CHH hypermethylation, and similar overlap with vegetative cell DEMETER targets indicates that the chromatin landscape that allows DEMetER access is mirrored in developing embryos, permitting CHH methylation catalysis at the same loci.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: April 9, 2023
2023 journal article
H2A.X promotes endosperm-specific DNA methylation in <i>Arabidopsis thaliana</i>
BMC PLANT BIOLOGY, 23(1).
author keywords: Epigenetics; DNA demethylation; H2A.X; DEMETER; DNA damage response; DNA glycosylase
TL;DR:
The authors' genome-wide methylation analyses suggest that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.
(via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 16, 2023
2023 article
H2A.Xmutants exhibit enhanced DNA demethylation inArabidopsis thaliana
Frost, J. M., Lee, J., Hsieh, P.-H., Lin, S. J. H., Min, Y., Bauer, M., … Fischer, R. L. (2023, January 9).
TL;DR:
It is shown that h2a.x mutants are more sensitive to genotoxic stress, consistent with previous reports, and data indicate that H2A.X is not required for DME function, but is important for DNA methylation homeostasis in the unique chromatin environment of Arabidopsis endosperm.
(via Semantic Scholar)
Source: ORCID
Added: January 10, 2023
2023 journal article
How ambient temperature affects the heading date of foxtail millet (Setaria italica)
Frontiers in Plant Science, 14.
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Source: ORCID
Added: March 4, 2023
2022 article
Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae
Shin, H., Park, J. E., Park, H. R., Choi, W. L., Yu, S. H., Koh, W., … Huh, J. H. (2022, April 28). NEW PHYTOLOGIST, Vol. 4.
author keywords: allopolyploidy; Brassicaceae; DNA methylation; epigenome; genome divergence; hybrid; xBrassicoraphanus
MeSH headings : Brassicaceae / genetics; DNA Methylation / genetics; Genome, Plant; Hybridization, Genetic
TL;DR:
The results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis–trans interactions, which suggests that a certain extent of genome divergence facilitates hybridization across species, which may explain the great diversification and expansion of angiosperms during evolution.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: May 10, 2022
2022 article
Loss of Linker Histone H1 in the Maternal Genome Influences DEMETER-Mediated Demethylation and Affects the Endosperm DNA Methylation Landscape
Hsieh, T.-F., Han, Q., Hung, Y.-H., Zhang, C., Bartels, A., Rea, M., … Xiao, W. (2022, October 20).
Source: ORCID
Added: October 21, 2022
2022 journal article
Loss of linker histone H1 in the maternal genome influences DEMETER-mediated demethylation and affects the endosperm DNA methylation landscape
FRONTIERS IN PLANT SCIENCE, 13.
author keywords: epigenetics; DNA demethylation; gene imprinting; DNA glycosylase; linker histone H1
TL;DR:
Endosperm methylome analysis revealed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-containing nucleosomes are barriers for DME dem methylation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 23, 2023
2021 journal article
Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Liberibacter Pathogens
MICROBIOLOGY SPECTRUM, 9(2).
author keywords: Liberibacter pathogens; Huanglongbing; zebra chip; toxins; prophages; pathogenesis; evolution; comparative genomics
MeSH headings : Bacterial Toxins / chemistry; Bacterial Toxins / genetics; Bacterial Toxins / metabolism; Citrus / microbiology; Endophytes / classification; Endophytes / genetics; Endophytes / physiology; Evolution, Molecular; Genome, Bacterial; Genomics; Liberibacter / chemistry; Liberibacter / classification; Liberibacter / genetics; Liberibacter / physiology; Phylogeny; Plant Diseases / microbiology
TL;DR:
An in-depth comparative phylogenomic analysis of Liberibacter pathogens along with their ancestral nonpathogenic species identified the prophage loci and several novel toxins that are evolutionarily associated with the emergence of the pathogens.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 20, 2021
2021 article
Comparative phylogenomic analysis reveals evolutionary genomic changes and novel toxin families in endophytic Liberibacter pathogens
Tan, Y., Wang, C., Schneider, T., Li, H., Souza, R. F., Tang, X., … Zhang, D. (2021, June 5). (Vol. 6). Vol. 6.
Source: ORCID
Added: June 6, 2021
2021 article
Epigenetic remodeling by DNA glycosylases during rice reproduction
Li, M., Cui, Q., Zhang, X.-Q., & Hsieh, T.-F. (2021, September 6). MOLECULAR PLANT, Vol. 14, pp. 1433–1435.
MeSH headings : Arabidopsis / enzymology; Arabidopsis / genetics; DNA Glycosylases / genetics; DNA Glycosylases / metabolism; DNA Methylation / physiology; DNA, Plant / genetics; DNA, Plant / metabolism; Epigenesis, Genetic; Oryza / enzymology; Oryza / genetics; Plant Development / physiology; Plant Proteins / genetics; Plant Proteins / metabolism
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: August 24, 2021
2020 journal article
Identification of mixed linkage beta-glucan quantitative trait loci and evaluation of AsCslF6 homoeologs in hexaploid oat
CROP SCIENCE, 60(2), 914–933.
Sources: Web Of Science, NC State University Libraries
Added: July 13, 2020
2019 journal article
Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice
Rice, 12(1).
author keywords: Rice; lncRNA; Epigenetic; Panicle; Pseudogene
TL;DR:
It is demonstrated that epigenetic modification of ESP is associated with the regulation of panicle architecture in rice, and the methylation status of 26 CGs and 13 CHGs within a continuous 313-bp region is essential for theregulation of ESP expression.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: April 22, 2019
2019 journal article
Epigenetics Regulates Reproductive Development in Plants
Plants, 8(12), 564.
author keywords: DNA methylation; dynamics; Polycomb group proteins; histone modifications; epigenetics; chromatin; siRNA; RdDM; gametogenesis; seed development
TL;DR:
Recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction are reviewed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Crossref, NC State University Libraries
Added: December 3, 2019
2019 journal article
Mutation in a putative glycosyltransferase-like gene causes programmed cell death and early leaf senescence in rice
Rice, 12(1).
author keywords: Rice; PCD; Glycosylation; Senescence; Ethylene
TL;DR:
Results highlight the importance of protein O-glycosylation in PCD and leaf senescence, and suggest a possible role of OsPSL in ethylene signaling.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: March 4, 2019
2019 journal article
Rice OsPEX1, an extensin-like protein, affects lignin biosynthesis and plant growth
Plant Molecular Biology, 100(1-2), 151–161.
author keywords: Rice; Semi-dwarf; Lignin; Lodging resistance; Leucine-rich repeat extensin-like protein; OsPEX1
MeSH headings : Base Sequence; Gene Expression Regulation, Plant; Genes, Plant; Glycoproteins / genetics; Glycoproteins / metabolism; Lignin / biosynthesis; Mutation / genetics; Oryza / genetics; Oryza / metabolism; Oryza / physiology; Phenotype; Plant Development; Plant Proteins / genetics; Plant Proteins / metabolism; Plant Stems / metabolism; Plants, Genetically Modified
TL;DR:
The identification and characterization of a rice semi-dominant dwarf mutant (pex1) with stiff culm is reported and it is demonstrated that modulating OsPEX1 expression could provide a tool for improving rice lodging resistance.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: June 4, 2019
2019 journal article
The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis
Proceedings of the National Academy of Sciences, 116(35), 17563–17571.
author keywords: gene imprinting; active DNA demethylation; endosperm development; epigenetic reprogramming; Arabidopsis thaliana
MeSH headings : Arabidopsis / classification; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / metabolism; Catalytic Domain; DNA Demethylation; Epigenesis, Genetic; Evolution, Molecular; Gene Expression Regulation, Plant; Heterochromatin / genetics; Heterochromatin / metabolism; Models, Molecular; N-Glycosyl Hydrolases / chemistry; N-Glycosyl Hydrolases / metabolism; Protein Binding; Protein Interaction Domains and Motifs; Trans-Activators / chemistry; Trans-Activators / metabolism
TL;DR:
A bipartite model for DME protein action is proposed and it is suggested that the DME N terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2018 journal article
Dynamic DNA Methylation in Plant Growth and Development
International Journal of Molecular Sciences, 19(7), 2144.
author keywords: DNA methylation; methylome; seed; development; gene expression; dynamics; epigenetics; transposable element; plant
MeSH headings : DNA Methylation; Epigenesis, Genetic; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Plant Development / genetics
TL;DR:
DNA methylation patterns in angiosperms are complex, dynamic, and an integral part of genome diversity after millions of years of evolution.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2018 journal article
Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems
Molecular Plant, 11(2), 245–256.
author keywords: CRISPR; gRNA2.0; MS2-VP64; TALE-VP64; multiplex; transcriptional activation
MeSH headings : CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Gene Expression Regulation, Plant / genetics; Gene Expression Regulation, Plant / physiology; Transcription Factors / genetics; Transcription Factors / metabolism; Transcriptional Activation / genetics; Transcriptional Activation / physiology
TL;DR:
This study revealed that certain endogenous genes are more amenable than others to transcriptional activation, and tightly regulated genes may cause target gene silencing when perturbed by activation probes, and these new tools could be used to investigate gene regulatory networks and their control mechanisms.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2018 chapter
Sexual and Non-sexual Reproduction
In Advances in Botanical Research (Vol. 88, pp. 117–163).
TL;DR:
With the advance in epigenome profiling techniques, dissection of epigenetic-based complex traits, and the development of molecular tools for locus-specific epigenome editing, the effects of epigenetics for underlying phenotypic traits can be unequivocally elucidated.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries, Web Of Science
Added: January 7, 2019
2017 journal article
A naturally occurring conditional albino mutant in rice caused by defects in the plastid-localized OsABCI8 transporter
Plant Molecular Biology, 94(1-2), 137–148.
author keywords: Rice; ABC transporter; Iron transport; Chloroplast development
MeSH headings : Amino Acid Sequence; Arabidopsis / metabolism; Biological Transport; Carrier Proteins / genetics; Carrier Proteins / metabolism; Chloroplasts; Cloning, Molecular; Gene Expression Regulation, Plant / physiology; Iron / metabolism; Mutation; Oryza / genetics; Phylogeny; Plant Proteins / genetics; Plant Proteins / metabolism; Plastids / metabolism
TL;DR:
It is demonstrated that OsABCI8 represents a conserved ABCI protein involved in transition metals transportation and/or homeostasis and suggest an important role of the plastid-localized Os ABCI8 for chloroplast development.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2017 chapter
Epigenetic Reprogramming During Plant Reproduction
In Plant Epigenetics (pp. 405–425).
author keywords: Epigenetics; Reprogramming; Gametogenesis; Reproduction; DNA Methylation; Active DNA Demethylation; Chromatin Remodeling; Transgenerational Inheritance; siRNAs
TL;DR:
In Arabidopsis, gene imprinting is a consequence of a large-scale epigenetic reprogramming via DEMETER-mediated active DNA demethylation during gametogenesis, believed to be critical for the maintenance of trans-generational epigenome integrity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2017 journal article
Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development
Proceedings of the National Academy of Sciences, 114(45), E9730–E9739.
author keywords: seed development; DNA methylation; soybean; Arabidopsis; transposon
MeSH headings : Arabidopsis / genetics; Base Sequence; DNA Methylation / genetics; DNA Methylation / physiology; DNA Transposable Elements / genetics; DNA Transposable Elements / physiology; DNA, Plant / metabolism; Gene Expression Profiling; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks; Gene Silencing; Genes, Plant / genetics; Genome, Plant / genetics; Germination / genetics; Plant Proteins / genetics; Plant Proteins / metabolism; RNA, Plant / genetics; RNA, Plant / metabolism; Seedlings / genetics; Seedlings / metabolism; Seeds / cytology; Seeds / genetics; Seeds / growth & development; Soybeans / genetics
TL;DR:
The results suggest that soybean and Arabidopsis seed methylomes are similar, and that DNA methylation does not play a significant role in regulating many genes important for seed development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2016 journal article
A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement
The Plant Genome, 9(2), 0.
MeSH headings : Avena / genetics; Chromosome Mapping; Chromosomes, Plant / genetics; Genetic Linkage; Genome, Plant / genetics; Genotype; North America; Polymorphism, Single Nucleotide; Polyploidy; Synteny
TL;DR:
A hexaploid oat consensus map is constructed from 12 populations representing 19 parents and represents the most common physical chromosome arrangements in oat.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2016 journal article
A Tug of war for DNA methylation
Nature Plants, 2(11).
Source: NC State University Libraries
Added: August 6, 2018
2016 journal article
Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution
Molecular Biology and Evolution, 33(11), 2947–2959.
author keywords: DNA methylation; human brain evolution; transcriptional divergence; differentially methylated regions; epigenomes
MeSH headings : Animals; Biological Evolution; Brain / physiology; CpG Islands; DNA Methylation; Epigenesis, Genetic; Evolution, Molecular; Female; Genomics; Humans; Macaca mulatta; Male; Pan troglodytes; Transcriptome
TL;DR:
These findings indicate that there is substantial reprogramming of epigenomic landscapes during human brain evolution involving noncoding regions, and their regulatory potential is on par with those of promoter DMRs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2016 journal article
Epigenetics: A tug of war for DNA methylation.
Nature Plants.
MeSH headings : DNA; DNA Methylation; DNA Mismatch Repair; DNA Modification Methylases / genetics; DNA Replication; Epigenesis, Genetic; Epigenomics; Humans; Methylation; Warfare
TL;DR:
Thousands of RNA-directed DNA methylation target sites masked by the active removal of methylated cytosines by a demethylating enzyme are uncovered.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: September 13, 2019
2016 journal article
FIE, a nuclear PRC2 protein, forms cytoplasmic complexes inArabidopsis thaliana
Journal of Experimental Botany, 67(21), 6111–6123.
author keywords: Cytoplasm; FIE; MEA; PcG; Polycomb complex; PRC2
MeSH headings : Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Chromatin / metabolism; Chromatography, Gel; Cytoplasm / metabolism; Immunoprecipitation; Microscopy, Confocal; Plants, Genetically Modified; Polycomb Repressive Complex 2; Repressor Proteins / metabolism
TL;DR:
FIE, a WD-40 subunit of the Arabidopsis PRC2 complexes known to take part in H3K27 methylation of nuclear chromatin, is also localized in cytoplasmic complexes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2015 journal article
A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation
Plant Physiology, 169(2), 971–985.
MeSH headings : Arabidopsis / genetics; Bacterial Proteins / genetics; CRISPR-Associated Protein 9; Clustered Regularly Interspaced Short Palindromic Repeats; DNA Methylation; DNA, Bacterial; Endonucleases / genetics; Gene Expression Regulation, Plant; Genetic Engineering / methods; Genome, Plant; Genomic Imprinting; Mutagenesis; Oryza / genetics; Plant Proteins / genetics; Plants, Genetically Modified; Promoter Regions, Genetic; RNA, Guide, Kinetoplastida; Tobacco / genetics
TL;DR:
A comprehensive molecular toolbox for multifaceted CRISPR/Cas9 applications in plants is developed and implemented, with a full suite of capabilities, including multiplexed gene editing and transcriptional activation or repression of plant endogenous genes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
2015 journal article
Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm
PLOS ONE, 10(2), e0117431.
Ed(s): M. Sun
MeSH headings : Alleles; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Base Sequence; DNA Methylation; Endosperm / metabolism; F-Box Proteins / genetics; Gene Expression Regulation, Plant; Genomic Imprinting; Polycomb-Group Proteins / metabolism; Transgenes / genetics; Ubiquitin-Protein Ligases / genetics
TL;DR:
It is reported that UPWARD CURly LEAF1 (UCL1), a gene encoding an E3 ligase that degrades the CURLY LEAF (CLF) polycomb protein, is a PEG, suggesting that divergent mechanisms for the regulation of PEGs evolved in Arabidopsis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2015 chapter
Whole-Genome DNA Methylation Profiling with Nucleotide Resolution
In Methods in Molecular Biology (Vol. 1284, pp. 27–40).
author keywords: 5-Methylcytosine; Epigenetics; SPRI; DNA methylome; Bisulfite conversion; Next-gen sequencing
MeSH headings : DNA Methylation; Epigenesis, Genetic; Epigenomics / methods; Gene Expression Profiling / methods; Genome; Genomic Library; High-Throughput Nucleotide Sequencing / methods
TL;DR:
Gene-specific methylation analysis by sequencing of bisulfite-treated genomic DNA has been instrumental in understanding how DNA methylation affects gene transcription, and techniques have been developed for genome-wide 5mC detection, and complete methylome at single base resolution has been reported for several organisms, providing unprecedented details on the dynamic nature ofDNA methylation during development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2014 journal article
The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes
Proceedings of the National Academy of Sciences, 111(45), 16166–16171.
author keywords: centromere disassembly; heterochromatin decondensation; chromosome dynamics; rDNA activation; pollen tip growth
MeSH headings : ATPases Associated with Diverse Cellular Activities; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Cycle Proteins / genetics; Cell Cycle Proteins / metabolism; Cell Nucleolus / genetics; Cell Nucleolus / metabolism; Centromere / genetics; Centromere / metabolism; Chromosomes, Plant / genetics; Chromosomes, Plant / metabolism; DNA, Plant / genetics; DNA, Plant / metabolism; DNA, Ribosomal / genetics; DNA, Ribosomal / metabolism; Genetic Loci / physiology; Heterochromatin / genetics; Heterochromatin / metabolism; Humans; Molecular Chaperones / genetics; Molecular Chaperones / metabolism; Pollen / genetics; Pollen / metabolism; RNA, Plant / biosynthesis; RNA, Plant / genetics; RNA, Ribosomal / biosynthesis; RNA, Ribosomal / genetics; Ribosomes / genetics; Ribosomes / metabolism; Sumoylation / physiology
TL;DR:
The results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2013 chapter
Epigenetic Control of Seed Gene Imprinting
In Seed Genomics (pp. 63–82).
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2013 journal article
Heritable Epigenetic Variation and its Potential Applications for Crop Improvement
Plant Breeding and Biotechnology, 1(4), 307–319.
TL;DR:
There is a potential for epigenetics to play a role in crop improvement, including regulation of transgene expression and creation of novel epialleles, and how the studies from two epigenetic populations are rapidly increasing the authors' understanding of epigenetic diversity is discussed.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2012 journal article
Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes
Science, 337(6100), 1360–1364.
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; DNA Methylation; DNA Transposable Elements / genetics; DNA, Plant / metabolism; Endosperm / cytology; Endosperm / genetics; Gene Expression Regulation, Plant; Gene Silencing; Germ Cells, Plant / metabolism; N-Glycosyl Hydrolases / genetics; N-Glycosyl Hydrolases / metabolism; RNA, Plant / metabolism; Trans-Activators / genetics; Trans-Activators / metabolism
TL;DR:
It is demonstrated that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2011 journal article
MethylCoder: software pipeline for bisulfite-treated sequences
Bioinformatics, 27(17), 2435–2436.
MeSH headings : Cytosine / metabolism; DNA / chemistry; DNA / metabolism; DNA Methylation; Genomics / methods; Sequence Alignment / methods; Sequence Analysis, DNA; Software; Sulfites
TL;DR:
MethylCoder is a software program that generates per-base methylation data given a set of bisulfite-treated reads and provides the option to use either of two existing short-read aligners, each with different strengths.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2011 journal article
Regulation of imprinted gene expression in Arabidopsis endosperm
Proceedings of the National Academy of Sciences, 108(5), 1755–1762.
author keywords: epigenetics; gene imprinting; angiosperm reproduction; DNA demethylation
MeSH headings : Arabidopsis / embryology; Arabidopsis / genetics; DNA Methylation; Gene Expression Regulation, Plant; Genes, Plant; Genomic Imprinting; Mutation; Ovule; Pollen; Reverse Transcriptase Polymerase Chain Reaction; Seeds / metabolism
TL;DR:
The results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2009 journal article
Genome-Wide Demethylation of Arabidopsis Endosperm
Science, 324(5933), 1451–1454.
MeSH headings : Arabidopsis / embryology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; DNA Methylation; DNA Transposable Elements; DNA, Plant / genetics; DNA, Plant / metabolism; Gene Expression Regulation, Plant; Gene Silencing; Genes, Plant; Genome, Plant; Genomic Imprinting; N-Glycosyl Hydrolases / genetics; N-Glycosyl Hydrolases / metabolism; RNA Interference; RNA, Small Interfering / genetics; RNA, Small Interfering / metabolism; Repetitive Sequences, Nucleic Acid; Seeds / genetics; Seeds / growth & development; Trans-Activators / genetics; Trans-Activators / metabolism; Transcription Initiation Site
TL;DR:
Almost the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences, indicating that CG demethylation is specific to maternal sequences.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2008 journal article
Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: Implications for somatic embryogenesis
Proceedings of the National Academy of Sciences, 105(8), 3151–3156.
author keywords: seed development; totipotency
TL;DR:
LEC2 causes rapid changes in auxin responses and induces cellular differentiation characteristic of the maturation phase of embryogenesis, and the relevance of these changes to the ability of LEC2 to promote somatic embryogenesis is discussed.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2008 journal article
Cellular Programming of Plant Gene Imprinting
Cell, 132(5), 735–744.
MeSH headings : Animals; Epigenesis, Genetic; Gene Expression Regulation, Plant; Genes, Plant; Genomic Imprinting; Histone Code; Magnoliopsida / cytology; Magnoliopsida / genetics; Magnoliopsida / physiology
TL;DR:
Gene imprinting, the differential expression of maternal and paternal alleles, independently evolved in mammals and in flowering plants to prevent parthenogenetic development of the endosperm.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2007 journal article
Endosperm gene imprinting and seed development
Current Opinion in Genetics & Development, 17(6), 480–485.
MeSH headings : DNA Methylation; Gene Silencing; Genomic Imprinting; Histones / metabolism; Models, Genetic; Plant Development; Plants / embryology; Plants / genetics; Polycomb-Group Proteins; Repressor Proteins / genetics; Repressor Proteins / physiology; Seeds / genetics; Seeds / growth & development
TL;DR:
Endosperm gene imprinting can be uncoupled from seed development when fertilization of the central cell is prevented, thereby preventing parthenogenic development of the endosperm.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2007 chapter
Genomic Imprinting in Arabidopsis thaliana and Zea mays
In Plant Cell Monographs (pp. 219–239).
TL;DR:
Locus-specific imprinting is found in both maize and Arabidopsis and mechanisms by which the parental alleles are distinguished from one another are focused on.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2006 journal article
DEMETER DNA Glycosylase Establishes MEDEA Polycomb Gene Self-Imprinting by Allele-Specific Demethylation
Cell, 124(3), 495–506.
MeSH headings : Alleles; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Base Pair Mismatch; Base Sequence; DNA Methylation; DNA, Plant / genetics; DNA, Plant / metabolism; Escherichia coli / genetics; Escherichia coli / metabolism; Gene Silencing; Genes, Plant; Genomic Imprinting; Models, Genetic; N-Glycosyl Hydrolases / genetics; N-Glycosyl Hydrolases / metabolism; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Trans-Activators / genetics; Trans-Activators / metabolism
TL;DR:
DME is responsible for endosperm maternal-allele-specific hypomethylation at the MEA gene, which establishes MEA imprinting by removing 5-methylcytosine to activate the maternal allele and is subsequently maintained in theendosperm by maternal MEA silencing the paternal allele.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2006 journal article
Patenting Applied to Genetic Sequence Information
Biotechnology and Genetic Engineering Reviews, 23(1), 317–330.
MeSH headings : Databases, Genetic / legislation & jurisprudence; Genetic Engineering / legislation & jurisprudence; Humans; Ownership / legislation & jurisprudence; Patents as Topic / legislation & jurisprudence; United States
Sources: Crossref, NC State University Libraries
Added: January 4, 2020
2005 journal article
BIOLOGY OF CHROMATIN DYNAMICS
Annual Review of Plant Biology, 56(1), 327–351.
author keywords: chromatin remodeling; epigenetic inheritance; histone modification; DNA methylation; RNA interference
MeSH headings : Chromatin / chemistry; Chromatin / genetics; Chromatin / physiology; DNA Methylation; Epigenesis, Genetic; Histones / metabolism; RNA Interference
TL;DR:
A large number of factors and protein complexes are now known to be involved in regulating the dynamic states of chromatin structure, and their biological functions and molecular mechanisms are beginning to be revealed.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2003 journal article
From flour to flower: how Polycomb group proteins influence multiple aspects of plant development
Trends in Plant Science, 8(9), 439–445.
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Flour; Flowers / physiology; Gene Expression Regulation, Developmental; Plant Development; Plant Proteins / genetics; Plant Proteins / physiology; Plants / genetics; Polycomb-Group Proteins; Repressor Proteins / genetics; Repressor Proteins / physiology; Reproduction
TL;DR:
Polycomb group (PcG) proteins form a cellular memory system that maintains the repressed state of homeotic gene expression and might function through a similar biochemical mechanism owing to their conserved structural and functional relationship to animal PcG proteins.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2003 chapter
Genomic analysis of Arabidopsis gene expression in response to a systemic fungicide
In Genomics of Plants and Fungi (pp. 251–268). CRC Press.
Source: ORCID
Added: September 13, 2019
2002 journal article
Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily
Plant Molecular Biology, 50(2), 237–248.
author keywords: DNA-binding domain; shoot meristem; transcriptional activation
MeSH headings : Amino Acid Sequence; Arabidopsis / genetics; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Base Sequence; Binding Sites / genetics; Cloning, Molecular; DNA, Complementary / chemistry; DNA, Complementary / genetics; DNA, Complementary / isolation & purification; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Electrophoretic Mobility Shift Assay; Gene Expression; In Situ Hybridization; Molecular Sequence Data; Multigene Family / genetics; Plant Proteins / genetics; Plant Proteins / metabolism; Protein Binding; RNA, Messenger / genetics; RNA, Messenger / metabolism; Saccharomyces cerevisiae / genetics; Seeds / genetics; Sequence Alignment; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Trans-Activators / genetics
TL;DR:
In vivo assays in yeast demonstrate that AtNAM encodes a transcription factor and that the NAC domain includes a specific DNA binding domain (DBD), which potentially folds into a helix-turn-helix motif that specifically binds to the CaMV 35S promoter.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2001 journal article
Gene expression in the developing mouse retina by EST sequencing and microarray analysis.
Nucleic Acids Research.
MeSH headings : Animals; Cell Cycle Proteins / genetics; DNA, Complementary / genetics; Expressed Sequence Tags; GAP-43 Protein / genetics; Gene Expression Profiling; Gene Expression Regulation, Developmental; Mice; Oligonucleotide Array Sequence Analysis / methods; Retina / embryology; Retina / metabolism; Signal Transduction / genetics; Transcription Factors / genetics; Transcription, Genetic
TL;DR:
A sequence analysis of an E14.5 retinal cDNA library of mice revealed a potential regulatory linkage between the transcription factor Brn-3b and expression of GAP-43, a protein associated with axon growth, which will be a valuable platform for gene expression profiling and a new source for gene discovery.
(via Semantic Scholar)
Source: ORCID
Added: September 13, 2019
2001 journal article
Identification of estrogen-induced genes downregulated by AhR agonists in MCF-7 breast cancer cells using suppression subtractive hybridization
Gene, 262(1-2), 207–214.
author keywords: antiestrogens; gene expression
MeSH headings : Animals; Anticarcinogenic Agents / pharmacology; Blotting, Northern; Breast Neoplasms / drug therapy; Breast Neoplasms / genetics; Down-Regulation; Estradiol / metabolism; Estradiol / pharmacology; Estrogens / metabolism; Estrogens / pharmacology; Female; Gene Expression Profiling / methods; Gene Expression Regulation, Neoplastic / drug effects; Humans; In Situ Hybridization / methods; Indoles / pharmacology; Polychlorinated Dibenzodioxins / pharmacology; Receptors, Aryl Hydrocarbon / agonists; Receptors, Aryl Hydrocarbon / genetics; Receptors, Aryl Hydrocarbon / metabolism; Tumor Cells, Cultured
TL;DR:
SSH has identified a diverse spectrum of new genes that are affected by inhibitory AhR-ER crosstalk and among this group are a subset of genes that may be critical for the in vivo antitumorigenic effects of AhR agonists.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
2000 journal article
The use of RT-PCR differential display in single-celled organisms and plant tissues
Differential Display: A Practical Approach, (224), 83.
Source: ORCID
Added: September 13, 2019
1999 journal article
Characterization and subcellular compartmentation of recombinant 4-hydroxyphenylpyruvate dioxygenase from Arabidopsis in transgenic tobacco.
Plant Physiology.
MeSH headings : 4-Hydroxyphenylpyruvate Dioxygenase / genetics; 4-Hydroxyphenylpyruvate Dioxygenase / metabolism; Amino Acid Sequence; Arabidopsis / enzymology; Arabidopsis / genetics; Base Sequence; Cloning, Molecular; DNA Primers / genetics; DNA, Complementary / genetics; DNA, Plant / genetics; Immunohistochemistry; Molecular Sequence Data; Plants, Genetically Modified; Plants, Toxic; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Sequence Homology, Amino Acid; Subcellular Fractions / enzymology; Tobacco / genetics
TL;DR:
The molecular and biochemical characterization of an Arabidopsis 4HPPD and the compartmentation of the recombinant protein in chlorophyllous tissues are reported and southern analysis strongly suggested that this 4HP PD is encoded by a single-copy gene.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: September 13, 2019
1998 chapter
Plant P-Hydroxyphenylpyruvate Dioxygenase: A Target for New Bleaching Herbicides
In Photosynthesis: Mechanisms and Effects (pp. 3861–3864).
TL;DR:
The biochemical characterisation of carrot recombinant HPPD, and the molecular characterisation and the sub-cellular localization of the corresponding enzyme from A. thaliana are reported here.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 13, 2019
1997 journal article
Molecular approaches to identify novel genes expressed in Arabidopsis thaliana.
SAAS Bulletin, Biochemistry and Biotechnology.
Source: ORCID
Added: September 13, 2019
1996 conference paper
Homeobox genes expressed in Arabidopsis embryo
PLANT PHYSIOLOGY, 111(2), 733–733.
Event: AMER SOC PLANT PHYSIOLOGISTS 15501 MONONA DRIVE, ROCKVILLE, MD 20855
Source: ORCID
Added: September 13, 2019
1996 journal article
Identification of novel mRNAs in immature seeds of Arabidopsis thaliana.
SAAS Bulletin, Biochemistry and Biotechnology.
Source: ORCID
Added: September 13, 2019
1991 journal article
Identification of phospholipase activities in the exotoxin of Edwardsiella tarda
Reports On Fish Disease Research, 29, 39–46.
Source: NC State University Libraries
Added: January 13, 2020
Employment
Updated: December 3rd, 2019 09:16
2018 - present
North Carolina State University Kannapolis, NC, US
Associate Professor
Department of Plant and Microbial Biology
2012 - 2018
North Carolina State University Kannapolis, NC, US
Assistant Professor
Plant and Microbial Biology
2007 - 2012
University of California Berkeley Berkeley, CA, US
Research Specialist
Plant and Microbial Biology
2001 - 2007
University of California Berkeley Berkeley, CA, US
Postgraduate Researcher
Plant and Microbial Biology
1998 - 2001
Texas A&M University College Station, Texas, US
Postdoctoral Research Associate
Biology
Education
Updated: July 3rd, 2019 16:37
1991 - 1998
Texas A&M University College Station, Texas, US
PhD
Biology
1983 - 1987
National Tsing-Hua University Hsinchu , TW
BS
Chemistry
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