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  1. Article ; Online: Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.

    Narsai, Reena / Secco, David / Schultz, Matthew D / Ecker, Joseph R / Lister, Ryan / Whelan, James

    The Plant journal : for cell and molecular biology

    2017  Volume 89, Issue 4, Page(s) 805–824

    Abstract: Detailed molecular profiling of Oryza sativa (rice) was carried out to uncover the features that are essential for germination and early seedling growth under anoxic conditions. Temporal analysis of the transcriptome and methylome from germination to ... ...

    Abstract Detailed molecular profiling of Oryza sativa (rice) was carried out to uncover the features that are essential for germination and early seedling growth under anoxic conditions. Temporal analysis of the transcriptome and methylome from germination to young seedlings under aerobic and anaerobic conditions revealed 82% similarity in the transcriptome and no differences in the epigenome up to 24 h. Following germination, significant changes in the transcriptome and DNA methylation were observed between 4-day aerobically and anaerobically grown coleoptiles. A link between the epigenomic state and cell division versus cell elongation is suggested, as no differences in DNA methylation were observed between 24-h aerobically and anaerobically germinating embryos, when there is little cell division. After that, epigenetic changes appear to correlate with differences between cell elongation (anaerobic conditions) versus cell division (aerobic conditions) in the coleoptiles. Re-oxygenation of 3-day anaerobically grown seedlings resulted in rapid transcriptomic changes in DNA methylation in these coleoptiles. Unlike the transcriptome, changes in DNA methylation upon re-oxygenation did not reflect those seen in aerobic coleoptiles, but instead, reverted to a pattern similar to dry seeds. Reversion to the 'dry seed' state of DNA methylation upon re-oxygenation may act to 'reset the clock' for the rapid molecular changes and cell division that result upon re-oxygenation.
    Language English
    Publishing date 2017-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 1088037-9
    ISSN 1365-313X ; 0960-7412
    ISSN (online) 1365-313X
    ISSN 0960-7412
    DOI 10.1111/tpj.13418
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  2. Article: 'Leveling' the playing field for analyses of single-base resolution DNA methylomes.

    Schultz, Matthew D / Schmitz, Robert J / Ecker, Joseph R

    Trends in genetics : TIG

    2012  Volume 28, Issue 12, Page(s) 583–585

    MeSH term(s) Cytosine/metabolism ; DNA Methylation ; Genome ; Sequence Analysis, DNA/methods ; Sequence Analysis, DNA/statistics & numerical data ; Sulfites
    Chemical Substances Sulfites ; Cytosine (8J337D1HZY) ; hydrogen sulfite (OJ9787WBLU)
    Language English
    Publishing date 2012-11-03
    Publishing country England
    Document type Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2012.10.012
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  3. Article ; Online: (with research data) Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.

    Secco, David / Wang, Chuang / Shou, Huixia / Schultz, Matthew D / Chiarenza, Serge / Nussaume, Laurent / Ecker, Joseph R / Whelan, James / Lister, Ryan

    eLife

    2015  Volume 4

    Abstract: Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite ... ...

    Abstract Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.
    MeSH term(s) 5-Methylcytosine/analysis ; Arabidopsis/physiology ; DNA Methylation ; DNA, Plant/chemistry ; DNA, Plant/metabolism ; Gene Expression Regulation ; Genome, Plant ; Oryza/physiology ; Phosphates/metabolism ; Regulatory Elements, Transcriptional ; Sequence Analysis, DNA ; Stress, Physiological
    Chemical Substances DNA, Plant ; Phosphates ; 5-Methylcytosine (6R795CQT4H)
    Language English
    Publishing date 2015-07-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.09343
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  4. Article ; Online: Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis.

    Hua, Zhihua / Pool, John E / Schmitz, Robert J / Schultz, Matthew D / Shiu, Shin-Han / Ecker, Joseph R / Vierstra, Richard D

    Proceedings of the National Academy of Sciences of the United States of America

    2013  Volume 110, Issue 42, Page(s) 16927–16932

    Abstract: Comparisons within expanding sequence databases have revealed a dynamic interplay among genomic and epigenomic forces in driving plant evolution. Such forces are especially obvious within the F-Box (FBX) superfamily, one of the largest and most ... ...

    Abstract Comparisons within expanding sequence databases have revealed a dynamic interplay among genomic and epigenomic forces in driving plant evolution. Such forces are especially obvious within the F-Box (FBX) superfamily, one of the largest and most polymorphic gene families in land plants, where its frequent lineage-specific expansions and contractions provide an excellent model to assess how genetic variation impacted gene function before and after speciation. Previous phylogenetic comparisons based on orthology, diversity, and expression patterns identified three plant FBX groups--Common, Lineage-Specific, and Pseudo(genized)--whose emergences are consistent with genomic drift evolution. Here, we examined this variance within Arabidopsis thaliana by evaluating SNPs for all 877 FBX loci from 432 naturally occurring accessions and their relationships to variations in natural selection, expression, and DNA/histone methylation. In line with their phenotypic importance, Common FBX loci have low polymorphism but high deleterious mutation rates indicative of stringent functional constraints. In contrast, the Lineage-Specific and Pseudo groups are enriched in genes with basal expression and higher SNP density and more correlated with methylation marks (RNA-directed DNA methylation and histone H3K27 trimethylation) that promote transcriptional silencing. Taken together, we propose that reversible epigenomic modifications helped shape FBX gene evolution by transcriptionally suppressing the adverse effects of gene dosage imbalance and harmful FBX alleles that arise during genomic drift, while simultaneously allowing innovations to emerge through epigenomic reprogramming.
    MeSH term(s) Arabidopsis/physiology ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; DNA Methylation/physiology ; Epigenesis, Genetic/physiology ; Evolution, Molecular ; F-Box Proteins/genetics ; F-Box Proteins/metabolism ; Genetic Drift ; Genetic Loci/physiology
    Chemical Substances Arabidopsis Proteins ; F-Box Proteins
    Language English
    Publishing date 2013-09-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1316009110
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  5. Article ; Online: Release factor one is nonessential in Escherichia coli.

    Johnson, David B F / Wang, Chong / Xu, Jianfeng / Schultz, Matthew D / Schmitz, Robert J / Ecker, Joseph R / Wang, Lei

    ACS chemical biology

    2012  Volume 7, Issue 8, Page(s) 1337–1344

    Abstract: Recoding a stop codon to an amino acid may afford orthogonal genetic systems for biosynthesizing new protein and organism properties. Although reassignment of stop codons has been found in extant organisms, a model organism is lacking to investigate the ... ...

    Abstract Recoding a stop codon to an amino acid may afford orthogonal genetic systems for biosynthesizing new protein and organism properties. Although reassignment of stop codons has been found in extant organisms, a model organism is lacking to investigate the reassignment process and to direct code evolution. Complete reassignment of a stop codon is precluded by release factors (RFs), which recognize stop codons to terminate translation. Here we discovered that RF1 could be unconditionally knocked out from various Escherichia coli stains, demonstrating that the reportedly essential RF1 is generally dispensable for the E. coli species. The apparent essentiality of RF1 was found to be caused by the inefficiency of a mutant RF2 in terminating all UAA stop codons; a wild type RF2 was sufficient for RF1 knockout. The RF1-knockout strains were autonomous and unambiguously reassigned UAG to encode natural or unnatural amino acids (Uaas) at multiple sites, affording a previously unavailable model for studying code evolution and a unique host for exploiting Uaas to evolve new biological functions.
    MeSH term(s) Amino Acids/chemistry ; Codon, Terminator ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genetic Techniques ; Genomics ; Green Fluorescent Proteins/metabolism ; Microscopy, Fluorescence/methods ; Models, Genetic ; Mutation ; Peptide Termination Factors/metabolism ; Plasmids/metabolism ; Protein Biosynthesis ; Time Factors
    Chemical Substances Amino Acids ; Codon, Terminator ; Escherichia coli Proteins ; Peptide Termination Factors ; prfA protein, E coli ; Green Fluorescent Proteins (147336-22-9)
    Language English
    Publishing date 2012-06-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/cb300229q
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  6. Article ; Online: Patterns of population epigenomic diversity.

    Schmitz, Robert J / Schultz, Matthew D / Urich, Mark A / Nery, Joseph R / Pelizzola, Mattia / Libiger, Ondrej / Alix, Andrew / McCosh, Richard B / Chen, Huaming / Schork, Nicholas J / Ecker, Joseph R

    Nature

    2013  Volume 495, Issue 7440, Page(s) 193–198

    Abstract: Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA ... ...

    Abstract Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.
    MeSH term(s) Arabidopsis/genetics ; DNA Methylation/genetics ; DNA Transposable Elements/genetics ; Epigenesis, Genetic/genetics ; Epigenomics ; Genetic Variation/genetics ; Genome, Plant/genetics ; Linkage Disequilibrium/genetics ; Pollen/genetics ; Polymorphism, Genetic/genetics ; Quantitative Trait Loci ; RNA, Messenger/analysis ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Seeds/genetics
    Chemical Substances DNA Transposable Elements ; RNA, Messenger ; RNA, Plant
    Language English
    Publishing date 2013-03-06
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature11968
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  7. Article ; Online: Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis.

    Kurihara, Yukio / Schmitz, Robert J / Nery, Joseph R / Schultz, Matthew D / Okubo-Kurihara, Emiko / Morosawa, Taeko / Tanaka, Maho / Toyoda, Tetsuro / Seki, Motoaki / Ecker, Joseph R

    G3 (Bethesda, Md.)

    2012  Volume 2, Issue 4, Page(s) 487–498

    Abstract: Eukaryotes possess several RNA surveillance mechanisms that prevent undesirable aberrant RNAs from accumulating. Arabidopsis XRN2, XRN3, and XRN4 are three orthologs of the yeast 5'-to-3' exoribonuclease, Rat1/Xrn2, that function in multiple RNA decay ... ...

    Abstract Eukaryotes possess several RNA surveillance mechanisms that prevent undesirable aberrant RNAs from accumulating. Arabidopsis XRN2, XRN3, and XRN4 are three orthologs of the yeast 5'-to-3' exoribonuclease, Rat1/Xrn2, that function in multiple RNA decay pathways. XRN activity is maintained by FIERY1 (FRY1), which converts the XRN inhibitor, adenosine 3', 5'-bisphosphate (PAP), into 5'AMP. To identify the roles of XRNs and FRY1 in suppression of non-coding RNAs, strand-specific genome-wide tiling arrays and deep strand-specific RNA-Seq analyses were carried out in fry1 and xrn single and double mutants. In fry1-6, about 2000 new transcripts were identified that extended the 3' end of specific mRNAs; many of these were also observed in genotypes that possess the xrn3-3 mutation, a partial loss-of-function allele. Mutations in XRN2 and XRN4 in combination with xrn3-3 revealed only a minor effect on 3' extensions, indicating that these genes may be partially redundant with XRN3. We also observed the accumulation of 3' remnants of many DCL1-processed microRNA (miRNA) precursors in fry1-6 and xrn3-3. These findings suggest that XRN3, in combination with FRY1, is required to prevent the accumulation of 3' extensions that arise from thousands of mRNA and miRNA precursor transcripts.
    Language English
    Publishing date 2012-04-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.111.001362
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  8. Article ; Online: Active DNA demethylation at enhancers during the vertebrate phylotypic period.

    Bogdanović, Ozren / Smits, Arne H / de la Calle Mustienes, Elisa / Tena, Juan J / Ford, Ethan / Williams, Ruth / Senanayake, Upeka / Schultz, Matthew D / Hontelez, Saartje / van Kruijsbergen, Ila / Rayon, Teresa / Gnerlich, Felix / Carell, Thomas / Veenstra, Gert Jan C / Manzanares, Miguel / Sauka-Spengler, Tatjana / Ecker, Joseph R / Vermeulen, Michiel / Gómez-Skarmeta, José Luis /
    Lister, Ryan

    Nature genetics

    2016  Volume 48, Issue 4, Page(s) 417–426

    Abstract: The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage. However, the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report ... ...

    Abstract The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage. However, the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of enhancers during the phylotypic period in zebrafish, Xenopus tropicalis and mouse. These enhancers are linked to developmental genes that display coordinated transcriptional and epigenomic changes in the diverse vertebrates during embryogenesis. Binding of Tet proteins to (hydroxy)methylated DNA and enrichment of 5-hydroxymethylcytosine in these regions implicated active DNA demethylation in this process. Furthermore, loss of function of Tet1, Tet2 and Tet3 in zebrafish reduced chromatin accessibility and increased methylation levels specifically at these enhancers, indicative of DNA methylation being an upstream regulator of phylotypic enhancer function. Overall, our study highlights a regulatory module associated with the most conserved phase of vertebrate embryogenesis and suggests an ancient developmental role for Tet dioxygenases.
    MeSH term(s) Animals ; Body Patterning ; DNA Methylation ; Enhancer Elements, Genetic ; Epigenesis, Genetic ; Gene Expression Regulation, Developmental ; Mice ; Xenopus ; Zebrafish ; Zebrafish Proteins/genetics ; Zebrafish Proteins/metabolism
    Chemical Substances Zebrafish Proteins
    Language English
    Publishing date 2016-02-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/ng.3522
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  9. Article ; Online: Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation.

    Schultz, Matthew D / He, Yupeng / Whitaker, John W / Hariharan, Manoj / Mukamel, Eran A / Leung, Danny / Rajagopal, Nisha / Nery, Joseph R / Urich, Mark A / Chen, Huaming / Lin, Shin / Lin, Yiing / Jung, Inkyung / Schmitt, Anthony D / Selvaraj, Siddarth / Ren, Bing / Sejnowski, Terrence J / Wang, Wei / Ecker, Joseph R

    Nature

    2016  Volume 530, Issue 7589, Page(s) 242

    Language English
    Publishing date 2016-02-11
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature16179
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  10. Article ; Online: Transgenerational epigenetic instability is a source of novel methylation variants.

    Schmitz, Robert J / Schultz, Matthew D / Lewsey, Mathew G / O'Malley, Ronan C / Urich, Mark A / Libiger, Ondrej / Schork, Nicholas J / Ecker, Joseph R

    Science (New York, N.Y.)

    2011  Volume 334, Issue 6054, Page(s) 369–373

    Abstract: Epigenetic information, which may affect an organism's phenotype, can be stored and stably inherited in the form of cytosine DNA methylation. Changes in DNA methylation can produce meiotically stable epialleles that affect transcription and morphology, ... ...

    Abstract Epigenetic information, which may affect an organism's phenotype, can be stored and stably inherited in the form of cytosine DNA methylation. Changes in DNA methylation can produce meiotically stable epialleles that affect transcription and morphology, but the rates of spontaneous gain or loss of DNA methylation are unknown. We examined spontaneously occurring variation in DNA methylation in Arabidopsis thaliana plants propagated by single-seed descent for 30 generations. We identified 114,287 CG single methylation polymorphisms and 2485 CG differentially methylated regions (DMRs), both of which show patterns of divergence compared with the ancestral state. Thus, transgenerational epigenetic variation in DNA methylation may generate new allelic states that alter transcription, providing a mechanism for phenotypic diversity in the absence of genetic mutation.
    MeSH term(s) Alleles ; Arabidopsis/genetics ; Arabidopsis/metabolism ; DNA Methylation ; DNA Transposable Elements ; DNA, Intergenic ; DNA, Plant/genetics ; DNA, Plant/metabolism ; Dinucleoside Phosphates/metabolism ; Epigenesis, Genetic ; Genes, Plant ; Genetic Variation ; Genome, Plant ; Linear Models ; Mutation ; Polymorphism, Genetic ; Promoter Regions, Genetic ; Transcription, Genetic
    Chemical Substances DNA Transposable Elements ; DNA, Intergenic ; DNA, Plant ; Dinucleoside Phosphates ; cytidylyl-3'-5'-guanosine (2382-65-2)
    Language English
    Publishing date 2011-09-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.1212959
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