166 results on '"Eichten, Steven"'
Search Results
2. Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species
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Waters, Amanda J, Bilinski, Paul, Eichten, Steven R, Vaughn, Matthew W, Ross-Ibarra, Jeffrey, Gehring, Mary, and Springer, Nathan M
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Genetics ,Alleles ,Base Sequence ,Bayes Theorem ,Crosses ,Genetic ,Evolution ,Molecular ,Genetic Variation ,Genetics ,Population ,Genomic Imprinting ,Hybridization ,Genetic ,Molecular Sequence Annotation ,Molecular Sequence Data ,Oryza ,Polymorphism ,Single Nucleotide ,Sequence Analysis ,RNA ,Species Specificity ,Zea mays - Abstract
In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons during reproduction, and in some cases imprinted expression of particular genes may provide a selective advantage such that it is conserved across species. Separate mechanisms for the origin of imprinted expression patterns and maintenance of these patterns may result in substantial variation in the targets of imprinting in different species. Here we present deep sequencing of RNAs isolated from reciprocal crosses of four diverse maize genotypes, providing a comprehensive analysis that allows evaluation of imprinting at more than 95% of endosperm-expressed genes. We find that over 500 genes exhibit statistically significant parent-of-origin effects in maize endosperm tissue, but focused our analyses on a subset of these genes that had >90% expression from the maternal allele (69 genes) or from the paternal allele (108 genes) in at least one reciprocal cross. Over 10% of imprinted genes show evidence of allelic variation for imprinting. A comparison of imprinting in maize and rice reveals that 13% of genes with syntenic orthologs in both species exhibit conserved imprinting. Genes that exhibit conserved imprinting between maize and rice have elevated nonsynonymous to synonymous substitution ratios compared with other imprinted genes, suggesting a history of more rapid evolution. Together, these data suggest that imprinting only has functional relevance at a subset of loci that currently exhibit imprinting in maize.
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- 2013
3. The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress
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Ganguly, Diep R., Crisp, Peter A., Eichten, Steven R., and Pogson, Barry J.
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- 2017
4. Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize
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He, Yan, Wang, Minghui, Dukowic-Schulze, Stefanie, Zhou, Adele, Tiang, Choon-Lin, Shilo, Shay, Sidhu, Gaganpreet K., Eichten, Steven, Bradbury, Peter, Springer, Nathan M., Buckler, Edward S., Levy, Avraham A., Sun, Qi, Pillardy, Jaroslaw, Kianian, Penny M. A., Kianian, Shahryar F., Chen, Changbin, and Pawlowski, Wojciech P.
- Published
- 2017
5. Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in ArabidopsisOPEN
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Crisp, Peter A., Ganguly, Diep R., Smith, Aaron B., Murray, Kevin D., Estavillo, Gonzalo M., Searle, Iain, Ford, Ethan, Bogdanović, Ozren, Lister, Ryan, Borevitz, Justin O., Eichten, Steven R., and Pogson, Barry J.
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- 2017
6. Twenty-four–nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids
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Greaves, Ian K., Eichten, Steven R., Groszmann, Michael, Wang, Aihua, Ying, Hua, Peacock, W. James, and Dennis, Elizabeth S.
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- 2016
7. Genetic Perturbation of the Maize Methylome
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Li, Qing, Eichten, Steven R., Hermanson, Peter J., Zaunbrecher, Virginia M., Song, Jawon, Wendt, Jennifer, Rosenbaum, Heidi, Madzima, Thelma F., Sloan, Amy E., Huang, Ji, Burgess, Daniel L., Richmond, Todd A., McGinnis, Karen M., Meeley, Robert B., Danilevskaya, Olga N., Vaughn, Matthew W., Kaeppler, Shawn M., Jeddeloh, Jeffrey A., and Springer, Nathan M.
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- 2014
8. Correction to: Genome-wide discovery and characterization of maize long non-coding RNAs
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Li, Lin, Eichten, Steven R., Shimizu, Rena, Petsch, Katherine, Yeh, Cheng-Ting, Wu, Wei, Chettoor, Antony M., Givan, Scott A., Cole, Rex A., Fowler, John E., Evans, Matthew M. S., Scanlon, Michael J., Yu, Jianming, Schnable, Patrick S., Timmermans, Marja C. P., Springer, Nathan M., and Muehlbauer, Gary J.
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- 2018
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9. Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations
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Eichten, Steven R., Briskine, Roman, Song, Jawon, Li, Qing, Swanson-Wagner, Ruth, Hermanson, Peter J., Waters, Amanda J., Starr, Evan, West, Patrick T., Tiffin, Peter, Myers, Chad L., Vaughn, Matthew W., and Springer, Nathan M.
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- 2013
10. Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27
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Makarevitch, Irina, Eichten, Steven R., Briskine, Roman, Waters, Amanda J., Danilevskaya, Olga N., Meeley, Robert B., Myers, Chad L., Vaughn, Matthew W., and Springer, Nathan M.
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- 2013
11. B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize
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Eichten, Steven R., Foerster, Juillian M., de Leon, Natalia, Kai, Ying, Yeh, Cheng-Ting, Liu, Sanzhen, Jeddeloh, Jeffrey A., Schnable, Patrick S., Kaeppler, Shawn M., and Springer, Nathan M.
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- 2011
12. Epigenomics: Methylationʼs mark on inheritance
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Eichten, Steven and Borevitz, Justin
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- 2013
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13. Genome-wide discovery and characterization of maize long non-coding RNAs
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Li, Lin, Eichten, Steven R, Shimizu, Rena, Petsch, Katherine, Yeh, Cheng-Ting, Wu, Wei, Chettoor, Antony M, Givan, Scott A, Cole, Rex A, Fowler, John E, Evans, Matthew M S, Scanlon, Michael J, Yu, Jianming, Schnable, Patrick S, Timmermans, Marja C P, Springer, Nathan M, and Muehlbauer, Gary J
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- 2014
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14. Additional file 1: of HOME: a histogram based machine learning approach for effective identification of differentially methylated regions
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Akanksha Srivastava, Karpievitch, Yuliya, Eichten, Steven, Borevitz, Justin, and Lister, Ryan
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Contains supplementary information that includes parameters tested for different DMR finders, Table S1 and S2, and Figure S1 to S7. (PDF 382â kb)
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- 2019
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15. HOME: A histogram based machine learning approach for effective identification of differentially methylated regions
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Srivastava, Akanksha, Karpievitch, Yuliya, Eichten, Steven, Borevitz, Justin, Lister, Ryan, Srivastava, Akanksha, Karpievitch, Yuliya, Eichten, Steven, Borevitz, Justin, and Lister, Ryan
- Abstract
Background The development of whole genome bisulfite sequencing has made it possible to identify methylation differences at single base resolution throughout an entire genome. However, a persistent challenge in DNA methylome analysis is the accurate identification of differentially methylated regions (DMRs) between samples. Sensitive and specific identification of DMRs among different conditions requires accurate and efficient algorithms, and while various tools have been developed to tackle this problem, they frequently suffer from inaccurate DMR boundary identification and high false positive rate. Results We present a novel Histogram Of MEthylation (HOME) based method that takes into account the inherent difference in the distribution of methylation levels between DMRs and non-DMRs to discriminate between the two using a Support Vector Machine. We show that generated features used by HOME are dataset-independent such that a classifier trained on, for example, a mouse methylome training set of regions of differentially accessible chromatin, can be applied to any other organism’s dataset and identify accurate DMRs. We demonstrate that DMRs identified by HOME exhibit higher association with biologically relevant genes, processes, and regulatory events compared to the existing methods. Moreover, HOME provides additional functionalities lacking in most of the current DMR finders such as DMR identification in non-CG context and time series analysis. HOME is freely available at https://github.com/ListerLab/HOME . Conclusion HOME produces more accurate DMRs than the current state-of-the-art methods on both simulated and biological datasets. The broad applicability of HOME to identify accurate DMRs in genomic data from any organism will have a significant impact upon expanding our knowledge of how DNA methylation dynamics affect cell development and differentiation.
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- 2019
16. Global diversity of the Brachypodium species complex as a resource for genome-wide association studies demonstrated for agronomic traits in response to climate
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Wilson, Philippa, Streich, Jared, Murray, Kevin, Eichten, Steven, Cheng, Riyan, Aitken, Nicola, Spokas, Kurt A., Warthmann, Norman, Gordon, Sean P., Vogel, John P., Borevitz, Justin, Wilson, Philippa, Streich, Jared, Murray, Kevin, Eichten, Steven, Cheng, Riyan, Aitken, Nicola, Spokas, Kurt A., Warthmann, Norman, Gordon, Sean P., Vogel, John P., and Borevitz, Justin
- Abstract
The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.
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- 2019
17. RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling
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Crisp, Peter, Smith, Aaron, Ganguly, Diep, Murray, Kevin, Eichten, Steven, Millar, Anthony, Pogson, Barry, Crisp, Peter, Smith, Aaron, Ganguly, Diep, Murray, Kevin, Eichten, Steven, Millar, Anthony, and Pogson, Barry
- Abstract
In plants, the molecular function(s) of the nucleus-localized 5′-3′ EXORIBONUCLEASES (XRNs) are unclear; however, their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using parallel analysis of RNA ends, we documented a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We found that a major consequence of reducing SAL1 or XRN activity was RNA Polymerase II 3′ read-through. This occurred at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis (Arabidopsis thaliana). Read-through is speculated to have a negative effect on transcript abundance; however, we did not observe this. Rather, we identified a strong association between read-through and increased transcript abundance of tandemly orientated downstream genes, strongly correlated with the proximity (less than 1,000 bp) and expression of the upstream gene. We observed read-through in the proximity of 903 genes up-regulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may account directly for up to 23% of genes up-regulated in sal1-8. Using APX2 and AT5G43770 as exemplars, we genetically uncoupled read-through loci from downstream genes to validate the principle of read-through-mediated mRNA regulation, providing one mechanism by which an ostensibly posttranscriptional exoribonuclease that targets uncapped RNAs could modulate gene expression.
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- 2018
18. Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits.
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Eichten, Steven R., Srivastava, Akanksha, Reddiex, Adam J., Ganguly, Diep R., Heussler, Alison, Streich, Jared C., Wilson, Pip B., and Borevitz, Justin O.
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BRACHYPODIUM , *GENETICS , *DNA fingerprinting , *FLOWERING time , *NUCLEOTIDE sequence , *DNA methylation - Abstract
Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation toward heritable phenotypic variation relative to genetic differences. [ABSTRACT FROM AUTHOR]
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- 2020
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19. DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity
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Eichten, Steven, Stuart, Tim, Srivastava, Akanksha, Lister, Ryan, Borevitz, Justin, Eichten, Steven, Stuart, Tim, Srivastava, Akanksha, Lister, Ryan, and Borevitz, Justin
- Abstract
DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon. Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertions or deletions are associated with nearby differential methylation. This study highlights unique relationships between genetic variation and DNA methylation variation within Brachypodium and provides a valuable map of DNA methylation across diverse resequenced accessions of this model cereal species.
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- 2016
20. Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation
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Stuart, Tim, Eichten, Steven R, Cahn, Jonathan, Karpievitch, Yuliya V, Borevitz, Justin O, Lister, Ryan, Stuart, Tim, Eichten, Steven R, Cahn, Jonathan, Karpievitch, Yuliya V, Borevitz, Justin O, and Lister, Ryan
- Abstract
Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.
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- 2016
21. Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics
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Crisp, Peter, Ganguly, Diep, Eichten, Steven, Borevitz, Justin, Pogson, Barry, Crisp, Peter, Ganguly, Diep, Eichten, Steven, Borevitz, Justin, and Pogson, Barry
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- 2016
22. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
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Swanson-Wagner, Ruth A., Eichten, Steven R., Kumari, Sunita, Tiffin, Peter, Stein, Joshua C., Ware, Doreen, and Springer, Nathan M.
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Corn -- Genetic aspects ,Corn -- Physiological aspects ,Variation (Biology) -- Analysis ,Health - Published
- 2010
23. Methylation's mark on inheritance
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Eichten, Steven and Borevitz, Justin
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Methylation -- Genetic aspects ,Genetic research ,Arabidopsis thaliana -- Physiological aspects -- Genetic aspects ,Epigenetic inheritance -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Epigenetic changes to the genome can have heritable effects. An epigenome-wide study of wild plants identifies shared patterns of such modifications and their associations with genetic information. We have long [...]
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- 2013
24. Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stresse
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Eichten, Steven, Springer, Nathan M, Eichten, Steven, and Springer, Nathan M
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- 2015
25. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes
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Li, Qing, Suzuki, Masako, Wendt, Jennifer, Patterson, Nicole, Eichten, Steven, Hermanson, Peter J, Green, Dawn, Jeddeloh, Jeffrey A., Richmond, Todd A, Rosenbaum, Heidi, Burgess, Daniel L, Springer, Nathan M, Greally, John M, Li, Qing, Suzuki, Masako, Wendt, Jennifer, Patterson, Nicole, Eichten, Steven, Hermanson, Peter J, Green, Dawn, Jeddeloh, Jeffrey A., Richmond, Todd A, Rosenbaum, Heidi, Burgess, Daniel L, Springer, Nathan M, and Greally, John M
- Abstract
We present a capture-based approach for bisulfiteconverted DNA that allows interrogation of predefined genomic locations, allowing quantitative and qualitative assessments of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at CG dinucleotides and in non-CG contexts (CHG, CHH) in mammalian and plant genomes. We show the technique works robustly and reproducibly using as little as 500 ng of starting DNA, with results correlating well with whole genome bisulfite sequencing data, and demonstrate that human DNA can be tested in samples contaminated with microbial DNA. This targeting approach will allow cell type-specific designs to maximize the value of 5mC and 5hmC sequencing.
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- 2015
26. Maintenance of pre‐existing DNA methylation states through recurring excess‐light stress.
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Ganguly, Diep R., Crisp, Peter A., Eichten, Steven R., and Pogson, Barry J.
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ARABIDOPSIS thaliana genetics ,EFFECT of stress on plants ,PLANT DNA ,EFFECT of drought on plants ,DNA methylation ,PLANT physiology ,ACCLIMATIZATION (Plants) - Abstract
Abstract: The capacity for plant stress priming and memory and the notion of this being underpinned by DNA methylation‐mediated memory is an appealing hypothesis for which there is mixed evidence. We previously established a lack of drought‐induced methylome variation in Arabidopsis thaliana (Arabidopsis); however, this was tied to only minor observations of physiological memory. There are numerous independent observations demonstrating that photoprotective mechanisms, induced by excess‐light stress, can lead to robust programmable changes in newly developing leaf tissues. Although key signalling molecules and transcription factors are known to promote this priming signal, an untested question is the potential involvement of chromatin marks towards the maintenance of light stress acclimation, or memory. Thus, we systematically tested our previous hypothesis of a stress‐resistant methylome using a recurring excess‐light stress, then analysing new, emerging, and existing tissues. The DNA methylome showed negligible stress‐associated variation, with the vast majority attributable to stochastic differences. Yet, photoacclimation was evident through enhanced photosystem II performance in exposed tissues, and nonphotochemical quenching and fluorescence decline ratio showed evidence of mitotic transmission. Thus, we have observed physiological acclimation in new and emerging tissues in the absence of substantive DNA methylome changes. [ABSTRACT FROM AUTHOR]
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- 2018
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27. Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize.
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Yan He, Minghui Wang, Dukowic-Schulzed, Stefanie, Adele Zhou, Choon-Lin Tiang, Shay Shilo, Sidhu, Gaganpreet K., Eichten, Steven, Bradbury, Peter, Springer, Nathan M., Buckler, Edward S., Levy, Avraham A., Qi Sun, Pillardy, Jaroslaw, Kianian, Penny M. A., Kianian, Shahryar F., Changbin Chen, and Pawlowski, Wojciech P.
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MEIOSIS ,DNA replication ,DNA repair ,DNA methylation ,GENETIC recombination - Abstract
Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly Gypsy retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome. [ABSTRACT FROM AUTHOR]
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- 2017
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28. Inheritance Patterns and Stability of DNA Methylation Variation in Maize Near-Isogenic Lines
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Li, Qing, Eichten, Steven, Hermanson, Peter J, Springer, Nathan M, Li, Qing, Eichten, Steven, Hermanson, Peter J, and Springer, Nathan M
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DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-inherited DMRs provide an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at these DMRs during the generations of the NIL population development. DNA methylation level was associated with local genotypes in nearly all of the >30,000 potential cases of inheritance. The majority of the DMRs were not associated with small RNAs. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits locally (cis) inherited patterns, is highly stable, and does not require active programming by small RNAs for maintenance. DNA methylation may contribute to heritable epigenetic information in many eukaryotic genomes. In this study, we have documented the inheritance patterns and trans-generational stability for nearly 1000 DNA methylation variants in a segregating maize population. At most loci studied, the DNA methylation differences are locally inherited and are not influenced by the other allele or other genomic regions. The inheritance of DNA methylation levels across generations is quite robust with almost no examples of unstable inheritance, suggesting that DNA methylation differences can be quite stably inherited, even in segregating populations.
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- 2014
29. Genomic distribution of H3K9me2 and DNA methylation in a maize genome
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West, Patrick T., Li, Qing, Ji, Lexiang, Eichten, Steven R., Song, Jawon, Vaughn, Matthew W., Schmitz, Robert J., Springer, Nathan M., West, Patrick T., Li, Qing, Ji, Lexiang, Eichten, Steven R., Song, Jawon, Vaughn, Matthew W., Schmitz, Robert J., and Springer, Nathan M.
- Abstract
DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.
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- 2014
30. Consistent and Heritable Alterations of DNA Methylation are Induced by Tissue Culture in Maize
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Stelpflug, Scott C., Eichten, Steven, Hermanson, Peter J, Springer, Nathan M, Kaeppler, Shawn M., Stelpflug, Scott C., Eichten, Steven, Hermanson, Peter J, Springer, Nathan M, and Kaeppler, Shawn M.
- Published
- 2014
31. Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize
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Hirsch, Candice N, Flint-Garcia, Sherry A., Beissinger, Timothy M., Eichten, Steven, Deshpande, Shweta, Barry, Kerrie, McMullen, Michael D., Holland, James B, Buckler, Edward S., Springer, Nathan M, Buell, C. Robin, de Leon, Natalia, Kaeppler, Shawn M., Hirsch, Candice N, Flint-Garcia, Sherry A., Beissinger, Timothy M., Eichten, Steven, Deshpande, Shweta, Barry, Kerrie, McMullen, Michael D., Holland, James B, Buckler, Edward S., Springer, Nathan M, Buell, C. Robin, de Leon, Natalia, and Kaeppler, Shawn M.
- Published
- 2014
32. Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species
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Massachusetts Institute of Technology. Department of Biology, Whitehead Institute for Biomedical Research, Gehring, Mary, Waters, Amanda J., Bilinski, Paul, Eichten, Steven R., Vaughn, Matthew W., Ross-Ibarra, Jeffrey, Springer, Nathan M., Massachusetts Institute of Technology. Department of Biology, Whitehead Institute for Biomedical Research, Gehring, Mary, Waters, Amanda J., Bilinski, Paul, Eichten, Steven R., Vaughn, Matthew W., Ross-Ibarra, Jeffrey, and Springer, Nathan M.
- Abstract
In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons during reproduction, and in some cases imprinted expression of particular genes may provide a selective advantage such that it is conserved across species. Separate mechanisms for the origin of imprinted expression patterns and maintenance of these patterns may result in substantial variation in the targets of imprinting in different species. Here we present deep sequencing of RNAs isolated from reciprocal crosses of four diverse maize genotypes, providing a comprehensive analysis that allows evaluation of imprinting at more than 95% of endosperm-expressed genes. We find that over 500 genes exhibit statistically significant parent-of-origin effects in maize endosperm tissue, but focused our analyses on a subset of these genes that had >90% expression from the maternal allele (69 genes) or from the paternal allele (108 genes) in at least one reciprocal cross. Over 10% of imprinted genes show evidence of allelic variation for imprinting. A comparison of imprinting in maize and rice reveals that 13% of genes with syntenic orthologs in both species exhibit conserved imprinting. Genes that exhibit conserved imprinting between maize and rice have elevated nonsynonymous to synonymous substitution ratios compared with other imprinted genes, suggesting a history of more rapid evolution. Together, these data suggest that imprinting only has functional relevance at a subset of loci that currently exhibit imprinting in maize., National Science Foundation (U.S.) (Grant MCB-1121952)
- Published
- 2014
33. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome
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Muñoz-Amatriaín, María, Eichten, Steven R, Wicker, Thomas, Richmond, Todd A, Mascher, Martin, Steuernagel, Burkhard, Scholz, Uwe, Ariyadasa, Ruvini, Spannagl, Manuel, Nussbaumer, Thomas, Mayer, Klaus FX, Taudien, Stefan, Platzer, Matthias, Jeddeloh, Jeffrey A, Springer, Nathan M, Muehlbauer, Gary J, Stein, Nils, Muñoz-Amatriaín, María, Eichten, Steven R, Wicker, Thomas, Richmond, Todd A, Mascher, Martin, Steuernagel, Burkhard, Scholz, Uwe, Ariyadasa, Ruvini, Spannagl, Manuel, Nussbaumer, Thomas, Mayer, Klaus FX, Taudien, Stefan, Platzer, Matthias, Jeddeloh, Jeffrey A, Springer, Nathan M, Muehlbauer, Gary J, and Stein, Nils
- Abstract
BACKGROUND There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.
- Published
- 2013
34. Epigenomics: Methylation's mark on inheritance
- Author
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Eichten , Steven, Borevitz, Justin, Eichten , Steven, and Borevitz, Justin
- Published
- 2013
35. Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations
- Author
-
Eichten, Steven, Briskine, Roman, Song, Jawon, Li, Qing, Swanson-Wagner, Ruth, Hermanson, Peter J, Waters, Amanda J, Starr, Evan, West, Patrick T, Tiffin, Peter, Myers, Chad L, Vaughn, Matthew W, Springer, Nathan M, Eichten, Steven, Briskine, Roman, Song, Jawon, Li, Qing, Swanson-Wagner, Ruth, Hermanson, Peter J, Waters, Amanda J, Starr, Evan, West, Patrick T, Tiffin, Peter, Myers, Chad L, Vaughn, Matthew W, and Springer, Nathan M
- Abstract
DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, genetic changes such as transposon insertions can also lead to changes in DNA methylation. Genome-wide profiles of DNA methylation for 20 maize (Zea mays) inbred lines were used to discover differentially methylated regions (DMRs). The methylation level for each of these DMRs was also assayed in 31 additional maize or teosinte genotypes, resulting in the discovery of 1966 common DMRs and 1754 rare DMRs. Analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable. A local association scan found that nearly half of the DMRs with common variation are significantly associated with single nucleotide polymorphisms found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the variation in DNA methylation. Analysis of gene expression in the same samples used for DNA methylation profiling identified over 300 genes with expression patterns that are significantly associated with DNA methylation variation. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic changes that are often stably inherited and can influence the expression of nearby genes.
- Published
- 2013
36. Variation in DNA methylation patterns is more common among maize inbreds than among tissues
- Author
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Eichten, Steven, Vaughn, Matthew W, Hermanson, Peter J, Springer, Nathan M, Eichten, Steven, Vaughn, Matthew W, Hermanson, Peter J, and Springer, Nathan M
- Abstract
Chromatin modifications, such as DNA methylation, can provide heritable, epigenetic regulation of gene expression in the absence of genetic changes. A role for DNA methylation in meiotically stable marking of repetitive elements and other sequences has been demonstrated in plants. Methylation of DNA is also proposed to play a role in development through providing a mitotic memory of gene expression states established during cellular differentiation. We sought to clarify the relative levels of DNA methylation variation among different genotypes and tissues in maize (Zea mays L.). We have assessed genomewide DNA methylation patterns in leaf, immature tassel, embryo, and endosperm tissues of two inbred maize lines: B73 and Mo17. There are hundreds of regions of differential methylation present between the two genotypes. In general, the same regions exhibit differential methylation between B73 and Mo17 in each of the tissues that were surveyed. In contrast, there are few examples of tissue-specific DNA methylation variation. Only a subset of regions with tissue-specific variation in DNA methylation show similar patterns in both genotypes of maize and even fewer are associated with altered gene expression levels among the tissues. Our data indicates a limited impact of DNA methylation on developmental gene regulation within maize.
- Published
- 2013
37. B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize
- Author
-
Eichten, Steven, Foerster, Jillian M., de Leon, Natalia, Kai, Ying, Yeh, Cheng-Ting, Liu, Sanzhen, Jeddeloh, Jeffrey A., Schnable, Patrick S., Kaeppler, Shawn M., Springer, Nathan M, Eichten, Steven, Foerster, Jillian M., de Leon, Natalia, Kai, Ying, Yeh, Cheng-Ting, Liu, Sanzhen, Jeddeloh, Jeffrey A., Schnable, Patrick S., Kaeppler, Shawn M., and Springer, Nathan M
- Abstract
Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.
- Published
- 2011
38. Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm
- Author
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Waters, Amanda J, Makarevitch, Irina, Eichten, Steven, Swanson-Wagner, Ruth, Yeh, Cheng-Ting, Xu, Wayne, Schnable, Patrick S., Vaughn, Matthew W, Gehring, Mary, Springer, Nathan M, Waters, Amanda J, Makarevitch, Irina, Eichten, Steven, Swanson-Wagner, Ruth, Yeh, Cheng-Ting, Xu, Wayne, Schnable, Patrick S., Vaughn, Matthew W, Gehring, Mary, and Springer, Nathan M
- Abstract
Imprinting describes the differential expression of alleles based on their parent of origin. Deep sequencing of RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set of ~12, 000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm, including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted, while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice (Oryza sativa) and Arabidopsis thaliana, and at least 10 examples of conserved imprinting between maize and each of the other species were identified.
- Published
- 2011
39. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
- Author
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Swanson-Wagner, Ruth, Eichten, Steven, Kumari, Sunita, Tiffin, Peter, Stein, Joshua C, Ware, Doreen, Springer, Nathan M, Swanson-Wagner, Ruth, Eichten, Steven, Kumari, Sunita, Tiffin, Peter, Stein, Joshua C, Ware, Doreen, and Springer, Nathan M
- Abstract
Individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. Array comparative genomic hybridization (CGH) was used to compare gene content and copy number variation among 19 diverse maize inbreds and 14 genotypes of the wild ancestor of maize, teosinte. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes present in B73, but missing from other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes, and the majority of events are observed in both maize and teosinte, suggesting that these variants predate domestication and that there is not strong selection acting against them. Many of the genes affected by CNV/PAV are either maize specific (thus possible annotation artifacts) or members of large gene families, suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation.
- Published
- 2010
40. Characterization of a novel maize retrotransposon family sprite that shows high levels of variability among maize inbred lines
- Author
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Springer, Nathan M, Eichten, Steven, Smith, A, papa, C. M., Steinway, S, Kaeppler, Shawn M., Springer, Nathan M, Eichten, Steven, Smith, A, papa, C. M., Steinway, S, and Kaeppler, Shawn M.
- Abstract
A novel LTR retrotransposon, SPRITE, was discovered inserted within an intron of the Mo17 allele of Zmet2. This retrotransposon does not affect the expression or function of the Mo17 Zmet2. There are 19 SPRITE elements in the B73 genome including nine with canonical LTRs and 10 with alternate LTR sequences. The individual SPRITE insertions are highly polymorphic in a sample of eight inbred lines. There is evidence for transcription of certain SPRITE elements following exposure with the DNA methylation or histone deacetylases inhibitors 5-aza-2-deoxycytidine or trichostatin A or after long-term tissue culture. The effects of these treatments cause differences in the specific elements that are activated.
- Published
- 2009
41. Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize.
- Author
-
Qing Li, Jawon Song, West, Patrick T., Zynda, Greg, Eichten, Steven R., Vaughn, Matthew W., and Springer, Nathan M.
- Subjects
DNA methylation ,CORN genetics ,EPIGENETICS ,QUANTITATIVE research ,GENE expression - Abstract
DNA methylation is a stable modification of chromatin that can contribute to epigenetic variation through the regulation of genes or transposons. Profiling of DNA methylation in five maize (Zea mays) inbred lines found that while DNA methylation levels for more than 99% of the analyzed genomic regions are similar, there are still 5,000 to 20,000 context-specific differentially methylated regions (DMRs) between any two genotypes. The analysis of identical-by-state genomic regions that have limited genetic variation provided evidence that DMRs can occur without local sequence variation, but they are less common than in regions with genetic variation. Characterization of the sequence specificity of DMRs, location of DMRs relative to genes and transposons, and patterns of DNA methylation in regions flanking DMRs reveals a distinct subset of DMRs. Transcriptome profiling of the same tissue revealed that only approximately 20% of genes with qualitative (on-off) differences in gene expression are associated with DMRs, and there is little evidence for association of DMRs with genes that show quantitative differences in gene expression. We also identify a set of genes that may represent cryptic information that is silenced by DNA methylation in the reference B73 genome. Many of these genes exhibit natural variation in other genotypes, suggesting the potential for selection to act upon existing epigenetic natural variation. This study provides insights into the origin and influences of DMRs in a crop species with a complex genome organization. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
42. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.
- Author
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Qing Li, Masako Suzuki, Wendt, Jennifer, Patterson, Nicole, Eichten, Steven R., Hermanson, Peter J., Green, Dawn, Jeddeloh, Jeffrey, Richmond, Todd, Rosenbaum, Heidi, Burgess, Daniel, Springer, Nathan M., and Greally, John M.
- Published
- 2015
- Full Text
- View/download PDF
43. Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress.
- Author
-
Eichten, Steven R. and Springer, Nathan M.
- Subjects
CORN analysis ,DNA methylation ,FORAGE plants ,METHYLATION ,CORN farming - Abstract
DNA methylation is a chromatin modification that is sometimes associated with epigenetic regulation of gene expression. As DNA methylation can be reversible at some loci, it is possible that methylation patterns may change within an organism that is subjected to environmental stress. In order to assess the effects of abiotic stress on DNA methylation patterns in maize (Zea mays), seeding plants were subjected to heat, cold, and UV stress treatments. Tissue was later collected from individual adult plants that had been subjected to stress or control treatments and used to perform DNA methylation profiling to determine whether there were consistent changes in DNA methylation triggered by specific stress treatments. DNA methylation profiling was performed by immunoprecipitation of methylated DNA followed by microarray hybridization to allow for quantitative estimates of DNA methylation abundance throughout the low-copy portion of the maize genome. By comparing the DNA methylation profiles of each individual plant to the average of the control plants it was possible to identify regions of the genome with variable DNA methylation. However, we did not find evidence of consistent DNA methylation changes resulting from the stress treatments used in this study. Instead, the data suggest that there is a low-rate of stochastic variation that is present in both control and stressed plants. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
44. Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation.
- Author
-
Eichten, Steven R., Schmitz, Robert J., and Springer, Nathan M.
- Subjects
- *
PLANT epigenetics , *PLANT chromatin , *PLANT genetics , *PLANT physiology , *PLANT RNA , *DNA modification & restriction - Abstract
Chromatin modifications and epigenetics may play important roles in many plant processes, including developmental regulation, responses to environmental stimuli, and local adaptation. Chromatin modifications describe biochemical changes to chromatin state, such as alterations in the specific type or placement of histones, modifications of DNA or histones, or changes in the specific proteins or RNAs that associate with a genomic region. The term epigenetic is often used to describe a variety of unexpected patterns of gene regulation or inheritance. Here, we specifically define epigenetics to include the key aspects of heritability (stable transmission of gene expression states through mitotic or meiotic cell divisions) and independence from DNA sequence changes. We argue against genetically equating chromatin and epigenetics; although many examples of epigenetics involve chromafin changes, those chromatin changes are not always heritable or may be influenced by genetic changes. Careful use of the terms chromatin modifications and epigenetics can help separate the biochemical mechanisms of regulation from the inheritance patterns of altered chromatin states. Here, we also highlight examples in which chromatin modifications and epigenetics affect important plant processes. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
45. Inheritance Patterns and Stability of DNA Methylation Variation in Maize Near-Isogenic Lines.
- Author
-
Qing Li, Eichten, Steven R., Hermanson, Peter J., and Springer, Nathan M.
- Subjects
- *
DNA methylation , *PLANT epigenetics , *MOLECULAR structure of chromatin , *EUKARYOTIC cell genetics ,CORN genetics - Abstract
DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-inherited DMRs provide an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at these DMRs during the generations of the NIL population development. DNA methylation level was associated with local genotypes in nearly all of the .30,000 potential cases of inheritance. The majority of the DMRs were not associated with small RNAs. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits locally (cis) inherited patterns, is highly stable, and does not require active programming by small RNAs for maintenance. DNA methylation may contribute to heritable epigenetic information in many eukaryotic genomes. In this study, we have documented the inheritance patterns and trans-generational stability for nearly 1000 DNA methylation variants in a segregating maize population. At most loci studied, the DNA methylation differences are locally inherited and are not influenced by the other allele or other genomic regions. The inheritance of DNA methylation levels across generations is quite robust with almost no examples of unstable inheritance, suggesting that DNA methylation differences can be quite stably inherited, even in segregating populations. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
46. Genome-wide discovery and characterization of maize long non-coding RNAs.
- Author
-
Lin Li, Eichten, Steven R., Shimizu, Rena, Petsch, Katherine, Cheng-Ting Yeh, Wei Wu, Chettoor, Antony M., Givan, Scott A., Cole, Rex A., Fowler, John E., Evans, Matthew M. S., Scanlon, Michael J., Jianming Yu, Schnable, Patrick S., Timmermans, Marja C. P., Springer, Nathan M., and Muehlbauer, Gary J.
- Published
- 2014
- Full Text
- View/download PDF
47. Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons.
- Author
-
Eichten, Steven R., Ellis, Nathanael A., Makarevitch, Irina, Cheng-Ting Yeh, Gent, Jonathan I., Lin Guo, McGinnis, Karen M., Xiaoyu Zhang, Schnable, Patrick S., Vaughn, Matthew W., Dawe, R. Kelly, and Springer, Nathan M.
- Subjects
- *
HETEROCHROMATIN , *HETEROCHROMATIC genes , *RETROTRANSPOSONS , *GENE silencing ,CORN genetics - Abstract
Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (retrotransposons) that are present in moderate to high copy numbers, and many are found in regions near genes, which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into DNA flanking each family of retrotransposons by profiling DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some retrotransposon families exhibit enrichment of heterochromatic marks within 800-1,200 base pairs of insertion sites, while other families exhibit very little evidence for the spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the heterochromatin in low-copy DNA flanking retrotransposons often results from the spreading of silencing marks rather than insertion-site preferences. Genes located near TEs that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of retrotransposon families may act as controlling elements influencing neighboring sequences, while the majority of retrotransposons have little effect on flanking sequences. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
48. B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize1[W][OA].
- Author
-
Eichten, Steven R., Foerster, Jillian M., de Leon, Natalia, Ying Kai, Cheng-Ting Yeh, Liu, Sanzhen, Jeddeloh, Jeffrey A., Schnable, Patrick S., Kaeppler, Shawn M., and Springer, Nathan M.
- Subjects
- *
CORN , *PHENOTYPES , *GENE mapping , *GENOMES , *GENETICS - Abstract
Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci ill 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
49. B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize1[W][OA].
- Author
-
Eichten, Steven R., Foerster, Jillian M., de Leon, Natalia, Ying Kai, Cheng-Ting Yeh, Liu, Sanzhen, Jeddeloh, Jeffrey A., Schnable, Patrick S., Kaeppler, Shawn M., and Springer, Nathan M.
- Subjects
CORN ,PHENOTYPES ,GENE mapping ,GENOMES ,GENETICS - Abstract
Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci ill 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
50. Identification and characterization of DNA methylation variation within maize
- Author
-
Eichten, Steven Richard
- Subjects
- Epigenetics, Genomics, Maize, Methylation, Variation
- Abstract
DNA methylation is a genetic modification known to repress the activity of transposable elements, repetitive sequences, and in some cases genes. Although DNA methylation is often found in common locations across different individuals, evidence has shown that DNA methylation can vary between individuals at certain loci and can therefore have the opportunity to create a unique regulatory environment for the surrounding sequence. Beyond this, the relationship between DNA methylation state and the genetic content of an individual is still unclear. DNA methylation may act as a downstream effect of certain genetic signals, or it may act independently of genetic state as an epigenetic modification. The goal of this thesis is to profile the DNA methylation landscape across maize (Zea mays) and identify the genomic regions that display differential DNA methylation patterns. These regions of differential methylation are then further studied to understand their stability across generations, their influences on gene expression, as well as their connection to the genetic context they are found. The chapters describe the identification of thousands of differentially methylated regions (DMRs) between maize lines. These DMRs are shown to occur throughout the genome and have high stability across generations. In contrast, few DMRs are found across different tissues within the same genotype. DMRs are shown to often be associated with the local genetic variation. This genetic relationship is highlighted, along with the discovery of a mechanism of genetic control by the spreading of DNA methylation from certain retrotransposable elements. These results indicate that DMRs are present in maize and are created through both epigenetic and genetic means.
- Published
- 2013
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