pENCODE: A Plant Encyclopedia of DNA Elements

Lane, A. Kelly; Niederhuth, Chad E.; Ji, Lexiang; Schmitz, Robert J.

doi:10.1146/annurev-genet-120213-092443

Cited by 39 publications

(23 citation statements)

References 143 publications

(180 reference statements)

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“…4 particularly compact genome that is not fully reflective of angiosperm diversity (Arabidopsis Genome 2000, Flowers andPurugganan 2008). The extent of natural variation of mechanisms that lead to epigenomic variation in plants, such as cytosine DNA methylation, is unknown and understanding this diversity is important to understanding the potential of epigenetic variation to contribute to phenotypic variation (Lane, Niederhuth et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Widespread natural variation of DNA methylation within angiosperms

Niederhuth¹,

Bewick²,

Ji³

et al. 2016

Preprint

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To understand the variation in genomic patterning of DNA methylation we compared methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time. These results show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

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Section: Introductionmentioning

confidence: 99%

Widespread natural variation of DNA methylation within angiosperms

Niederhuth¹,

Bewick²,

Ji³

et al. 2016

Preprint

Self Cite

115

226

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“…Epigenomicsis an emerging field that is expanding our abilities to explain observed phenotypic variation through the identification of multiple cellular products such as RNAs, protein: DNA interactions, chromatin modifications, and chromatin accessibility (Lane et al, 2014). DNA methylation is one of the most intensely investigated areas in this field as numerous phenotypes and cellular mechanisms have been explained as a result of changes in DNA methylation.…”

Section: Conclusion and Future Prospectsmentioning

confidence: 99%

“…The first plant reference genome was generated for Arabidopsis thaliana in 2000(Arabidopsis Genome, 2000); since then, more than 40 high-quality plant reference genomes have been published (Goodstein et al, 2012). Utilizing these publicly available reference genomes, the first genome-wide maps of DNA methylation were produced for a number of plant species revealing that all studied plants use DNA methylation (Lane et al, 2014), but not necessarily in the exact same way (Gent et al, 2013; Takuno and Gaut, 2013; West et al, 2014). DNA methylationis one of the most extensively studied chromatin modifications in plants (Niederhuth and Schmitz, 2014).…”

Section: Introductionmentioning

confidence: 99%

Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

Neumann

Schmitz

2015

Molecular Plant

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DNA methylation is a keychromatin modification in plant genomes that ismeiotically and mitotically heritable, and at times is associated with gene expression and morphological variation. Benefitting from the increased availability of high-quality reference genome assemblies and methods to profile single base resolution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methylation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes that once identified can be targeted for reactivation leading to phenotypic variation.

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“…Since CREs are difficult to identify by sequence alone, various Encyclopedia of DNA Elements (ENCODE)-like projects have emerged with the goal of annotating the non-coding, functional genome in a given species by generating spatiotemporal maps of chromatin accessibility, TF occupancy, protein and DNA modifications, and gene expression [4,5]. Although similar datasets are beginning to mature for a number of plant species [6][7][8][9], our knowledge of gene regulation in plants remains limited, and notably in our most economically important crops [10].…”

Section: Introductionmentioning

confidence: 99%

The regulatory landscape of early maize inflorescence development

Parvathaneni

Bertolini

Shamimuzzaman

et al. 2019

Preprint

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The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen-and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profiled accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classified approximately 1.6 percent of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach mapped regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor (TF) occupancy data were used to annotate regulatory factors, such as combinatorial TF binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity revealed new SNP-trait associations in known regulators of inflorescence development as well as new candidates. These analyses provide a comprehensive look into the cisregulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

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pENCODE: A Plant Encyclopedia of DNA Elements

Cited by 39 publications

References 143 publications

Widespread natural variation of DNA methylation within angiosperms

Widespread natural variation of DNA methylation within angiosperms

Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

The regulatory landscape of early maize inflorescence development

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