PlantDHS: a database for DNase I hypersensitive sites in plants

Zhang, Tao; Jiang, Jiming

doi:10.1093/nar/gkv962

Cited by 64 publications

(44 citation statements)

References 52 publications

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“…Their increased JSD suggests that inaccessible regions tend to harbor more methylation polymorphisms than accessible regions. This is confirmed by a negative correlation of JSD with DNAse1- [30] and ATAC-seq [31] signal levels ( Fig. 3b, see Fig.…”

Section: Inaccessible Chromatin Accumulates Methylation Polymorphismssupporting

confidence: 61%

Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements

Kartal

Schmid

Grossniklaus

2019

Preprint

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The epigenome modulates the activity of genes and supports the stability of the genome. The epigenome can also contain phenotypically relevant, heritable marks that may vary at the organismic and population level. Such non-genetic standing variation may be relevant to ecological and evolutionary processes. To identify loci susceptible to selection, it is common to profile large populations at the genome scale, yet methods to perform such scans for epigenetic diversity are barely tapped. Here, we develop a scalable, information-theoretic approach to assess epigenome diversity based on Jensen-Shannon divergence (JSD) and demonstrate its practicality by measuring cell type-specific methylation diversity in the model plant Arabidopsis thaliana. DNA methylation diversity tends to be increased in the CG as compared to the non-CG (CHG and CHH) sequence context but the tissue or cell type has an impact on diversity at non-CG sites. Less accessible, more heterochromatic states of chromatin exhibit increased diversity. Genes tend to carry more single-methylation polymorphisms when they harbor gene body-like chromatin signatures and flank transposable elements (TEs). In conclusion, the analysis of DNA methylation with JSD in Arabidopsis demonstrates that the genomic location of a gene dominates its methylation diversity, in particular the proximity to TEs which are increasingly viewed as drivers of evolution. Importantly, the JSD-based approach we implemented here is applicable to any population-level epigenomic data set to analyze variation in epigenetic marks among individuals, tissues, or cells of any organism, including the epigenetic heterogeneity of cells in healthy or diseased organs such as tumors.

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Section: Inaccessible Chromatin Accumulates Methylation Polymorphismssupporting

confidence: 61%

Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements

Kartal

Schmid

Grossniklaus

2019

Preprint

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“…DHS regions, DNase-Seq and MNase-Seq were obtained from PlantDHS.org (Zhang et al, 2016) . Position of the highest DNase signal in flower tissue was used to identify the DHS summit (DHSS) in each DHS region.…”

Section: Dhs Annotationmentioning

confidence: 99%

“…The X-axis is organized as in B. The Y-axis shows the average normalized MNase-seq and DNAse-seq signal from(Zhang et al, 2016) , separated by color. MNase-seq signal is proportional to the nucleosome occupancy, whereas DNase-seq signal denotes NDRs.…”

mentioning

confidence: 99%

Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

Thieffry

Bornholdt

Ivanov

et al. 2019

Preprint

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In animals, transcription by RNA polymerase II initiates bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are rapidly degraded by the nuclear exosome. Similarly, active enhancer regions in animals initiate transcription of exosome-sensitive enhancer RNAs (eRNAs). Previous studies based on nascent RNA approaches concluded that Arabidopsis thaliana does not produce PROMPTs . Here, we used steady-state RNA sequencing methods in mutants defective in nuclear RNA decay, including by the exosome, to reassess the existence of PROMPTs and eRNAs in A. thaliana . While PROMPTs are overall rare in A. thaliana , about 100 clear cases of exosome-sensitive PROMPTs and 113 loci producing eRNA-like transcripts were identified. In addition, we found~200 transcription start sites within 3'-UTR-encoding regions that produce unspliced exosome-sensitive antisense RNAs covering much of the cognate pre-mRNA. A typical representative of this class of RNAs is the previously characterized non-coding RNA controlling the expression of the key seed dormancy regulator, DELAY OF GERMINATION1 . Exosome-sensitive antisense RNAs are overrepresented in transcription factor genes, suggesting a potential for widespread control of gene expression.Lastly, we assess the use of alternative promoters in A. thaliana and compare the accuracy of existing TSS annotations.

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“…for Transposase-Accessible Chromatin (ATAC-SEQ) have been employed in C3 species 88 and provided insight into the patterns of transcription factor binding associated with 89 development (Zhang et al, 2012a;Pajoro et al, 2014;Zhang et al, 2012bZhang et al, , 2016, heat 90 stress (Sullivan et al, 2014) and root cell differentiation (Maher et al, 2017). By carrying out 91…”

Section: Introduction 54mentioning

confidence: 99%

Genome-wide transcription factor binding in leaves from C₃ and C₄ grasses

Burgess

Reyna-Llorens

Stevenson

et al. 2017

Preprint

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The majority of plants use C3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor and Setaria italica as well as C3Brachypodium distachyon. In C4 species, while bundle sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that impact gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.One sentence summaryGenome-wide patterns of transcription factor binding in vivo defined by DNaseI for leaves of C3 and C4 grasses

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PlantDHS: a database for DNase I hypersensitive sites in plants

Cited by 64 publications

References 52 publications

Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements

Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements

Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

Genome-wide transcription factor binding in leaves from C₃ and C₄ grasses

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PlantDHS: a database for DNase I hypersensitive sites in plants

Cited by 64 publications

References 52 publications

Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements

Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements

Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

Genome-wide transcription factor binding in leaves from C3 and C4 grasses

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Genome-wide transcription factor binding in leaves from C₃ and C₄ grasses