Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data

Nordström, Karl; Schmidt, Florian; Gasparoni, Nina; Salhab, Abdulrahman; Gasparoni, Gilles; Kattler, Kathrin; Müller, Fabian; Ebert, Peter; Costa, Ivan G.; Pfeifer, Nico; Lengauer, Thomas; Schulz, Marcel H.; Walter, Jörn

doi:10.1101/547596

Cited by 5 publications

(5 citation statements)

References 76 publications

(74 reference statements)

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“…Several previous studies showed that open chromatin regions identified by DNase I and Tn5 largely overlap in both animal and plant species [6,63,64]. We demonstrate that MH-seq reads cover the majority of the open chromatin regions identified DNase-seq and ATAC-seq.…”

Section: Discussionmentioning

confidence: 49%

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

Zhao

Zhang

et al. 2020

Genome Biol

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Background: Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. Results: We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. Conclusion: MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.

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Section: Discussionmentioning

confidence: 49%

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

Zhao

Zhang

et al. 2020

Genome Biol

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“…The nucleosome occupancy and methylome sequencing assay. For the nucleosome occupancy and methylome sequencing (NOMe-seq) assay, we adapted current protocols 34,56 . A detailed experimental procedure can be found at https:// www.protocols.io/view/nome-seq-of-fixed-cells-brdwm27e.…”

Section: Rna Extraction Real-time Quantitative Pcr and Rna-seq Librar...mentioning

confidence: 99%

Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler

et al. 2022

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How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. Here, to systematically map the regulatory landscape of neural differentiation in the mouse neocortex, we profiled gene expression and chromatin accessibility in single cells and integrated these data with measurements of enhancer activity, DNA methylation and three-dimensional genome architecture in purified cell populations. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. We characterize specific neuronal transcription factors associated with extensive and frequently coordinated changes across multiple epigenetic modalities. In addition, we functionally demonstrate a new role for Neurog2 in directly mediating enhancer activity, DNA demethylation, increasing chromatin accessibility and facilitating chromatin looping in vivo. Our work provides a global view of the gene regulatory logic of lineage specification in the cerebral cortex.

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“…Textbooks describe gene inactivation by a hierarchical chromatin folding from open 10nm fibres to condensed and higher occupied 30nm filaments. Active transcription accompanied by open, accessible chromatin in mammals was highly supported in the last years by many studies of DNA accessibility using ATAC, NOMe, DNAse-Seq or methods free of enzymatic steps like sedimentation velocity centrifugation [30,34,45]. Our data does not support this model for Paramecium Mac chromatin suggesting a totally different chromatin associated mechanism of gene inactivation.…”

Section: Genomic and Epigenomic Paradoxesmentioning

confidence: 52%

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

Drews

Salhab

Karunanithi

et al. 2021

Preprint

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The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin our study characterizes the functional epigenomic organisation necessary for gene regulation and proper PolII activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) revealed no narrow peaks but broad domains along gene bodies, whereas intergenic regions were devoid of nucleosomes. Our data implicates H3K4me3 levels inside ORFs to be the main factor to associate with gene expression and H3K27me3 appears to occur as a bistable domain with H3K4me3 in plastic genes. Surprisingly, silent and lowly expressed genes show low nucleosome occupancy suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Due to a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different to other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data implies that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. This could represent a buffer for paused Pol II along ORFs in absence of elongation factors of higher eukaryotes.

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Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data

Cited by 5 publications

References 76 publications

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

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