NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule

Requena, Francisco; Asenjo, Helena G; Barturen, Guillermo; Martorell-Marugán, Jordi; Carmona-Sáez, Pedro; Landeira, David

doi:10.1038/s41598-019-44597-2

Cited by 5 publications

(7 citation statements)

References 38 publications

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“…Nuclei extraction and M.CviPI treatment were performed as described previously 90 . Briefly, isolated nuclei were incubated with 200 U of M.CviPI (NEB, M0227L) for 15 min at 37 °C.…”

Section: Methodsmentioning

confidence: 99%

Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

et al. 2021

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CpG islands (CGIs) represent a widespread feature of vertebrate genomes, being associated with ~70% of all gene promoters. CGIs control transcription initiation by conferring nearby promoters with unique chromatin properties. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance is barely known. Here we show that oCGIs are an essential component of poised enhancers (PEs) that augment their long-range regulatory activity and control the responsiveness of their target genes. Using a knock-in strategy in mouse embryonic stem cells (ESCs), we introduced PEs with or without oCGIs within topologically associating domains (TADs) harboring genes with different types of promoters. Analysis of the resulting cell lines revealed that oCGIs act as tethering elements that promote the physical and functional communication between PEs and distally located genes, particularly those with large CGI clusters in their promoters. Therefore, by acting as genetic determinants of gene-enhancer compatibility, CGIs can contribute to gene expression control under both physiological and potentially pathological conditions.

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“…Nuclei extraction and M.CviPI treatment were performed as described previously 90 . Briefly, isolated nuclei were incubated with 200 U of M.CviPI (NEB, M0227L) for 15 min at 37 °C.…”

Section: Methodsmentioning

confidence: 99%

Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

et al. 2021

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“…Line plots, also commonly used to visualize methylation and accessibility status [e.g. as implemented in the aaRon R package ( Statham et al , 2015 ) or the NOMePlot software( Requena et al , 2019 )] either present the status of a single molecule at a time or of a moving population average of statuses across all molecules (Supplementary Fig. S6).…”

Section: Resultsmentioning

confidence: 99%

“…Previously developed methods utilize the output from Bismark but are limited to a relatively small number of reads or provide summary plots rather than site-level data ( Huang et al , 2018 ; Wong et al , 2016 ). Two other such visualization tools are the NOMePlot ( Requena et al , 2019 ) and MethylViewer ( Pardo et al , 2011 ) applications, which were designed to simultaneously visualize CG methylation/GC accessibility patterns. Despite their integrated pipelines, the commonly used ‘lollipop’ plots are not intuitive in highlighting the joint occupancy and methylation states along a continuous DNA strand, especially when considering hundreds or thousands of molecules.…”

Section: Introductionmentioning

confidence: 99%

Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data

et al. 2021

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Summary Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methods that allow profiling of these epigenetic mechanisms in the same reaction and at the single-molecule or single-cell level continue to emerge. However, a challenge lies in jointly visualizing and analyzing the heterogeneous nature of the data and extracting regulatory insight. Here, we present methylscaper, a visualization framework for simultaneous analysis of DNA methylation and chromatin accessibility landscapes. Methylscaper implements a weighted principal component analysis that orders DNA molecules, each providing a record of the chromatin state of one epiallele, and reveals patterns of nucleosome positioning, transcription factor occupancy, and DNA methylation. We demonstrate methylscaper’s utility on a long-read, single-molecule methyltransferase accessibility protocol for individual templates (MAPit-BGS) dataset and a single-cell nucleosome, methylation, and transcription sequencing (scNMT-seq) dataset. In comparison to other procedures, methylscaper is able to readily identify chromatin features that are biologically relevant to transcriptional status while scaling to larger datasets. Availability and Implementation Methylscaper, is implemented in R (version > 4.1) and available on Bioconductor: https://bioconductor.org/packages/methylscaper/, GitHub: https://github.com/rhondabacher/methylscaper/, and Web: https://methylscaper.com. Supplementary information Supplementary data are available at Bioinformatics online.

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“…Finally, the PCR product were cloned into the pGEM-T vector (Promega) and sequenced with M13 reverse primer. NOMe-PCR data was analysed with the NOMePlot web app tool (http://www.landeiralab.ugr.es/soſtware) 94 .…”

Section: Nome-pcrmentioning

confidence: 99%

Orphan CpG islands boost the regulatory activity of poised enhancers and dictate the responsiveness of their target genes

Rada-Iglesias

2020

Preprint

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ARTICLECpG islands (CGIs) represent a distinctive and widespread genetic feature of vertebrate genomes, being associated with ∼70% of all annotated gene promoters1. CGIs have been proposed to control transcription initiation by conferring nearby promoters with unique chromatin properties2–4. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance and mechanism of action are barely known5–7. Here we show that oCGIs are an essential component of poised enhancers (PEs)8, 9 that boost their long-range regulatory activity and dictate the responsiveness of their target genes. Using a CRISPR/Cas9 knock-in strategy in mESC, we introduced PEs with or without oCGIs within topological associating domains (TADs) harbouring genes with different types of promoters. By evaluating the chromatin, topological and regulatory properties of the engineered PEs, we uncover that, rather than increasing their local activation, oCGIs boost the physical and functional communication between PEs and distally located developmental genes. Furthermore, we demonstrate that developmental genes with CpG rich promoters are particularly responsive to PEs and that such responsiveness depends on the presence of oCGIs. Therefore, our work unveils a novel role for CGIs as genetic determinants of the compatibility between genes and enhancers, thus providing major insights into how developmental gene expression programs are deployed under both physiological and pathological conditions10–12.

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NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule

Cited by 5 publications

References 38 publications

Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data

Orphan CpG islands boost the regulatory activity of poised enhancers and dictate the responsiveness of their target genes

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