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Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [green fruit]

ABSTRACT: The biggest advantage of DAP-seq is that it’s capable of measuring the influence of DNA methylation on TF binding, without disturbing of other epigenetic markers. Here, by utilizing DNA affinity purification sequencing, we generated two binding sets which were incubated with DNA libraries that representing methylomes in different developmental stage. And we made the most of our data to predict DNA methylation impact on TF binding in two dimensions: prediction by comparing genome-wide binding signal in motif-matched regions with or without methylation in single stage, and prediction by comparing binding signal variation in motif-matched regions with or without methylation variation.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE172249 | GEO | 2023/06/30

REPOSITORIES: GEO

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Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [red fruit]

Project description:The biggest advantage of DAP-seq is that it’s capable of measuring the influence of DNA methylation on TF binding, without disturbing of other epigenetic markers. Here, by utilizing DNA affinity purification sequencing, we generated two binding sets which were incubated with DNA libraries that representing methylomes in different developmental stage. And we made the most of our data to predict DNA methylation impact on TF binding in two dimensions: prediction by comparing genome-wide binding signal in motif-matched regions with or without methylation in single stage, and prediction by comparing binding signal variation in motif-matched regions with or without methylation variation.

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Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [Bisulfite-seq]

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Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [pre-experiment]

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Base-resolution methylation patterns accurately predict transcription factor bindings in vivo

Project description:Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo. However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. However, technical limitations of these methods prevent them from being applied broadly, especially in clinical settings. We conducted a comprehensive survey involving multiple cell lines, TFs, and methylation types and found that there are intimate relationships between TF binding and methylation level changes around the binding sites. Exploiting the connection between DNA methylation and TF binding, we proposed a novel supervised learning approach to predict TF-DNA interaction using data from base-resolution whole-genome methylation sequencing experiments. We devised beta-binomial models to characterize methylation data around TF binding sites and the background. Along with other static genomic features, we adopted a random forest framework to predict TF-DNA interaction. After conducting comprehensive tests, we saw that the proposed method accurately predicts TF binding and performs favorably versus competing methods. Examine Oct4 genome-wide binding in mouse embryonic stem cells (E14)

2015-03-02 | E-GEOD-65093 | biostudies-arrayexpress

Base-resolution methylation patterns accurately predict transcription factor bindings in vivo

2015-03-02 | GSE65093 | GEO

Project description:Transcription factor (TF) binding specificities (motifs) are essential to the analysis of noncoding DNA and gene regulation. Accurate prediction of TF sequence specificities is critical, because the hundreds of sequenced eukaryotic genomes encompass hundreds of thousands of TFs, and assaying each is currently infeasible. There is ongoing controversy regarding the efficacy of motif prediction methods, as well as the degree of motif diversification among related species. Here, we describe Similarity Regression (SR), a significantly improved method for predicting motifs. We have updated and expanded the Cis-BP database using SR, and validate its predictive capacity with new data from diverse eukaryotic TFs. SR inherently quantifies TF motif evolution, and we show that previous claims of near-complete conservation of motifs between human and Drosophila are grossly inflated, with nearly half the motifs in each species absent from the other. We conclude that diversification in DNA binding motifs is pervasive, and present a new tool and updated resource to study TF diversity and gene regulation across eukaryotes.

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Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [ChIP-seq]

Project description:Here we generated ChIP-seq data of a tomato ERF family TF Sl-ERF_F_4 in red fruit stage and green fruit stage to validate the accuracy of DAP-seq data.

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Mechanisms of active DNA demethylation in human monocytes

Project description:The differentiation of human blood monocytes (MO), the post-mitotic precursors of macrophages (MAC) and dendritic cells (moDC), is accompanied by the active turnover of DNA methylation, but the extent, consequences and mechanisms of DNA methylation changes remain unclear. Here we profile and compare epigenetic landscapes during IL-4/GM-CSF-driven MO differentiation across the genome and detect several thousand regions that are actively demethylated during culture, both with or without accompanying changes in chromatin accessibility or transcription factor (TF) binding. We further identify TF that are globally associated with DNA demethylation processes. While interferon regulatory factor 4 (IRF4) is found to control hallmark DC functions with less impact on DNA methylation, early growth response 2 (EGR2), proves essential for MO differentiation as well as DNA methylation turnover at its binding sites. EGR2 is shown to interact with the 5mC hydroxylase TET2 and its consensus sequences show a characteristic DNA methylation footprint at demethylated sites with or without detectable protein binding. Our findings reveal a novel and essential role for EGR2 as epigenetic pioneer in human MO and suggest that active DNA demethylation can be initiated by TET2 recruiting TF both at stable and transient binding sites.

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BANP is an essential transcription factor that opens chromatin and activates CpG island regulated genes

Project description:While the majority of RNA polymerase II initiation events in mammalian genomes take place within CpG island (CGI) promoters, our understanding of their regulation remains limited. Here we combine single-molecule footprinting with interaction proteomics to identify BANP as a critical CGI regulator and the long sought-after TF that binds the orphan CGCG element in mouse and human. We show that BANP drives the activity of essential metabolic genes in the mouse genome in pluripotent and terminally differentiated cells. However, BANP binding is strongly repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for its absence at aberrantly methylated CGIs in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. Our results establish Banp as a critical activator and put forth a model whereby CGI promoter activity relies on methylation-sensitive TFs capable of chromatin opening.

2021-06-16 | PXD024794 | Pride

DNA binding factors shape the mouse methylome at distal regulatory regions [strand-specific-RNA-seq]

Project description:To gain insights into the interplay between DNA methylation and gene regulation we generated a basepair resolution reference map of the mouse methylome in stem cells and neurons. High genome coverage allowed for a novel quantitative analysis of local methylation states, which identified Low Methylated Regions (LMR) with an average methylation of 30%. These regions are evolutionary conserved, reside outside of CpG islands and distal to promoters. They represent regulatory regions evidenced by their DNaseI hypersensitivity and chromatin marks of enhancer elements. LMRs are occupied by transcription factors (TF) and their reduced methylation requires TF binding while introduction of TF binding sites creates LMRs de novo. This dependency on TF activity is further evident when comparing the methylomes of embryonic stem cells and derived neuronal cells. LMRs present in both cell types are occupied by broadly expressed factors, while LMRs present at only one state are occupied by cell-type specific TFs. Methylome data can thus enhance the prediction of occupied TF binding sites and identification of active regulatory regions genome-wide. Our study provides reference methylomes for the mouse at two cell states, identifies a novel and highly dynamic feature of the epigenome that defines distal regulatory elements and shows that transcription factor binding dynamically shapes mammalian methylomes. Strand specific expression profiling by high throughput sequencing.

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