Refine regulatory elements across the genome
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus Homo sapiens
PROVIDER: GSE149028 | GEO | 2023/04/20
REPOSITORIES: GEO
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Project description:Proper cell fate determination relies on precise spatial and temporal genome-wide cooperativities among regulatory elements (REs) and their targeted genes. However, the lengths of REs defined by different methods are varied, which indicates sequence redundancy contained and the context of the genome will be unintelligible. To figure this out, we developed a method termed as MAE-seq (Massive Active Enhancers by Sequencing) to experimentally identify functional REs at a 25-bp scale. In this study, more than 626,879 active enhancers are identified in mouse embryonic stem cells. Comparative analysis indicates most of histone modification datasets could be annotated by MAE-Seq loci. Additionally, 35.03% (219,623) are identified as de novo ones without any epigenetic modification. Validation results show that these 25-bp sequences could act as a functional unit, which shows identical or similar expression patterns as the previously defined larger elements. Additionally, we examined the functions of some novel elements that can up-regulate gene activities. By integrating with Hi-C data, over 55.64% novel elements may have distal association with different targeted genes. As an example, we find Cdh1 gene is interacting with one novel and two known REs in mESCs. And their biological effects are investigated via CRISPR-Cas9. It indicates these distal associations can coordinate Cdh1 gene expression and mESCs proliferation. Therefore, our study provides an experimental approach to refine the REs at 25-bp resolution and it will be a great improvement to unscramble the underlying genome context.
2023-01-06 | GSE193494 | GEO
Project description:Enhancer loci identified by ChIP-Seq or other experimental methods occupy hundreds of base pairs on the genome. It is the paradox comparing with the motif analysis, which usually contains only a few or tens nucleotides, achieved by bioinformatics analysis. To address this issue, we develop an experimental method, termed as massive active enhancer sequencing (MAE-Seq), to designate active enhancer sequences from arbitrary sources of 25bp random DNA libraries. These sequences are constructed in a mini-promoter vector with fluorescent reporter. After transfection, positive cells are sorted out and for sequencing. With the results, we successfully identify hundreds known accurate active enhancer sequences as expected. Besides that, large amounts of unmarked regulatory elements (UREs) that might control gene expression without epigenetic features are also been spotted. In conclusion, MAE-Seq would be useful to refine enhancer sequences and precisely annotate the genome in eukaryotes.
2023-03-29 | GSE129453 | GEO
Project description:Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from around 35-55 bp in most eu- and heterochromatin domains (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 bp in nucleosome-depleted regions (NDRs) found at active enhancers and promoters (Schones et al, 2008; Hansen He et al, 2010). To investigate whether and how nucleosome linker DNA affects chromatin recognition by nuclear proteins we performed an additional set of affinity purifications using di-nucleosomes incorporating different DNA linkers. Here, we investigated the effect of a 200 bp di-nucleosome linker DNA represented by scrambled DNA or SV40 enhancer DNA sequence on the nuclear protein binding to di-nucleosome decorated with enhancer-associated modifications, including H3K4me1 and H3K27ac.
2023-12-12 | PXD041443 | Pride
Project description:To identify candidate enhancer elements we analyzed the distribution of two histone modifications associated with enhancers - H3K4me1 and H3K27ac - and one histone modification associated with active transcription - H4 acetylation. ChIP-seq for H3K4me1, H3K27ac and H4ac, and input DNA controls, from 2 cell types (DCs & fibroblasts) under 2 conditions (unstimulated & stimulated)
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Project description:Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing
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Project description:<p>Transcription factor p63 is a key regulator of epidermal keratinocyte proliferation and differentiation. Mutations in the p63 DNA-binding domain are associated with Ectrodactyly Ectodermal Dysplasia Cleft Lip/Palate (EEC) syndrome. Underlying molecular mechanism of these mutations however remain unclear. Here we characterized the transcriptome and epigenome of p63 mutant keratinocytes derived from EEC patients. The transcriptome of p63 mutant keratinocytes deviated from the normal epidermal cell identity. Epigenomic analyses showed an altered enhancer landscape in p63 mutant keratinocytes contributed by loss of p63-bound active enhancers and by unexpected gain of enhancers. The gained enhancers were frequently bound by deregulated transcription factors such as RUNX1. Reversing RUNX1 overexpression partially rescued deregulated gene expression and the altered enhancer landscape. Our findings identify an unreported disease mechanism whereby mutant p63 rewires the enhancer landscape and affects epidermal cell identity, consolidating the pivotal role of p63 in controlling the enhancer landscape of epidermal keratinocytes.</p>
| phs001737 | dbGaP
Project description:To identify candidate enhancer elements we analyzed the distribution of two histone modifications associated with enhancers - H3K4me1 and H3K27ac - and one histone modification associated with active transcription - H4 acetylation.
2012-11-19 | GSE32380 | GEO
Project description:Cis-Regulatory Elements (CREs) precisely control transcription levels, temporal dynamics, and cell-cell variation - often referred to as transcriptional noise. However, the combination of regulatory proteins and epigenetic features necessary to control different transcription attributes is not fully understood. Here, single-cell RNA-seq (scRNA-seq) is conducted during a time course of estrogen treatment to identify genomic predictors of expression timing and noise. We find that multiple active enhancers predict faster temporal responses. Synthetic modulation of enhancer activity verifies that activating enhancers accelerates expression responses, while inhibiting enhancers results in a delayed response. Noise is controlled by a balance of promoter and enhancer activity. Active promoters are found at genes with low noise levels, whereas active enhancers are associated with high noise. Finally, we observe that co-expression across single cells is an emergent property dependent on chromatin looping, timing, and noise levels. Overall, our results indicate a fundamental tradeoff between a gene’s ability to quickly respond to incoming signals and maintain low variation across cells.
2023-10-12 | GSE245120 | GEO
Project description:Cis-Regulatory Elements (CREs) precisely control transcription levels, temporal dynamics, and cell-cell variation - often referred to as transcriptional noise. However, the combination of regulatory proteins and epigenetic features necessary to control different transcription attributes is not fully understood. Here, single-cell RNA-seq (scRNA-seq) is conducted during a time course of estrogen treatment to identify genomic predictors of expression timing and noise. We find that multiple active enhancers predict faster temporal responses. Synthetic modulation of enhancer activity verifies that activating enhancers accelerates expression responses, while inhibiting enhancers results in a delayed response. Noise is controlled by a balance of promoter and enhancer activity. Active promoters are found at genes with low noise levels, whereas active enhancers are associated with high noise. Finally, we observe that co-expression across single cells is an emergent property dependent on chromatin looping, timing, and noise levels. Overall, our results indicate a fundamental tradeoff between a gene’s ability to quickly respond to incoming signals and maintain low variation across cells.
2023-03-15 | GSE227244 | GEO
Project description:Cis-Regulatory Elements (CREs) precisely control transcription levels, temporal dynamics, and cell-cell variation - often referred to as transcriptional noise. However, the combination of regulatory proteins and epigenetic features necessary to control different transcription attributes is not fully understood. Here, single-cell RNA-seq (scRNA-seq) is conducted during a time course of estrogen treatment to identify genomic predictors of expression timing and noise. We find that multiple active enhancers predict faster temporal responses. Synthetic modulation of enhancer activity verifies that activating enhancers accelerates expression responses, while inhibiting enhancers results in a delayed response. Noise is controlled by a balance of promoter and enhancer activity. Active promoters are found at genes with low noise levels, whereas active enhancers are associated with high noise. Finally, we observe that co-expression across single cells is an emergent property dependent on chromatin looping, timing, and noise levels. Overall, our results indicate a fundamental tradeoff between a gene’s ability to quickly respond to incoming signals and maintain low variation across cells.
2023-03-15 | GSE227243 | GEO