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Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts

ABSTRACT: Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts

PROVIDER: PRJNA623134 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10180804_1.fastq.gz	Fastqsanger.gz
	SRR10180804_2.fastq.gz	Fastqsanger.gz
	SRR10180805_1.fastq.gz	Fastqsanger.gz
	SRR10180805_2.fastq.gz	Fastqsanger.gz
	SRR10180806_1.fastq.gz	Fastqsanger.gz

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Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [HiChIP]

Project description:Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [HiChIP]

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Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [Hi-C]

Project description:Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [Hi-C]

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Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [HiChIP]

Project description:Silencers active in the Drosophila embryonic mesoderm were identified by reporter assays in dissociated embryonic cells. We find that, despite the presence of ChIP peaks for known transcriptional corepressors and marks of repressed chromatin, the only significantly enriched source of mesodermal silencers is non-mesodermal enhancers. We present evidence that a subset of silencers acts by looping to target promoters.

2019-09-25 | GSE137949 | GEO

Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [Hi-C]

Project description:We generated HiC data from sorted mesodermal and non-mesodermal cells from stage 11-12 Drosophila embryos to explore the distribution of genomic contacts of silencers and non-silencers (identified elsewhere in the manuscript).

2019-09-25 | GSE137955 | GEO

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.

Project description:A major challenge in biology is to understand how complex gene expression patterns are encoded in the genome. While transcriptional enhancers have been studied extensively, few transcriptional silencers have been identified, and they remain poorly understood. Here, we used a novel strategy to screen hundreds of sequences for tissue-specific silencer activity in whole Drosophila embryos. Almost all of the transcriptional silencers that we identified were also active enhancers in other cellular contexts. These elements are bound by more transcription factors than non-silencers. A subset of these silencers forms long-range contacts with promoters. Deletion of a silencer caused derepression of its target gene. Our results challenge the common practice of treating enhancers and silencers as separate classes of regulatory elements and suggest the possibility that thousands or more bifunctional CRMs remain to be discovered in Drosophila and 104-105 in humans.

| S-EPMC6980774 | biostudies-literature

Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-09-25 | GSE137958 | GEO

Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

Project description:Enhancers and silencers often depend on the same transcription factors (TFs) and are imperfectly distinguished from each other by genomic assays of TF binding or chromatin state. To identify sequence features that define enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF CRX and found instances of enhancer, silencer, or no activity. Both enhancers and silencers contain more TF motifs than inactive sequences, but enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. Our results indicate that enhancers contain motifs for a diverse but degenerate collection of TFs, while silencers depend on a smaller and less diverse collection of TFs.

2021-01-30 | GSE165812 | GEO

Histone H4 lysine 20 monomethylation is not a mark of transcriptional silencers

Project description:Silencers are cis-regulatory elements that down-regulate the expression of target genes. While thousands of silencers have been identified experimentally, a predictive chromatin signature has not been found. H4K20me1 was previously reported to be enriched in silencers, but through reanalysis we found that this enrichment is marginal and was primarily driven by the biased selection of elements used in the screen. We generated H4K20me1 ChIP-seq in Drosophila S2 cells and confirmed that H4K20me1 does not mark transcriptional silencers but instead is associated with active transcription. Transcriptional silencers remain a poorly annotated and difficult to predict class of cis-regulatory elements.

2025-02-19 | GSE284058 | GEO

human genome-wide silencers

Project description:Silencers, the yin to enhancers' yang, play a pivotal role in fine-tuning gene expression throughout the genome. However, despite their recognized importance, comprehensive identification of these regulatory elements in the genome is still in its early stages. We developed a method called Ss-STARR-seq to directly determine the activity of silencers in the whole genome. In this study, we applied Ss-STARR-seq to human cell lines K562, LNCaP, and 293T, and identified 134,171, 137,753, and 125,307 silencers on a genome-wide scale, respectively, these silencers function in various cells in a cell-specific manner. Silencers exhibited a substantial enrichment of transcriptional-inhibitory motifs, including REST, and demonstrated overlap with the binding sites of repressor transcription factors within the endogenous environment. Interestingly, H3K27me3 did not reflect silencer activity but facilitated the silencer's inhibitory role on gene expression. Additionally, the silencer did not have any significant histone markers at the genome-wide level. Our findings unveil that aspect-silencers not only transition into enhancers throughout diverse cell lines but also achieve functional conversion with insulators. Regarding to biological effects, knockout experiments underscored the functional redundancy and specificity of silencers in regulating gene expression and cell proliferation. In summary, this study pioneers the elucidation of the genome-wide silencer landscape in human cells, delineates their global regulatory features, and identifies specific silencers influencing cancer cell proliferation.

2024-12-06 | GSE283488 | GEO

smRNAs generated by single-stranded and double-stranded silencers

Project description:To investigate possible smRNAs linked to TMM silencing by single-stranded and double-stranded silencers, we determined sequences of smRNAs by the Illumina high-throughput sequencing platform and compared silencing efficiency of different strategies. We found that single-stranded silencer alone could promote the production of smRNAs. smRNA profiles of 2-week-old wide type seedlings (WT) and different silencers were generated by Illumina Genome Analyzer IIx.

2013-12-23 | E-GEOD-39398 | biostudies-arrayexpress

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