ArticleGenome research2019
Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it, 98 citations in OpenAlex.
- Genetic factors contributing to skeletal class III malocclusion: a systematic review and meta-analysis.Clinical oral investigations · 2021Pooled it
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Article
- Crosstalk BetweenCancers · 2026Review
- Article
- ZFP612 controls neuropathic pain through epigenetic repression of Il1rl1 within the silencer-promoter loop in primary sensory neurons of male mice.Nature communications · 2025Article
- Runx2 downregulates Lpl expression through super-silencer formation to alter lipid metabolism in Zhu Schwann cells after nerve injury.Cellular & molecular biology letters · 2025Article
- Super-silencers are crucial for development and carcinogenesis in B cells.Nature communications · 2025Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.Nature communications · 2025Article
- Genome-Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Uncovering the whole genome silencers of human cells via Ss-STARR-seq.Nature communications · 2025Article
- Histone H4 lysine 20 monomethylation is not a mark of transcriptional silencers.bioRxiv : the preprint server for biology · 2025Article
- In silico screening system based on a transcription factors regulatory network only using transcriptomic data.PloS one · 2025Article
- Review
- Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth.Nature structural & molecular biology · 2025Article
- An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation.bioRxiv : the preprint server for biology · 2024Article
- Repressor elements provide insights into tissue development and phenotypes in pigs.Zoological research · 2024Article
- Chromatin structure and 3D architecture define the differential functions of PU.1 regulatory elements in blood cell lineages.Epigenetics & chromatin · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Compared to enhancers, silencers are notably difficult to identify and validate experimentally. In search for human silencers, we utilized H3K27me3-DNase I hypersensitive site (DHS) peaks with tissue specificity negatively correlated with the expression of nearby genes across 25 diverse cell lines. These regions are predicted to be silencers since they are physically linked, using Hi-C loops, or associated, using expression quantitative trait loci (eQTL) results, with a decrease in gene expression much more frequently than general H3K27me3-DHSs. Also, these regions are enriched for the binding sites of transcriptional repressors (such as CTCF, MECOM, SMAD4, and SNAI3) and depleted of the binding sites of transcriptional activators. Using sequence signatures of these regions, we constructed a computational model and predicted approximately 10,000 additional silencers per cell line and demonstrated that the majority of genes linked to these silencers are expressed at a decreased level. Furthermore, single nucleotide polymorphisms (SNPs) in predicted silencers are significantly associated with disease phenotypes. Finally, our results show that silencers commonly interact with enhancers to affect the transcriptional dynamics of tissue-specific genes and to facilitate fine-tuning of transcription in the human genome.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.