ArticleG3 (Bethesda, Md.)2018
A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes.
Article in G3 (Bethesda, Md.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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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.
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Who cites it
28 citing papers in PubMed, 46 citations in OpenAlex.
- The KMT2F histone methyltransferase interacts with the RNA polymerase I machinery to promote ribosomal RNA transcription.PLoS biology · 2026Article
- Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF.Science advances · 2026Article
- Interpreting the Origins and Functions of Noncoding RNAs From the Ribosomal Genes.Journal of cellular physiology · 2025Review
- Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters.Molecular cell · 2024Article
- Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping.Nature methods · 2024Article
- Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters.bioRxiv : the preprint server for biology · 2024Article
- Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability.NAR genomics and bioinformatics · 2024Article
- The Long Non-Coding RNA MALAT1 Modulates NR4A1 Expression through a Downstream Regulatory Element in Specific Cancer Cell Types.International journal of molecular sciences · 2024Article
- Repression of rRNA gene transcription by endothelial SPEN deficiency normalizes tumor vasculature via nucleolar stress.The Journal of clinical investigation · 2023Article
- Construction and validation of customized genomes for human and mouse ribosomal DNA mapping.The Journal of biological chemistry · 2023Article
- Regulation of RNA Polymerase I Stability and Function.Cancers · 2022Review
- The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans.Life science alliance · 2022Article
- Control of ribosomal RNA synthesis by hematopoietic transcription factors.Molecular cell · 2022Article
- Mechanism of RNA polymerase I selection by transcription factor UAF.Science advances · 2022Article
- Human Cytomegalovirus Infection Elicits Global Changes in Host Transcription by RNA Polymerases I, II, and III.Viruses · 2022Article
- Ribosomal DNA promoter recognition is determined in vivo by cooperation between UBTF1 and SL1 and is compromised in the UBTF-E210K neuroregression syndrome.PLoS genetics · 2022Article
- Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Zooming in: PAGE-Northern Blot Helps to Analyze Anti-Sense Transcripts Originating from Human rIGS under Transcriptional Stress.Non-coding RNA · 2021Article
- Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription.Genes · 2021Review
- The Role of rDNA Clusters in Global Epigenetic Gene Regulation.Frontiers in genetics · 2021Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The combination of Chromatin Immunoprecipitation and Massively Parallel Sequencing, or ChIP-Seq, has greatly advanced our genome-wide understanding of chromatin and enhancer structures. However, its resolution at any given genetic locus is limited by several factors. In applying ChIP-Seq to the study of the ribosomal RNA genes, we found that a major limitation to resolution was imposed by the underlying variability in sequence coverage that very often dominates the protein-DNA interaction profiles. Here, we describe a simple numerical deconvolution approach that, in large part, corrects for this variability, and significantly improves both the resolution and quantitation of protein-DNA interaction maps deduced from ChIP-Seq data. This approach has allowed us to determine the
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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.