ArticleScientific reports2016
Integrative analyses shed new light on human ribosomal protein gene regulation.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
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- A systematic study of HIF1A cofactors in hypoxic cancer cells.Scientific reports · 2022Article
- A revisit to universal single-copy genes in bacterial genomes.Scientific reports · 2022Article
- Drp1 regulates transcription of ribosomal protein genes in embryonic hearts.Journal of cell science · 2022Article
- A systematic study of motif pairs that may facilitate enhancer-promoter interactions.Journal of integrative bioinformatics · 2022Article
- NFAT-dependent and -independent exhaustion circuits program maternal CD8 T cell hypofunction in pregnancy.The Journal of experimental medicine · 2022Article
- Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription.Genes · 2021Review
- Interpretation of deep learning in genomics and epigenomics.Briefings in bioinformatics · 2021Review
- Regulation of ribosomal protein genes: An ordered anarchy.Wiley interdisciplinary reviews. RNA · 2021Review
- An intriguing characteristic of enhancer-promoter interactions.BMC genomics · 2021Article
- High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death.Physiological genomics · 2020Article
- Shared distal regulatory regions may contribute to the coordinated expression of human ribosomal protein genes.Genomics · 2020Article
- Untangling the effects of cellular composition on coexpression analysis.Genome research · 2020Article
- Article
- EPIP: a novel approach for condition-specific enhancer-promoter interaction prediction.Bioinformatics (Oxford, England) · 2019Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Ribosomal protein genes (RPGs) are important house-keeping genes that are well-known for their coordinated expression. Previous studies on RPGs are largely limited to their promoter regions. Recent high-throughput studies provide an unprecedented opportunity to study how human RPGs are transcriptionally modulated and how such transcriptional regulation may contribute to the coordinate gene expression in various tissues and cell types. By analyzing the DNase I hypersensitive sites under 349 experimental conditions, we predicted 217 RPG regulatory regions in the human genome. More than 86.6% of these computationally predicted regulatory regions were partially corroborated by independent experimental measurements. Motif analyses on these predicted regulatory regions identified 31 DNA motifs, including 57.1% of experimentally validated motifs in literature that regulate RPGs. Interestingly, we observed that the majority of the predicted motifs were shared by the predicted distal and proximal regulatory regions of the same RPGs, a likely general mechanism for enhancer-promoter interactions. We also found that RPGs may be differently regulated in different cells, indicating that condition-specific RPG regulatory regions still need to be discovered and investigated. Our study advances the understanding of how RPGs are coordinately modulated, which sheds light to the general principles of gene transcriptional regulation in mammals.
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Registered trials
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