ArticleNature communications2020
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.bioRxiv : the preprint server for biology · 2026Article
- Strategies for constructing context-specific protein-protein interaction networks.Briefings in bioinformatics · 2026Review
- Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells.Genome research · 2026Article
- Predictive markers for the efficacy of CAR T-cell therapy: the interplay between CAR T-cell fitness and systemic immunity.Blood advances · 2025Review
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts.Nature cell biology · 2024Article
- 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network.Science advances · 2024Article
- Cohesin prevents cross-domain gene coactivation.Nature genetics · 2024Article
- Molecular models of bidirectional promoter regulation.Current opinion in structural biology · 2024Review
- Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy.iScience · 2024Article
- Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome.Genome research · 2023Article
- Article
- Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis.Evolutionary biology · 2023Article
- Human variation in population-wide gene expression data predicts gene perturbation phenotype.iScience · 2022Article
- Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis.Communications biology · 2022Article
- Cotranslational Mechanisms of Protein Biogenesis and Complex Assembly in Eukaryotes.Annual review of biomedical data science · 2022Review
- The limits of human microRNA annotation have been met.RNA (New York, N.Y.) · 2022Article
- Making sense of the linear genome, gene function and TADs.Epigenetics & chromatin · 2022Article
- baredSC: Bayesian approach to retrieve expression distribution of single-cell data.BMC bioinformatics · 2022Article
- A Deep Insight Into Regulatory T Cell Metabolism in Renal Disease: Facts and Perspectives.Frontiers in immunology · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells.
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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.