ArticleiScience2018
RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome.
Article in iScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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.
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Who cites it
25 citing papers in PubMed.
- Nuclear speckle dynamics are controlled by polyphosphate inhibition of CLK proteins.Nucleic acids research · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- RBBP6 anchors pre-mRNA 3' end processing to nuclear speckles for efficient gene expression.Molecular cell · 2025Article
- Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency.Science advances · 2024Article
- Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.Nature communications · 2023Article
- Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle.Retrovirology · 2023Review
- Phase Separation: Direct and Indirect Driving Force for High-Order Chromatin Organization.Genes · 2023Review
- Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study.Nucleus (Austin, Tex.) · 2022Article
- Detecting TAD-like domains from RNA-associated interactions.Nucleic acids research · 2022Article
- Localization and functions of native and eGFP-tagged capsid proteins in HIV-1 particles.PLoS pathogens · 2022Article
- Nuclear speckles - a driving force in gene expression.Journal of cell science · 2022Review
- Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture.Cold Spring Harbor perspectives in biology · 2022Review
- Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision.Current opinion in genetics & development · 2021Review
- Insight into membraneless organelles and their associated proteins: Drivers, Clients and Regulators.Computational and structural biotechnology journal · 2021Article
- Coordination of transcription, processing, and export of highly expressed RNAs by distinct biomolecular condensates.Emerging topics in life sciences · 2020Article
- Stress-induced RNA-chromatin interactions promote endothelial dysfunction.Nature communications · 2020Article
- Article
- HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains.Nature communications · 2020Article
- Nuclear hubs built on RNAs and clustered organization of the genome.Current opinion in cell biology · 2020Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
It remains challenging to identify all parts of the nuclear genome that are in proximity to nuclear speckles, due to physical separation between the nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNA (snRNAs) and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA [nuclear speckle-associated RNA]), may extend to sufficient proximity to the genome. Leveraging a transcriptome-genome interaction assay (mapping of RNA-genome interactions [MARGI]), we identified clusters of nsaRNA-interacting genomic sequences (nsaPeaks). Posttranscriptional pre-mRNAs, which also accumulate to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Our combined DNA fluorescence in situ hybridization and immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs are located in sufficient proximity to the nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles.
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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.