ArticleJournal of cellular biochemistry2008
Identifying functional neighborhoods within the cell nucleus: proximity analysis of early S-phase replicating chromatin domains to sites of transcription, RNA polymerase II, HP1gamma, matrin 3 and SAF-A.
Article in Journal of cellular biochemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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
32 citing papers in PubMed, 53 citations in OpenAlex.
- Matrin-3 forms spherical and wormlike assemblies that are modulated by RNA binding and ALS/FTD-associated mutations.Molecular cell · 2025Article
- Epigenetic Regulation of Erythropoiesis: From Developmental Programs to Therapeutic Targets.International journal of molecular sciences · 2025Review
- Erythropoiesis: insights from a genomic perspective.Experimental & molecular medicine · 2024Review
- Nuclear structures and their emerging roles in cell differentiation and development.BMB reports · 2024Review
- The role of Matrin-3 in physiology and its dysregulation in disease.Biochemical Society transactions · 2024Review
- Review
- Matrin-3 acts as a potential biomarker and promotes hepatocellular carcinoma progression by interacting with cell cycle-regulating genes.Cell cycle (Georgetown, Tex.) · 2024Article
- Review
- Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture.Nature communications · 2021Article
- Matrin 3 in neuromuscular disease: physiology and pathophysiology.JCI insight · 2021Review
- Matrin3: Disorder and ALS Pathogenesis.Frontiers in molecular biosciences · 2021Review
- Chromosome territories and the global regulation of the genome.Genes, chromosomes & cancer · 2019Review
- The exon junction complex factor Y14 is dynamic in the nucleus of the beetleMolecular cytogenetics · 2017Article
- Nucleolus-like body of mouse oocytes contains lamin A and B and TRF2 but not actin and topo II.Molecular cytogenetics · 2016Article
- Nuclear matrix protein Matrin 3 is a regulator of ZAP-mediated retroviral restriction.Retrovirology · 2015Article
- Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB.The EMBO journal · 2015Article
- Mice with an isoform-ablating Mecp2 exon 1 mutation recapitulate the neurologic deficits of Rett syndrome.Human molecular genetics · 2014Article
- Nuclear trafficking of retroviral RNAs and Gag proteins during late steps of replication.Viruses · 2013Review
- Alterations in replication timing of cancer-related genes in malignant human breast cancer cells.Journal of cellular biochemistry · 2013Article
- The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components.Molecular & cellular proteomics : MCP · 2013Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1gamma, nascent transcript sites (TS), active DNA replicating sites in early S-phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture.
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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.