ArticleGenome research2009
Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed, 69 citations in OpenAlex.
- Combined 3D DNA FISH, Single-Molecule RNA FISH, and Immunofluorescence.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Recent advances in the spatial organization of the mammalian genome.Journal of biosciences · 2020Review
- Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions.Biophysical journal · 2017Article
- Locus-specific gene repositioning in prostate cancer.Molecular biology of the cell · 2016Article
- Chromosomes at Work: Organization of Chromosome Territories in the Interphase Nucleus.Journal of cellular biochemistry · 2016Article
- Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool.Frontiers in genetics · 2016Review
- An Overview of Genome Organization and How We Got There: from FISH to Hi-C.Microbiology and molecular biology reviews : MMBR · 2015Review
- Chromatin at the nuclear periphery and the regulation of genome functions.Histochemistry and cell biology · 2015Review
- Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization.Genes & development · 2014Article
- Distinct nuclear orientation patterns for mouse chromosome 11 in normal B lymphocytes.BMC cell biology · 2014Article
- The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease.Journal of cellular physiology · 2014Review
- Imaging RNA Polymerase II transcription sites in living cells.Current opinion in genetics & development · 2014Review
- p63 and Brg1 control developmentally regulated higher-order chromatin remodelling at the epidermal differentiation complex locus in epidermal progenitor cells.Development (Cambridge, England) · 2014Article
- Epigenetic layers and players underlying neurodevelopment.Trends in neurosciences · 2013Review
- Understanding the regulatory and transcriptional complexity of the genome through structure.Genome research · 2013Review
- Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional differentiation.Genome research · 2013Article
- Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers.Cell reports · 2013Article
- Anterior-posterior differences in HoxD chromatin topology in limb development.Development (Cambridge, England) · 2012Article
- Navigating the epigenetic landscape of pluripotent stem cells.Nature reviews. Molecular cell biology · 2012Review
- Higher-order chromatin structure: bridging physics and biology.Current opinion in genetics & development · 2012Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Position within chromosome territories and localization at transcription factories are two facets of nuclear organization that have been associated with active gene expression. However, there is still debate about whether this organization is a cause or consequence of transcription. Here we induced looping out from chromosome territories (CTs), by the activation of Hox loci during differentiation, to investigate consequences on neighboring loci. We show that, even though flanking genes are caught up in the wave of nuclear reorganization, there is no effect on their expression. However, there is a differential organization of active and inactive alleles of these genes. Inactive alleles are preferentially retained within the CT, whereas actively transcribing alleles, and those associated with transcription factories, are found both inside and outside of the territory. We suggest that the alleles relocated further to the exterior of the CT are those that were already active and already associated with transcription factories before the induction of differentiation. Hence active gene regions may loop out from CTs because they are able to, and not because they need to in order to facilitate gene expression.
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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.