ArticleNucleic acids research2004
Visualization of individual DNA loops and a map of loop domains in the human dystrophin gene.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 65 citations in OpenAlex.
- Chromatin Architectural Factors as Safeguards against Excessive Supercoiling during DNA Replication.International journal of molecular sciences · 2020Review
- Gene functioning and storage within a folded genome.Cellular & molecular biology letters · 2017Review
- A requiem to the nuclear matrix: from a controversial concept to 3D organization of the nucleus.Chromosoma · 2014Review
- Epigenetic landscape for initiation of DNA replication.Chromosoma · 2014Review
- Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes.PloS one · 2011Article
- DNA moves sequentially towards the nuclear matrix during DNA replication in vivo.BMC cell biology · 2011Article
- Continued stabilization of the nuclear higher-order structure of post-mitotic neurons in vivo.PloS one · 2011Article
- Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure.Nucleic acids research · 2010Article
- Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach.DNA research : an international journal for rapid publication of reports on genes and genomes · 2010Article
- Intrinsically bent DNA sites in the Drosophila melanogaster third chromosome amplified domain.Molecular genetics and genomics : MGG · 2009Article
- The organization in micro-loops of an extended fragment of chicken chromosome 14, including the alpha globin gene cluster in the erythroid cells.Acta naturae · 2009Article
- Chromatin loop domain organization within the 4q35 locus in facioscapulohumeral dystrophy patients versus normal human myoblasts.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Loop formation by the transgene WAP:6xHishGH in transgenic rabbit fibroblasts, revealed by fluorescence in situ hybridization to nuclear halos.Journal of applied genetics · 2006Article
- Distribution of gyrase and topoisomerase IV on bacterial nucleoid: implications for nucleoid organization.Nucleic acids research · 2006Article
- Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix.Nucleic acids research · 2005Article
- Specific spatial organization of chromosomes in nuclei of primary human fibroblasts is maintained by nuclear matrix.Doklady. Biochemistry and biophysicsArticle
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The organization of the human dystrophin gene into loop domains has been studied using two different experimental approaches: excision of DNA loops mediated by nuclear matrix-bound topoisomerase II and in situ hybridization of different probes with histone-depleted nuclei (nuclear halos). Our objective was to examine if the DNA loops mapped by this biochemical approach coincide with loops visualized by microscopy. The results obtained using both approaches were in good agreement. Eight loops separated by attachment regions of different length were mapped in the upstream part (up to exon 54) of the gene by topoisomerase II-mediated excision. One of these loops was then directly visualized by in situ hybridization of the corresponding bacmid clone with nuclear halos. This is the first direct demonstration that a DNA domain mapped as a loop using a biochemical approach corresponds to a loop visible on cytological preparations. The validity of this result and of the whole map of loop domains was confirmed by in situ hybridization using probes derived from other attachment regions or loops mapped by topoisomerase II-mediated cleavage; these probes hybridized on the core or halo region, respectively, of nuclear halos. Our results demonstrate that a single transcription unit may be organized into several loops and that DNA loop attachment regions may be fairly long. Three out of four replication origins mapped in this gene co-localize with loop attachment regions, and the major deletion hot spot is harbored in an attachment region. These results strongly suggest that partitioning of genomic DNA into specific loops attached to a skeletal structure is a characteristic feature of eukaryotic chromosome organization in interphase.
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