scholarly journals Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH

2002 ◽  
Vol 159 (5) ◽  
pp. 753-763 ◽  
Author(s):  
Nicola L. Mahy ◽  
Paul E. Perry ◽  
Wendy A. Bickmore
Keyword(s):  
Spatial Organization ◽  
Cell Types ◽  
Gene Density ◽  
Epidermal Differentiation ◽  
Chromosome 1 ◽  
Chromosome Territories ◽  
Chromosome 11 ◽  
Epidermal Differentiation Complex ◽  
High Gene ◽  
Complex Locus

Genes can be transcribed from within chromosome territories; however, the major histocompatibilty complex locus has been reported extending away from chromosome territories, and the incidence of this correlates with transcription from the region. A similar result has been seen for the epidermal differentiation complex region of chromosome 1. These data suggested that chromatin decondensation away from the surface of chromosome territories may result from, and/or may facilitate, transcription of densely packed genes subject to coordinate regulation. To investigate whether localization outside of the visible confines of chromosome territories can also occur for regions that are not coordinately regulated, we have examined the spatial organization of human 11p15.5 and the syntenic region on mouse chromosome 7. This region is gene rich but its genes are not coordinately expressed, rather overall high levels of transcription occur in several cell types. We found that chromatin from 11p15.5 frequently extends away from the chromosome 11 territory. Localization outside of territories was also detected for other regions of high gene density and high levels of transcription. This is shown to be partly dependent on ongoing transcription. We suggest that local gene density and transcription, rather than the activity of individual genes, influences the organization of chromosomes in the nucleus.

scholarly journals Bioinformatics Approach towards Transcriptomics of Filaggrin

2016 ◽  
Vol 2 (3) ◽  
pp. 8 ◽  
Author(s):  
Dito Anurogo ◽  
Arli Aditya Parikesit
Keyword(s):  
Lipid Synthesis ◽  
Atopic Disease ◽  
Epidermal Differentiation ◽  
Chromosome 1 ◽  
Atopic Diseases ◽  
Structural Protein ◽  
Microbial Infection ◽  
Epidermal Differentiation Complex ◽  
Increased Risk ◽  
And Function

Filaggrin, or filaments which combines protein, is one of the important structural protein that works for the development, maintenance, and the formation of the skin as an intact barrier. Filaggrin breakdown products regulate the hydration of the skin; contribute to the acidic pH of the skin, which in turn is essential for the activity of various proteases in the stratum corneum desquamation and lipid synthesis. Filaggrin produced by keratinocytes granular as a major precursor called profilaggrin, encoded by the FLG gene, located in the epidermal differentiation complex on chromosome 1 (1q21 locus). The locus contains a group of genes involved in epidermal differentiation. Filaggrin deficiency has some consequences on the organization and function of epidermal with important implications such as increased risk for atopic disease or a microbial infection. FLG mutation, a gene that encodes filaggrin, has been shown to cause ichthyosis vulgaris, increasing the risk of atopic dermatitis and other atopic diseases. This research examined the FLG gene based bioinformatics approach to search for conserved region of representative mammals that encode coding (m) and non-coding (nc) RNAs. Expected mRNA expression can be used as a diagnostic and therapeutic agent against deficiencies and filaggrin mutations.Key words: filaggrin, FLG, profilaggrin, filaggrin deficiency, bioinformatics.

scholarly journals Nuclear Organization of Mammalian Genomes

1999 ◽  
Vol 146 (6) ◽  
pp. 1211-1226 ◽  
Author(s):  
Nicolas Sadoni ◽  
Sabine Langer ◽  
Christine Fauth ◽  
Giorgio Bernardi ◽  
Thomas Cremer ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Chromosome Structure ◽  
Nuclear Architecture ◽  
Replication Timing ◽  
Cell Types ◽  
Higher Order ◽  
Chromosome Territories ◽  
Mitotic Chromosomes ◽  
Organizational Principle ◽  
Mammalian Genomes

We investigated the nuclear higher order compartmentalization of chromatin according to its replication timing (Ferreira et al. 1997) and the relations of this compartmentalization to chromosome structure and the spatial organization of transcription. Our aim was to provide a comprehensive and integrated view on the relations between chromosome structure and functional nuclear architecture. Using different mammalian cell types, we show that distinct higher order compartments whose DNA displays a specific replication timing are stably maintained during all interphase stages. The organizational principle is clonally inherited. We directly demonstrate the presence of polar chromosome territories that align to build up higher order compartments, as previously suggested (Ferreira et al. 1997). Polar chromosome territories display a specific orientation of early and late replicating subregions that correspond to R- or G/C-bands of mitotic chromosomes. Higher order compartments containing G/C-bands replicating during the second half of the S phase display no transcriptional activity detectable by BrUTP pulse labeling and show no evidence of transcriptional competence. Transcriptionally competent and active chromatin is confined to a coherent compartment within the nuclear interior that comprises early replicating R-band sequences. As a whole, the data provide an integrated view on chromosome structure, nuclear higher order compartmentalization, and their relation to the spatial organization of functional nuclear processes.

scholarly journals Epidermal differentiation complex (locus 1q21) gene expression in head and neck cancer and normal mucosa

2014 ◽  
Vol 52 (2) ◽  
pp. 79-89 ◽  
Author(s):  
Tomasz Tyszkiewicz ◽  
Michal Jarzab ◽  
Cezary Szymczyk ◽  
Monika Kowal ◽  
Jolanta Krajewska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Head And Neck Cancer ◽  
Head And Neck ◽  
Neck Cancer ◽  
Normal Mucosa ◽  
Epidermal Differentiation ◽  
Epidermal Differentiation Complex ◽  
Complex Locus

scholarly journals Spatial organization of active and inactive genes and noncoding DNA within chromosome territories

2002 ◽  
Vol 157 (4) ◽  
pp. 579-589 ◽  
Author(s):  
Nicola L. Mahy ◽  
Paul E. Perry ◽  
Susan Gilchrist ◽  
Richard A. Baldock ◽  
Wendy A. Bickmore
Keyword(s):  
Spatial Organization ◽  
Wilms Tumor ◽  
Cell Types ◽  
Domain Model ◽  
Chromosome Territories ◽  
Noncoding Dna ◽  
Transcription Machinery ◽  
Accessibility Barriers ◽  
High Resolution Analysis ◽  
Genitourinary Anomalies

The position of genes within the nucleus has been correlated with their transcriptional activity. The interchromosome domain model of nuclear organization suggests that genes preferentially locate at the surface of chromosome territories. Conversely, high resolution analysis of chromatin fibers suggests that chromosome territories do not present accessibility barriers to transcription machinery. To clarify the relationship between the organization of chromosome territories and gene expression, we have used fluorescence in situ hybridization to analyze the spatial organization of a contiguous ∼1 Mb stretch of the Wilms' tumor, aniridia, genitourinary anomalies, mental retardation syndrome region of the human genome and the syntenic region in the mouse. These regions contain constitutively expressed genes, genes with tissue-restricted patterns of expression, and substantial regions of intergenic DNA. We find that there is a spatial organization within territories that is conserved between mouse and humans: certain sequences do preferentially locate at the periphery of the chromosome territories in both species. However, we do not detect genes necessarily at the periphery of chromosome territories or at the surface of subchromosomal domains. Intraterritory organization is not different among cell types that express different combinations of the genes under study. Our data demonstrate that transcription of both ubiquitous and tissue-restricted genes is not confined to the periphery of chromosome territories, suggesting that the basal transcription machinery and transcription factors can readily gain access to the chromosome interior.

Mutagenic transgene insertion into a region of high gene density and multiple linkage disruptions on mouse chromosome 11

2002 ◽  
Vol 97 (1-2) ◽  
pp. 100-105 ◽  
Author(s):  
N. Kleiter ◽  
I. Artner ◽  
N. Gmachl ◽  
N. Ghaffari-Tabrizi ◽  
K. Kratochwil
Keyword(s):  
Mouse Chromosome ◽  
Gene Density ◽  
Chromosome 11 ◽  
High Gene ◽  
Mouse Chromosome 11 ◽  
High Gene Density ◽  
Transgene Insertion
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