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Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods.

Shopland LS, Johnson CV, Byron M, McNeil J, Lawrence JB - J. Cell Biol. (2003)

Bottom Line: Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not.All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences.Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic "neighborhoods."

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, University of Massachusetts Medical Center, Worcester, MA 01655, USA.

ABSTRACT
Typically, eukaryotic nuclei contain 10-30 prominent domains (referred to here as SC-35 domains) that are concentrated in mRNA metabolic factors. Here, we show that multiple specific genes cluster around a common SC-35 domain, which contains multiple mRNAs. Nonsyntenic genes are capable of associating with a common domain, but domain "choice" appears random, even for two coordinately expressed genes. Active genes widely separated on different chromosome arms associate with the same domain frequently, assorting randomly into the 3-4 subregions of the chromosome periphery that contact a domain. Most importantly, visualization of six individual chromosome bands showed that large genomic segments ( approximately 5 Mb) have striking differences in organization relative to domains. Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not. All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences. Similarly, late-replicating DNA generally avoids SC-35 domains. These findings suggest a functional rationale for gene clustering in chromosomal bands, which relates to nuclear clustering of genes with SC-35 domains. Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic "neighborhoods."

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Specificity of chromosome band probes. Probes from indicated bands were hybridized to spreads of human metaphase chromosomes (stained with DAPI, blue) of peripheral blood lymphocytes to assess their specificity. (A) 7p21, 17q21 (both green), and 17q22–24 (red); (B) 3p14 (red), 7q21 (green), and 19q13.3 (green); (C) 6p21.3 (red). Probes for 7p21 and 7q21 weakly detected additional bands, but 7p21 DNA was identified in interphase based on signal size, intensity, and cohybridization of the neighboring ACTB locus. Signals from 7q21 probe were not evaluated in interphase nuclei. (D–J) Enlarged views of single chromosomes, shown to scale, hybridized with different band probes as indicated and compared with DAPI bands (blue or white) indicates that they are largely either R- or G- band DNA. In D, the COL1A1 gene (red) is cohybridized with 17q21 (green), showing that this gene maps to the telomeric end of this band, proximal to 17q22–24 (E). Bars, 5 μm.
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fig3: Specificity of chromosome band probes. Probes from indicated bands were hybridized to spreads of human metaphase chromosomes (stained with DAPI, blue) of peripheral blood lymphocytes to assess their specificity. (A) 7p21, 17q21 (both green), and 17q22–24 (red); (B) 3p14 (red), 7q21 (green), and 19q13.3 (green); (C) 6p21.3 (red). Probes for 7p21 and 7q21 weakly detected additional bands, but 7p21 DNA was identified in interphase based on signal size, intensity, and cohybridization of the neighboring ACTB locus. Signals from 7q21 probe were not evaluated in interphase nuclei. (D–J) Enlarged views of single chromosomes, shown to scale, hybridized with different band probes as indicated and compared with DAPI bands (blue or white) indicates that they are largely either R- or G- band DNA. In D, the COL1A1 gene (red) is cohybridized with 17q21 (green), showing that this gene maps to the telomeric end of this band, proximal to 17q22–24 (E). Bars, 5 μm.

Mentions: Our data indicating that synteny can favor the association of specific genes with a common SC-35 domain led us to speculate that even closer chromosomal “linkage” might further correlate with domain co-association. Interestingly, genes are clustered along the chromosome and are enriched in certain cytogenetic bands (R-bands). Therefore, we tested whether individual chromosome bands show differences in their relationship to SC-35 domains, and whether gene-rich R-bands in particular tend to show more association with these structures than gene-poor G-bands. We developed an approach to detect specific chromosome bands in interphase nuclei relative to SC-35 domains (see Materials and methods). Probes generated from specific cytogenetic bands microdissected from metaphase chromosomes (Guan et al., 1993) were selected based on gene density (Table II). The chosen R-band probes were from 6p21.3, 17q21, and 19q13.3; G-band probes were from 3p14 and 7p21; and one probe, from 17q22–24, contained ∼1/3 R-band and 2/3 G-band material (Fig. 3). Two of these bands, 17q21 and 17q22–24, were also chosen because they are adjacent to one another and flank the COL1A1 gene, which maps to the telomeric end of 17q21 (Fig. 3 D), near its junction with 17q22–24.


Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods.

Shopland LS, Johnson CV, Byron M, McNeil J, Lawrence JB - J. Cell Biol. (2003)

Specificity of chromosome band probes. Probes from indicated bands were hybridized to spreads of human metaphase chromosomes (stained with DAPI, blue) of peripheral blood lymphocytes to assess their specificity. (A) 7p21, 17q21 (both green), and 17q22–24 (red); (B) 3p14 (red), 7q21 (green), and 19q13.3 (green); (C) 6p21.3 (red). Probes for 7p21 and 7q21 weakly detected additional bands, but 7p21 DNA was identified in interphase based on signal size, intensity, and cohybridization of the neighboring ACTB locus. Signals from 7q21 probe were not evaluated in interphase nuclei. (D–J) Enlarged views of single chromosomes, shown to scale, hybridized with different band probes as indicated and compared with DAPI bands (blue or white) indicates that they are largely either R- or G- band DNA. In D, the COL1A1 gene (red) is cohybridized with 17q21 (green), showing that this gene maps to the telomeric end of this band, proximal to 17q22–24 (E). Bars, 5 μm.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2172856&req=5

fig3: Specificity of chromosome band probes. Probes from indicated bands were hybridized to spreads of human metaphase chromosomes (stained with DAPI, blue) of peripheral blood lymphocytes to assess their specificity. (A) 7p21, 17q21 (both green), and 17q22–24 (red); (B) 3p14 (red), 7q21 (green), and 19q13.3 (green); (C) 6p21.3 (red). Probes for 7p21 and 7q21 weakly detected additional bands, but 7p21 DNA was identified in interphase based on signal size, intensity, and cohybridization of the neighboring ACTB locus. Signals from 7q21 probe were not evaluated in interphase nuclei. (D–J) Enlarged views of single chromosomes, shown to scale, hybridized with different band probes as indicated and compared with DAPI bands (blue or white) indicates that they are largely either R- or G- band DNA. In D, the COL1A1 gene (red) is cohybridized with 17q21 (green), showing that this gene maps to the telomeric end of this band, proximal to 17q22–24 (E). Bars, 5 μm.
Mentions: Our data indicating that synteny can favor the association of specific genes with a common SC-35 domain led us to speculate that even closer chromosomal “linkage” might further correlate with domain co-association. Interestingly, genes are clustered along the chromosome and are enriched in certain cytogenetic bands (R-bands). Therefore, we tested whether individual chromosome bands show differences in their relationship to SC-35 domains, and whether gene-rich R-bands in particular tend to show more association with these structures than gene-poor G-bands. We developed an approach to detect specific chromosome bands in interphase nuclei relative to SC-35 domains (see Materials and methods). Probes generated from specific cytogenetic bands microdissected from metaphase chromosomes (Guan et al., 1993) were selected based on gene density (Table II). The chosen R-band probes were from 6p21.3, 17q21, and 19q13.3; G-band probes were from 3p14 and 7p21; and one probe, from 17q22–24, contained ∼1/3 R-band and 2/3 G-band material (Fig. 3). Two of these bands, 17q21 and 17q22–24, were also chosen because they are adjacent to one another and flank the COL1A1 gene, which maps to the telomeric end of 17q21 (Fig. 3 D), near its junction with 17q22–24.

Bottom Line: Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not.All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences.Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic "neighborhoods."

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, University of Massachusetts Medical Center, Worcester, MA 01655, USA.

ABSTRACT
Typically, eukaryotic nuclei contain 10-30 prominent domains (referred to here as SC-35 domains) that are concentrated in mRNA metabolic factors. Here, we show that multiple specific genes cluster around a common SC-35 domain, which contains multiple mRNAs. Nonsyntenic genes are capable of associating with a common domain, but domain "choice" appears random, even for two coordinately expressed genes. Active genes widely separated on different chromosome arms associate with the same domain frequently, assorting randomly into the 3-4 subregions of the chromosome periphery that contact a domain. Most importantly, visualization of six individual chromosome bands showed that large genomic segments ( approximately 5 Mb) have striking differences in organization relative to domains. Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not. All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences. Similarly, late-replicating DNA generally avoids SC-35 domains. These findings suggest a functional rationale for gene clustering in chromosomal bands, which relates to nuclear clustering of genes with SC-35 domains. Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic "neighborhoods."

Show MeSH