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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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Transcripts from multiple genes can associate with the same SC-35 domain. (A) One focus of lamin A/C RNA (red) associates with the edge of an accumulation of COL1A1 transcripts (green), which serves as a marker for an SC-35 domain. (B) Triple labeling also shows that transcripts from ACTB (green) and COL1A2 (red) accumulate within the same SC-35 domain (blue). (C) Chromosome 7 territories detected with a whole chromosome paint (red) contact 3–4 SC-35 domains (green) per nucleus. Bars, 5 μm.
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fig2: Transcripts from multiple genes can associate with the same SC-35 domain. (A) One focus of lamin A/C RNA (red) associates with the edge of an accumulation of COL1A1 transcripts (green), which serves as a marker for an SC-35 domain. (B) Triple labeling also shows that transcripts from ACTB (green) and COL1A2 (red) accumulate within the same SC-35 domain (blue). (C) Chromosome 7 territories detected with a whole chromosome paint (red) contact 3–4 SC-35 domains (green) per nucleus. Bars, 5 μm.

Mentions: Are the COL1A1 and COL1A2 genes associated with one common or two closely abutting structures? These genes, which are restricted to the SC-35 domain edge, both produce transcripts that accumulate within the domain interior (Xing et al., 1995; Shopland et al., 2002). We found that their transcripts can intermingle within the same SC-35 domain (Fig. 1 B), demonstrating that they occupy a common structure. This was also observed for COL1A2 and β-actin (ACTB) transcripts (Fig. 2 B, see following section). Three-dimensional deconvolution to remove out of focus light further confirmed these observations (Fig. 1 C; see also Video 1, available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). These data provide direct evidence that SC-35 domains are structures around which multiple mRNA-encoding genes cluster, and which contain multiple mRNAs. The COL1A1 and COL1A2 genes provide the most rigorous test of our hypothesis because they produce very highly expressed and heavily spliced nuclear RNA accumulations (Smith et al., 1999), which could be thought more likely to generate the appearance of a “domain” from an individual gene (Huang and Spector, 1996). However, these findings directly demonstrate that even in these cases, there are multiple genes clustered with each individual domain.


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)

Transcripts from multiple genes can associate with the same SC-35 domain. (A) One focus of lamin A/C RNA (red) associates with the edge of an accumulation of COL1A1 transcripts (green), which serves as a marker for an SC-35 domain. (B) Triple labeling also shows that transcripts from ACTB (green) and COL1A2 (red) accumulate within the same SC-35 domain (blue). (C) Chromosome 7 territories detected with a whole chromosome paint (red) contact 3–4 SC-35 domains (green) per nucleus. Bars, 5 μm.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2172856&req=5

fig2: Transcripts from multiple genes can associate with the same SC-35 domain. (A) One focus of lamin A/C RNA (red) associates with the edge of an accumulation of COL1A1 transcripts (green), which serves as a marker for an SC-35 domain. (B) Triple labeling also shows that transcripts from ACTB (green) and COL1A2 (red) accumulate within the same SC-35 domain (blue). (C) Chromosome 7 territories detected with a whole chromosome paint (red) contact 3–4 SC-35 domains (green) per nucleus. Bars, 5 μm.
Mentions: Are the COL1A1 and COL1A2 genes associated with one common or two closely abutting structures? These genes, which are restricted to the SC-35 domain edge, both produce transcripts that accumulate within the domain interior (Xing et al., 1995; Shopland et al., 2002). We found that their transcripts can intermingle within the same SC-35 domain (Fig. 1 B), demonstrating that they occupy a common structure. This was also observed for COL1A2 and β-actin (ACTB) transcripts (Fig. 2 B, see following section). Three-dimensional deconvolution to remove out of focus light further confirmed these observations (Fig. 1 C; see also Video 1, available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). These data provide direct evidence that SC-35 domains are structures around which multiple mRNA-encoding genes cluster, and which contain multiple mRNAs. The COL1A1 and COL1A2 genes provide the most rigorous test of our hypothesis because they produce very highly expressed and heavily spliced nuclear RNA accumulations (Smith et al., 1999), which could be thought more likely to generate the appearance of a “domain” from an individual gene (Huang and Spector, 1996). However, these findings directly demonstrate that even in these cases, there are multiple genes clustered with each individual domain.

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