Limits...
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."

Show MeSH
COL1A1 and COL1A2 genes associate with a single, common domain. (A) WI-38 diploid fibroblasts were hybridized with differently labeled genomic probes of COL1A1 (red) and COL1A2 gene (green) and stained for SC-35 (blue). One homologue of each gene is simultaneously associated with the same SC-35 domain in the cell shown. (B) Transcripts from the COL1A1 (green) and COL1A2 (red) genes, detected with differentially labeled cDNA probes, intermingle within an SC-35 domain (blue). Overlap between the three colors appears white. (C) Three-dimensional deconvolution shows intermingling COL1A1 (green) and COL1A2 (red) transcripts in two focal planes. Regions of colocalization appear yellow. To view a three-dimensional reconstruction of this stack, see supplemental material (available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). Bars, 5 μm.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2172856&req=5

fig1: COL1A1 and COL1A2 genes associate with a single, common domain. (A) WI-38 diploid fibroblasts were hybridized with differently labeled genomic probes of COL1A1 (red) and COL1A2 gene (green) and stained for SC-35 (blue). One homologue of each gene is simultaneously associated with the same SC-35 domain in the cell shown. (B) Transcripts from the COL1A1 (green) and COL1A2 (red) genes, detected with differentially labeled cDNA probes, intermingle within an SC-35 domain (blue). Overlap between the three colors appears white. (C) Three-dimensional deconvolution shows intermingling COL1A1 (green) and COL1A2 (red) transcripts in two focal planes. Regions of colocalization appear yellow. To view a three-dimensional reconstruction of this stack, see supplemental material (available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). Bars, 5 μm.

Mentions: First, we directly tested the hypothesis that SC-35 domains are structures around which multiple, specific genes cluster by examining whether two nonsyntenic genes, collagen type I, α1 (COL1A1; chromosome 17) and collagen type I, α2 (COL1A2; chromosome 7), can simultaneously associate with the same SC-35 domain. Individually, each of these loci is known to associate with an SC-35 domain at high frequencies (98 and 87% of loci in diploid fibroblasts, respectively; Table I), and these are significantly greater than predicted or empirically observed random interactions (Xing et al., 1995; Shopland et al., 2002). We performed three-color analyses of these two genes and SC-35 in diploid fibroblasts. Results show that COL1A1 and COL1A2 position at the edge of the same SC-35 domain in a significant subset of cells (∼10%; Fig. 1 A, Table I, and see following section).


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)

COL1A1 and COL1A2 genes associate with a single, common domain. (A) WI-38 diploid fibroblasts were hybridized with differently labeled genomic probes of COL1A1 (red) and COL1A2 gene (green) and stained for SC-35 (blue). One homologue of each gene is simultaneously associated with the same SC-35 domain in the cell shown. (B) Transcripts from the COL1A1 (green) and COL1A2 (red) genes, detected with differentially labeled cDNA probes, intermingle within an SC-35 domain (blue). Overlap between the three colors appears white. (C) Three-dimensional deconvolution shows intermingling COL1A1 (green) and COL1A2 (red) transcripts in two focal planes. Regions of colocalization appear yellow. To view a three-dimensional reconstruction of this stack, see supplemental material (available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). Bars, 5 μm.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2172856&req=5

fig1: COL1A1 and COL1A2 genes associate with a single, common domain. (A) WI-38 diploid fibroblasts were hybridized with differently labeled genomic probes of COL1A1 (red) and COL1A2 gene (green) and stained for SC-35 (blue). One homologue of each gene is simultaneously associated with the same SC-35 domain in the cell shown. (B) Transcripts from the COL1A1 (green) and COL1A2 (red) genes, detected with differentially labeled cDNA probes, intermingle within an SC-35 domain (blue). Overlap between the three colors appears white. (C) Three-dimensional deconvolution shows intermingling COL1A1 (green) and COL1A2 (red) transcripts in two focal planes. Regions of colocalization appear yellow. To view a three-dimensional reconstruction of this stack, see supplemental material (available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). Bars, 5 μm.
Mentions: First, we directly tested the hypothesis that SC-35 domains are structures around which multiple, specific genes cluster by examining whether two nonsyntenic genes, collagen type I, α1 (COL1A1; chromosome 17) and collagen type I, α2 (COL1A2; chromosome 7), can simultaneously associate with the same SC-35 domain. Individually, each of these loci is known to associate with an SC-35 domain at high frequencies (98 and 87% of loci in diploid fibroblasts, respectively; Table I), and these are significantly greater than predicted or empirically observed random interactions (Xing et al., 1995; Shopland et al., 2002). We performed three-color analyses of these two genes and SC-35 in diploid fibroblasts. Results show that COL1A1 and COL1A2 position at the edge of the same SC-35 domain in a significant subset of cells (∼10%; Fig. 1 A, Table I, and see following section).

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