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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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Differential distribution of R- and G-band DNA with respect to SC-35 domains in interphase nuclei. (A and B) Probe of R-band 17q21 DNA (red in A, white in B) hybridized to WI-38 fibroblasts shows two highly extended homologues, each with different morphologies. The left homologue contacts four SC-35 domains (green). The right band surrounds half of one SC-35 domain and also contacts another. (C and D) Two 6p21.3 R-bands (red, white) each have a thin string of DNA extending from the more compact, main body of the band. In one case (top band), the extended region almost completely surrounds an SC-35 domain (green). (E) A tetraploid nucleus hybridized to detect 17q21 DNA (green) shows all four bands contacting multiple SC-35 domains (blue). The COL1A1 gene (red, right inset) is located at the tip of a DNA extension that contacts an SC-35 domain at a single point, in contrast to another homologue (left inset). (F and G) The G-band probe for 3p14 (red in F, white in G) shows two bands minimally contacting SC-35 domains (green). (H and I) Similar to other G-bands, probe for 7p21 (red, white) was detected in focal planes other than those containing SC-35 domains (green), which thus appear out of focus. (J) Hybridization to detect 17q22–24 DNA (red) and the adjacent COL1A1 gene (green) shows that although some of these bands can extensively contact the SC-35 domain (blue) associated with COL1A1 (top inset), others are clearly separated (bottom inset). (K) Three-dimensional deconvolution and reconstruction of 17q21 R-band signal (red) and surrounding SC-35 domains (green) shows that this band extends significantly in the X-Y plane (left), but when viewed along the Z-axis (right), appears largely restricted to the planes containing SC-35 domains. (L) A three-dimensional reconstruction as in K shows an example of a G-band, 3p14 (red), located above and separated from the nearest SC-35 domain (green). For rotational movies of K and L, see supplemental material (available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). Bars, 5 μm.
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fig4: Differential distribution of R- and G-band DNA with respect to SC-35 domains in interphase nuclei. (A and B) Probe of R-band 17q21 DNA (red in A, white in B) hybridized to WI-38 fibroblasts shows two highly extended homologues, each with different morphologies. The left homologue contacts four SC-35 domains (green). The right band surrounds half of one SC-35 domain and also contacts another. (C and D) Two 6p21.3 R-bands (red, white) each have a thin string of DNA extending from the more compact, main body of the band. In one case (top band), the extended region almost completely surrounds an SC-35 domain (green). (E) A tetraploid nucleus hybridized to detect 17q21 DNA (green) shows all four bands contacting multiple SC-35 domains (blue). The COL1A1 gene (red, right inset) is located at the tip of a DNA extension that contacts an SC-35 domain at a single point, in contrast to another homologue (left inset). (F and G) The G-band probe for 3p14 (red in F, white in G) shows two bands minimally contacting SC-35 domains (green). (H and I) Similar to other G-bands, probe for 7p21 (red, white) was detected in focal planes other than those containing SC-35 domains (green), which thus appear out of focus. (J) Hybridization to detect 17q22–24 DNA (red) and the adjacent COL1A1 gene (green) shows that although some of these bands can extensively contact the SC-35 domain (blue) associated with COL1A1 (top inset), others are clearly separated (bottom inset). (K) Three-dimensional deconvolution and reconstruction of 17q21 R-band signal (red) and surrounding SC-35 domains (green) shows that this band extends significantly in the X-Y plane (left), but when viewed along the Z-axis (right), appears largely restricted to the planes containing SC-35 domains. (L) A three-dimensional reconstruction as in K shows an example of a G-band, 3p14 (red), located above and separated from the nearest SC-35 domain (green). For rotational movies of K and L, see supplemental material (available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). Bars, 5 μm.

Mentions: Visualization of these chromosome bands showed striking differences in their morphological organization relative to the SC-35 domains, demonstrating that different genomic segments have clearly distinct structural relationships to these compartments. Although we observed differences between all bands examined, in general, the organization of the R-bands relative to SC-35 domains was significantly different from that of the G-bands (Fig. 4). The vast majority of R-bands examined contact domains either at a single point (Fig. 4 E, right inset) or by extending for a considerable distance along the domain edge (Fig. 4 A, left; Fig. 4 E, left inset). In contrast, the G-bands most often contact domains at a single point, if at all (Fig. 4, F–I).


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)

Differential distribution of R- and G-band DNA with respect to SC-35 domains in interphase nuclei. (A and B) Probe of R-band 17q21 DNA (red in A, white in B) hybridized to WI-38 fibroblasts shows two highly extended homologues, each with different morphologies. The left homologue contacts four SC-35 domains (green). The right band surrounds half of one SC-35 domain and also contacts another. (C and D) Two 6p21.3 R-bands (red, white) each have a thin string of DNA extending from the more compact, main body of the band. In one case (top band), the extended region almost completely surrounds an SC-35 domain (green). (E) A tetraploid nucleus hybridized to detect 17q21 DNA (green) shows all four bands contacting multiple SC-35 domains (blue). The COL1A1 gene (red, right inset) is located at the tip of a DNA extension that contacts an SC-35 domain at a single point, in contrast to another homologue (left inset). (F and G) The G-band probe for 3p14 (red in F, white in G) shows two bands minimally contacting SC-35 domains (green). (H and I) Similar to other G-bands, probe for 7p21 (red, white) was detected in focal planes other than those containing SC-35 domains (green), which thus appear out of focus. (J) Hybridization to detect 17q22–24 DNA (red) and the adjacent COL1A1 gene (green) shows that although some of these bands can extensively contact the SC-35 domain (blue) associated with COL1A1 (top inset), others are clearly separated (bottom inset). (K) Three-dimensional deconvolution and reconstruction of 17q21 R-band signal (red) and surrounding SC-35 domains (green) shows that this band extends significantly in the X-Y plane (left), but when viewed along the Z-axis (right), appears largely restricted to the planes containing SC-35 domains. (L) A three-dimensional reconstruction as in K shows an example of a G-band, 3p14 (red), located above and separated from the nearest SC-35 domain (green). For rotational movies of K and L, see supplemental material (available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). Bars, 5 μm.
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Related In: Results  -  Collection

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fig4: Differential distribution of R- and G-band DNA with respect to SC-35 domains in interphase nuclei. (A and B) Probe of R-band 17q21 DNA (red in A, white in B) hybridized to WI-38 fibroblasts shows two highly extended homologues, each with different morphologies. The left homologue contacts four SC-35 domains (green). The right band surrounds half of one SC-35 domain and also contacts another. (C and D) Two 6p21.3 R-bands (red, white) each have a thin string of DNA extending from the more compact, main body of the band. In one case (top band), the extended region almost completely surrounds an SC-35 domain (green). (E) A tetraploid nucleus hybridized to detect 17q21 DNA (green) shows all four bands contacting multiple SC-35 domains (blue). The COL1A1 gene (red, right inset) is located at the tip of a DNA extension that contacts an SC-35 domain at a single point, in contrast to another homologue (left inset). (F and G) The G-band probe for 3p14 (red in F, white in G) shows two bands minimally contacting SC-35 domains (green). (H and I) Similar to other G-bands, probe for 7p21 (red, white) was detected in focal planes other than those containing SC-35 domains (green), which thus appear out of focus. (J) Hybridization to detect 17q22–24 DNA (red) and the adjacent COL1A1 gene (green) shows that although some of these bands can extensively contact the SC-35 domain (blue) associated with COL1A1 (top inset), others are clearly separated (bottom inset). (K) Three-dimensional deconvolution and reconstruction of 17q21 R-band signal (red) and surrounding SC-35 domains (green) shows that this band extends significantly in the X-Y plane (left), but when viewed along the Z-axis (right), appears largely restricted to the planes containing SC-35 domains. (L) A three-dimensional reconstruction as in K shows an example of a G-band, 3p14 (red), located above and separated from the nearest SC-35 domain (green). For rotational movies of K and L, see supplemental material (available at http://www.jcb.org/cgi/content/full/jcb.200303131/DC1). Bars, 5 μm.
Mentions: Visualization of these chromosome bands showed striking differences in their morphological organization relative to the SC-35 domains, demonstrating that different genomic segments have clearly distinct structural relationships to these compartments. Although we observed differences between all bands examined, in general, the organization of the R-bands relative to SC-35 domains was significantly different from that of the G-bands (Fig. 4). The vast majority of R-bands examined contact domains either at a single point (Fig. 4 E, right inset) or by extending for a considerable distance along the domain edge (Fig. 4 A, left; Fig. 4 E, left inset). In contrast, the G-bands most often contact domains at a single point, if at all (Fig. 4, F–I).

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