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High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

van Koningsbruggen S, Gierlinski M, Schofield P, Martin D, Barton GJ, Ariyurek Y, den Dunnen JT, Lamond AI - Mol. Biol. Cell (2010)

Bottom Line: We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy.The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner.Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

ABSTRACT
The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

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Related in: MedlinePlus

Comparison of nucleolar-genomic ratio count rates for different repeat sequences with either multiple or unique hits. Each bar shows the nucleolar-genomic ratio of unique or multiple hit fraction to repeat sequences (see Figure 4A for details). Only repeat classes with nucleolar-genomic ratio greater than 2 are shown. Most notably, rRNA genes are significantly enriched in the nucleolar set.
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Figure 5: Comparison of nucleolar-genomic ratio count rates for different repeat sequences with either multiple or unique hits. Each bar shows the nucleolar-genomic ratio of unique or multiple hit fraction to repeat sequences (see Figure 4A for details). Only repeat classes with nucleolar-genomic ratio greater than 2 are shown. Most notably, rRNA genes are significantly enriched in the nucleolar set.

Mentions: We also compared the frequency of matches to the repeat sequences from genomic and nucleolar sets. Figure 5 shows the most pronounced classes, with a nucleolar-genomic hit ratio greater than 2. These include satellite repeats and rRNA genes. This distribution was expected, because NORs are clustered around the short arms of the acrocentric chromosomes, which contain tandem repeats of rRNA genes and satellite DNA. The clear enrichment of rRNA genes confirms the separation of nucleolar from total genomic DNA in these experiments.


High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

van Koningsbruggen S, Gierlinski M, Schofield P, Martin D, Barton GJ, Ariyurek Y, den Dunnen JT, Lamond AI - Mol. Biol. Cell (2010)

Comparison of nucleolar-genomic ratio count rates for different repeat sequences with either multiple or unique hits. Each bar shows the nucleolar-genomic ratio of unique or multiple hit fraction to repeat sequences (see Figure 4A for details). Only repeat classes with nucleolar-genomic ratio greater than 2 are shown. Most notably, rRNA genes are significantly enriched in the nucleolar set.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2965689&req=5

Figure 5: Comparison of nucleolar-genomic ratio count rates for different repeat sequences with either multiple or unique hits. Each bar shows the nucleolar-genomic ratio of unique or multiple hit fraction to repeat sequences (see Figure 4A for details). Only repeat classes with nucleolar-genomic ratio greater than 2 are shown. Most notably, rRNA genes are significantly enriched in the nucleolar set.
Mentions: We also compared the frequency of matches to the repeat sequences from genomic and nucleolar sets. Figure 5 shows the most pronounced classes, with a nucleolar-genomic hit ratio greater than 2. These include satellite repeats and rRNA genes. This distribution was expected, because NORs are clustered around the short arms of the acrocentric chromosomes, which contain tandem repeats of rRNA genes and satellite DNA. The clear enrichment of rRNA genes confirms the separation of nucleolar from total genomic DNA in these experiments.

Bottom Line: We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy.The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner.Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

ABSTRACT
The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

Show MeSH
Related in: MedlinePlus