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The C. elegans dosage compensation complex mediates interphase X chromosome compaction.

Lau AC, Nabeshima K, Csankovszki G - Epigenetics Chromatin (2014)

Bottom Line: In addition, we show that SET-1, SET-4, and SIR-2.1, histone modifiers whose activity is regulated by the DCC, need to be present for the compaction of the X chromosome territory.These results support the idea that condensin I(DC), and the histone modifications regulated by the DCC, mediate interphase X chromosome compaction.Our results link condensin-mediated chromosome compaction, an activity connected to mitotic chromosome condensation, to chromosome-wide repression of gene expression in interphase.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 Michigan.

ABSTRACT

Background: Dosage compensation is a specialized gene regulatory mechanism which equalizes X-linked gene expression between sexes. In Caenorhabditis elegans, dosage compensation is achieved by the activity of the dosage compensation complex (DCC). The DCC localizes to both X chromosomes in hermaphrodites to downregulate gene expression by half. The DCC contains a subcomplex (condensin I(DC)) similar to the evolutionarily conserved condensin complexes which play fundamental roles in chromosome dynamics during mitosis and meiosis. Therefore, mechanisms related to mitotic chromosome condensation have been long hypothesized to mediate dosage compensation. However experimental evidence was lacking.

Results: Using 3D FISH microscopy to measure the volumes of X and chromosome I territories and to measure distances between individual loci, we show that hermaphrodite worms deficient in DCC proteins have enlarged interphase X chromosomes when compared to wild type. By contrast, chromosome I is unaffected. Interestingly, hermaphrodite worms depleted of condensin I or II show no phenotype. Therefore X chromosome compaction is specific to condensin I(DC). In addition, we show that SET-1, SET-4, and SIR-2.1, histone modifiers whose activity is regulated by the DCC, need to be present for the compaction of the X chromosome territory.

Conclusion: These results support the idea that condensin I(DC), and the histone modifications regulated by the DCC, mediate interphase X chromosome compaction. Our results link condensin-mediated chromosome compaction, an activity connected to mitotic chromosome condensation, to chromosome-wide repression of gene expression in interphase.

No MeSH data available.


Related in: MedlinePlus

X chromatin compaction is evident at all genomic distances examined. (A) FISH probe pairs across the X chromosome. The position of YAC probes (red and white boxes) used in FISH is indicated. (B) 2D projections of 3D stacked images. Representative stained diploid nuclei of adult hermaphrodite wild type and dpy-21(e428) worms. Nuclei stained with probes pairs across the X chromosome (red and white) and counterstained with DAPI (blue) to label DNA. Scale bars equal 1 μm. (C) Boxplots indicating the distribution of 3D loci distances for wild type (n = 20) and dpy-21(e428) (n = 20) diploid nuclei. Boxes show the median and interquartile range of the data. Asterisks indicate level of statistical significance by t-test analysis (one asterisk, P <0.05; two asterisks, P <0.01; three asterisks, P <0.001).
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Fig4: X chromatin compaction is evident at all genomic distances examined. (A) FISH probe pairs across the X chromosome. The position of YAC probes (red and white boxes) used in FISH is indicated. (B) 2D projections of 3D stacked images. Representative stained diploid nuclei of adult hermaphrodite wild type and dpy-21(e428) worms. Nuclei stained with probes pairs across the X chromosome (red and white) and counterstained with DAPI (blue) to label DNA. Scale bars equal 1 μm. (C) Boxplots indicating the distribution of 3D loci distances for wild type (n = 20) and dpy-21(e428) (n = 20) diploid nuclei. Boxes show the median and interquartile range of the data. Asterisks indicate level of statistical significance by t-test analysis (one asterisk, P <0.05; two asterisks, P <0.01; three asterisks, P <0.001).

Mentions: To further investigate the genomic scale at which condensin operates we performed 3D FISH with pairs of X chromosome YAC probes separated by genomic distances ranging from 0.5 Mb to 7.2 Mb (Figure 4A and B). Such analysis has been previously used to demonstrate a role for polycomb repressive complexes in compacting chromatin in mouse embryonic stem cells, and a role for condensin II to promote compaction of chromosome territories in Drosophila[39, 56]. Since this analysis is not possible in polyploidy intestinal nuclei we analyzed the pairs of probes in wild type and dpy-21(e428) mutant diploid tail tip cells. Eighty-three percent of wild type diploid cells and 79% of dpy-21(e428) diploid cells had two clear spots for each probe, while others had either no spots due to high background or had one spot (presumably due to the overlap of two closely spaced spots). Nuclei with 0 or one spot were excluded from our analysis. No nuclei had three or four spots. These observations indicate that these cells have an unreplicated diploid DNA content. At all four genomic distances we detected a significant increase in distances in dpy-21(e428) mutants compared to wild type (Figure 4C). This more dispersed distribution of the two loci found in dpy-21(e428) correlates with the larger X chromosome territories found in the dosage compensation mutants. These data suggest that dosage compensation can be linked to levels of higher-order X chromatin compaction, both at the level of whole chromosomes and at a genomic scale as small as 0.5 Mb and as large as 7.2 Mb.Figure 4


The C. elegans dosage compensation complex mediates interphase X chromosome compaction.

Lau AC, Nabeshima K, Csankovszki G - Epigenetics Chromatin (2014)

X chromatin compaction is evident at all genomic distances examined. (A) FISH probe pairs across the X chromosome. The position of YAC probes (red and white boxes) used in FISH is indicated. (B) 2D projections of 3D stacked images. Representative stained diploid nuclei of adult hermaphrodite wild type and dpy-21(e428) worms. Nuclei stained with probes pairs across the X chromosome (red and white) and counterstained with DAPI (blue) to label DNA. Scale bars equal 1 μm. (C) Boxplots indicating the distribution of 3D loci distances for wild type (n = 20) and dpy-21(e428) (n = 20) diploid nuclei. Boxes show the median and interquartile range of the data. Asterisks indicate level of statistical significance by t-test analysis (one asterisk, P <0.05; two asterisks, P <0.01; three asterisks, P <0.001).
© Copyright Policy - open-access
Related In: Results  -  Collection

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Fig4: X chromatin compaction is evident at all genomic distances examined. (A) FISH probe pairs across the X chromosome. The position of YAC probes (red and white boxes) used in FISH is indicated. (B) 2D projections of 3D stacked images. Representative stained diploid nuclei of adult hermaphrodite wild type and dpy-21(e428) worms. Nuclei stained with probes pairs across the X chromosome (red and white) and counterstained with DAPI (blue) to label DNA. Scale bars equal 1 μm. (C) Boxplots indicating the distribution of 3D loci distances for wild type (n = 20) and dpy-21(e428) (n = 20) diploid nuclei. Boxes show the median and interquartile range of the data. Asterisks indicate level of statistical significance by t-test analysis (one asterisk, P <0.05; two asterisks, P <0.01; three asterisks, P <0.001).
Mentions: To further investigate the genomic scale at which condensin operates we performed 3D FISH with pairs of X chromosome YAC probes separated by genomic distances ranging from 0.5 Mb to 7.2 Mb (Figure 4A and B). Such analysis has been previously used to demonstrate a role for polycomb repressive complexes in compacting chromatin in mouse embryonic stem cells, and a role for condensin II to promote compaction of chromosome territories in Drosophila[39, 56]. Since this analysis is not possible in polyploidy intestinal nuclei we analyzed the pairs of probes in wild type and dpy-21(e428) mutant diploid tail tip cells. Eighty-three percent of wild type diploid cells and 79% of dpy-21(e428) diploid cells had two clear spots for each probe, while others had either no spots due to high background or had one spot (presumably due to the overlap of two closely spaced spots). Nuclei with 0 or one spot were excluded from our analysis. No nuclei had three or four spots. These observations indicate that these cells have an unreplicated diploid DNA content. At all four genomic distances we detected a significant increase in distances in dpy-21(e428) mutants compared to wild type (Figure 4C). This more dispersed distribution of the two loci found in dpy-21(e428) correlates with the larger X chromosome territories found in the dosage compensation mutants. These data suggest that dosage compensation can be linked to levels of higher-order X chromatin compaction, both at the level of whole chromosomes and at a genomic scale as small as 0.5 Mb and as large as 7.2 Mb.Figure 4

Bottom Line: In addition, we show that SET-1, SET-4, and SIR-2.1, histone modifiers whose activity is regulated by the DCC, need to be present for the compaction of the X chromosome territory.These results support the idea that condensin I(DC), and the histone modifications regulated by the DCC, mediate interphase X chromosome compaction.Our results link condensin-mediated chromosome compaction, an activity connected to mitotic chromosome condensation, to chromosome-wide repression of gene expression in interphase.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 Michigan.

ABSTRACT

Background: Dosage compensation is a specialized gene regulatory mechanism which equalizes X-linked gene expression between sexes. In Caenorhabditis elegans, dosage compensation is achieved by the activity of the dosage compensation complex (DCC). The DCC localizes to both X chromosomes in hermaphrodites to downregulate gene expression by half. The DCC contains a subcomplex (condensin I(DC)) similar to the evolutionarily conserved condensin complexes which play fundamental roles in chromosome dynamics during mitosis and meiosis. Therefore, mechanisms related to mitotic chromosome condensation have been long hypothesized to mediate dosage compensation. However experimental evidence was lacking.

Results: Using 3D FISH microscopy to measure the volumes of X and chromosome I territories and to measure distances between individual loci, we show that hermaphrodite worms deficient in DCC proteins have enlarged interphase X chromosomes when compared to wild type. By contrast, chromosome I is unaffected. Interestingly, hermaphrodite worms depleted of condensin I or II show no phenotype. Therefore X chromosome compaction is specific to condensin I(DC). In addition, we show that SET-1, SET-4, and SIR-2.1, histone modifiers whose activity is regulated by the DCC, need to be present for the compaction of the X chromosome territory.

Conclusion: These results support the idea that condensin I(DC), and the histone modifications regulated by the DCC, mediate interphase X chromosome compaction. Our results link condensin-mediated chromosome compaction, an activity connected to mitotic chromosome condensation, to chromosome-wide repression of gene expression in interphase.

No MeSH data available.


Related in: MedlinePlus