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Chromatin associations in Arabidopsis interphase nuclei.

Schubert V, Rudnik R, Schubert I - Front Genet (2014)

Bottom Line: We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances.The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns.Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Stadt Seeland, Germany.

ABSTRACT
The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA repair. To test whether such associations are present in plants we analyzed Arabidopsis thaliana interphase nuclei by FISH using probes from different chromosomes. We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances. The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns. Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus. Nevertheless, chromatin movement enables a flexible spatial genome arrangement in plant nuclei.

No MeSH data available.


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Heterologous associations in cis and trans. (A) Schemes of chromosomes 1, 3, and 5 showing euchromatin segments (probed by BACs) containing high (connected by bold red lines) or low (bold green lines) co-expressing genes (encoded proteins in parentheses). The percentage of association in cis or trans in 2C and 4C nuclei is indicated (for number of nuclei analyzed see Table S3). The thin black lines indicate combinations with missing co-expression data. (B) Examples of 2C and 4C nuclei showing different configurations of euchromatic segments probes by BACS F28P5, T29H11, and F13K9. The segments may be associated (arrows) or separated. Compare 2C values with the simulated random values according to the RSD model for loci at different arms of the same chromosome (17.2%) and for loci located at different chromosomes (9.9%) (*P < 0.05, **P < 0.01; ***P < 0.001).
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Figure 5: Heterologous associations in cis and trans. (A) Schemes of chromosomes 1, 3, and 5 showing euchromatin segments (probed by BACs) containing high (connected by bold red lines) or low (bold green lines) co-expressing genes (encoded proteins in parentheses). The percentage of association in cis or trans in 2C and 4C nuclei is indicated (for number of nuclei analyzed see Table S3). The thin black lines indicate combinations with missing co-expression data. (B) Examples of 2C and 4C nuclei showing different configurations of euchromatic segments probes by BACS F28P5, T29H11, and F13K9. The segments may be associated (arrows) or separated. Compare 2C values with the simulated random values according to the RSD model for loci at different arms of the same chromosome (17.2%) and for loci located at different chromosomes (9.9%) (*P < 0.05, **P < 0.01; ***P < 0.001).

Mentions: To test whether euchromatin segments of A. thaliana bearing high or low co-expressing genes show a different association frequency, we performed FISH experiments with suitable BAC combinations as probes and determined their association frequency. The selected BACs contain genes coding for the SMC complex subunit SMC4A (a condensin subunit; Schubert, 2009) and the potential CTCF insulator factors C2H2 and REF6 (www.arabidopsis.org) which are known to act in a concerted manner and to be involved in chromatin organization and transcriptional regulation (Poon and Mekhail, 2011; Huang et al., 2013). With these genes as reference (except Ref6 because data were not available) highly and lowly co-expressing genes were determined based on the Comprehensive Systems Biology database (CSB.DB; Steinhauser et al., 2004) (Table S2). Then the BACs bearing these genes were labeled in different colors and hybridized in five different combinations of probes from chromosomes 1, 3, and 5 in cis or trans to 2C and 4C leaf nuclei (Figure 5).


Chromatin associations in Arabidopsis interphase nuclei.

Schubert V, Rudnik R, Schubert I - Front Genet (2014)

Heterologous associations in cis and trans. (A) Schemes of chromosomes 1, 3, and 5 showing euchromatin segments (probed by BACs) containing high (connected by bold red lines) or low (bold green lines) co-expressing genes (encoded proteins in parentheses). The percentage of association in cis or trans in 2C and 4C nuclei is indicated (for number of nuclei analyzed see Table S3). The thin black lines indicate combinations with missing co-expression data. (B) Examples of 2C and 4C nuclei showing different configurations of euchromatic segments probes by BACS F28P5, T29H11, and F13K9. The segments may be associated (arrows) or separated. Compare 2C values with the simulated random values according to the RSD model for loci at different arms of the same chromosome (17.2%) and for loci located at different chromosomes (9.9%) (*P < 0.05, **P < 0.01; ***P < 0.001).
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 5: Heterologous associations in cis and trans. (A) Schemes of chromosomes 1, 3, and 5 showing euchromatin segments (probed by BACs) containing high (connected by bold red lines) or low (bold green lines) co-expressing genes (encoded proteins in parentheses). The percentage of association in cis or trans in 2C and 4C nuclei is indicated (for number of nuclei analyzed see Table S3). The thin black lines indicate combinations with missing co-expression data. (B) Examples of 2C and 4C nuclei showing different configurations of euchromatic segments probes by BACS F28P5, T29H11, and F13K9. The segments may be associated (arrows) or separated. Compare 2C values with the simulated random values according to the RSD model for loci at different arms of the same chromosome (17.2%) and for loci located at different chromosomes (9.9%) (*P < 0.05, **P < 0.01; ***P < 0.001).
Mentions: To test whether euchromatin segments of A. thaliana bearing high or low co-expressing genes show a different association frequency, we performed FISH experiments with suitable BAC combinations as probes and determined their association frequency. The selected BACs contain genes coding for the SMC complex subunit SMC4A (a condensin subunit; Schubert, 2009) and the potential CTCF insulator factors C2H2 and REF6 (www.arabidopsis.org) which are known to act in a concerted manner and to be involved in chromatin organization and transcriptional regulation (Poon and Mekhail, 2011; Huang et al., 2013). With these genes as reference (except Ref6 because data were not available) highly and lowly co-expressing genes were determined based on the Comprehensive Systems Biology database (CSB.DB; Steinhauser et al., 2004) (Table S2). Then the BACs bearing these genes were labeled in different colors and hybridized in five different combinations of probes from chromosomes 1, 3, and 5 in cis or trans to 2C and 4C leaf nuclei (Figure 5).

Bottom Line: We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances.The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns.Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Stadt Seeland, Germany.

ABSTRACT
The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA repair. To test whether such associations are present in plants we analyzed Arabidopsis thaliana interphase nuclei by FISH using probes from different chromosomes. We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances. The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns. Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus. Nevertheless, chromatin movement enables a flexible spatial genome arrangement in plant nuclei.

No MeSH data available.


Related in: MedlinePlus