Limits...
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.


Related in: MedlinePlus

Interstitial chromatin associations. (A–D) Schemes of chromosomes 1 and 3 showing interstitial positions of single BAC and BAC contig inserts in different color as used for FISH. (A1) Parts of both ~100 kb euchromatin segments are elongated in one homolog each thus showing a second signal (arrows) in an 2C nucleus. (B1) The ~100 kb segments T7N9 and F11P17 located on different arms of chromosome 1 may both be cohesive (left) or one may be separated (right, T7N9) in 4C nuclei. In the right nucleus all four F11P17 sister chromatid segments are cohesive and associated (arrow) indicated by the location apart (~5 μm, double arrow) from the lower located homolog position marked by the two T7N9 signals (asterisk). (C1) The top 4C nucleus contains the 760 kb contig of both homologs in close vicinity. The bottom nucleus displays the same contig, but the T1F9 segment of one homolog moved apart from its contig position (~2.5 μm, double arrow) toward the second homolog (arrow). (D1) Examples of chromatin configurations in 4C nuclei labeled by ~2.8 Mb (X) and ~2.6 Mb BAC (Y) contigs, respectively, in combination with the segment T7N9 from the same chromosome arm. In the first nucleus the green contigs are associated with the T7N9 segment, in the second nucleus the segments are located at the edges of the contigs, and in the third nucleus two of the non-cohesive T7N9 segments are present distantly from the contigs. The fourth and fifth nuclei demonstrate, that the T7N9 segments, although located ~3.3 Mb apart from the ~2.6 Mb contig may be localized within this domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4230181&req=5

Figure 3: Interstitial chromatin associations. (A–D) Schemes of chromosomes 1 and 3 showing interstitial positions of single BAC and BAC contig inserts in different color as used for FISH. (A1) Parts of both ~100 kb euchromatin segments are elongated in one homolog each thus showing a second signal (arrows) in an 2C nucleus. (B1) The ~100 kb segments T7N9 and F11P17 located on different arms of chromosome 1 may both be cohesive (left) or one may be separated (right, T7N9) in 4C nuclei. In the right nucleus all four F11P17 sister chromatid segments are cohesive and associated (arrow) indicated by the location apart (~5 μm, double arrow) from the lower located homolog position marked by the two T7N9 signals (asterisk). (C1) The top 4C nucleus contains the 760 kb contig of both homologs in close vicinity. The bottom nucleus displays the same contig, but the T1F9 segment of one homolog moved apart from its contig position (~2.5 μm, double arrow) toward the second homolog (arrow). (D1) Examples of chromatin configurations in 4C nuclei labeled by ~2.8 Mb (X) and ~2.6 Mb BAC (Y) contigs, respectively, in combination with the segment T7N9 from the same chromosome arm. In the first nucleus the green contigs are associated with the T7N9 segment, in the second nucleus the segments are located at the edges of the contigs, and in the third nucleus two of the non-cohesive T7N9 segments are present distantly from the contigs. The fourth and fifth nuclei demonstrate, that the T7N9 segments, although located ~3.3 Mb apart from the ~2.6 Mb contig may be localized within this domain.

Mentions: For testing to what degree homologous and heterologous chromatin associations appear between distinct chromatin segments of different genetic positions, we labeled euchromatin segments of different sizes (~80 kb, ~760 kb, ~2.6 Mb, ~2.8 Mb) in different colors and combined them for FISH (Figure 3).


Chromatin associations in Arabidopsis interphase nuclei.

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

Interstitial chromatin associations. (A–D) Schemes of chromosomes 1 and 3 showing interstitial positions of single BAC and BAC contig inserts in different color as used for FISH. (A1) Parts of both ~100 kb euchromatin segments are elongated in one homolog each thus showing a second signal (arrows) in an 2C nucleus. (B1) The ~100 kb segments T7N9 and F11P17 located on different arms of chromosome 1 may both be cohesive (left) or one may be separated (right, T7N9) in 4C nuclei. In the right nucleus all four F11P17 sister chromatid segments are cohesive and associated (arrow) indicated by the location apart (~5 μm, double arrow) from the lower located homolog position marked by the two T7N9 signals (asterisk). (C1) The top 4C nucleus contains the 760 kb contig of both homologs in close vicinity. The bottom nucleus displays the same contig, but the T1F9 segment of one homolog moved apart from its contig position (~2.5 μm, double arrow) toward the second homolog (arrow). (D1) Examples of chromatin configurations in 4C nuclei labeled by ~2.8 Mb (X) and ~2.6 Mb BAC (Y) contigs, respectively, in combination with the segment T7N9 from the same chromosome arm. In the first nucleus the green contigs are associated with the T7N9 segment, in the second nucleus the segments are located at the edges of the contigs, and in the third nucleus two of the non-cohesive T7N9 segments are present distantly from the contigs. The fourth and fifth nuclei demonstrate, that the T7N9 segments, although located ~3.3 Mb apart from the ~2.6 Mb contig may be localized within this domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230181&req=5

Figure 3: Interstitial chromatin associations. (A–D) Schemes of chromosomes 1 and 3 showing interstitial positions of single BAC and BAC contig inserts in different color as used for FISH. (A1) Parts of both ~100 kb euchromatin segments are elongated in one homolog each thus showing a second signal (arrows) in an 2C nucleus. (B1) The ~100 kb segments T7N9 and F11P17 located on different arms of chromosome 1 may both be cohesive (left) or one may be separated (right, T7N9) in 4C nuclei. In the right nucleus all four F11P17 sister chromatid segments are cohesive and associated (arrow) indicated by the location apart (~5 μm, double arrow) from the lower located homolog position marked by the two T7N9 signals (asterisk). (C1) The top 4C nucleus contains the 760 kb contig of both homologs in close vicinity. The bottom nucleus displays the same contig, but the T1F9 segment of one homolog moved apart from its contig position (~2.5 μm, double arrow) toward the second homolog (arrow). (D1) Examples of chromatin configurations in 4C nuclei labeled by ~2.8 Mb (X) and ~2.6 Mb BAC (Y) contigs, respectively, in combination with the segment T7N9 from the same chromosome arm. In the first nucleus the green contigs are associated with the T7N9 segment, in the second nucleus the segments are located at the edges of the contigs, and in the third nucleus two of the non-cohesive T7N9 segments are present distantly from the contigs. The fourth and fifth nuclei demonstrate, that the T7N9 segments, although located ~3.3 Mb apart from the ~2.6 Mb contig may be localized within this domain.
Mentions: For testing to what degree homologous and heterologous chromatin associations appear between distinct chromatin segments of different genetic positions, we labeled euchromatin segments of different sizes (~80 kb, ~760 kb, ~2.6 Mb, ~2.8 Mb) in different colors and combined them for FISH (Figure 3).

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