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Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure.

Grand RS, Pichugina T, Gehlen LR, Jones MB, Tsai P, Allison JR, Martienssen R, O'Sullivan JM - Nucleic Acids Res. (2014)

Bottom Line: These models suggest that groups of genes with high and low, or differentially regulated transcript levels have preferred positions within the S. pombe nucleus.We conclude that the S. pombe nucleus is spatially divided into functional sub-nuclear domains that correlate with gene activity.The observation that chromosomal interactions are maintained even when chromosomes are fully condensed in M phase implicates genome organization in epigenetic inheritance and bookmarking.

View Article: PubMed Central - PubMed

Affiliation: Liggins institute, University of Auckland, Grafton Auckland 1032, NZ Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0745, NZ.

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Differentially regulated genes colocalize in a cell cycle-specific manner. Genes that had a ≥2-fold change in transcript level during each cell cycle transition were identified (Supplementary File 5). We then determined whether genes with up- or downregulated transcript levels colocalized at a frequency significantly different from randomly selected genomic regions. A significantly high level of (A) inter- and (B) intrachromosomal colocalization was detected between genes that were upregulated during the G1→G2 transition. (C) Interchromosomal colocalization of downregulated genes occurred at a significantly high level in captured interactions that were shared by M and G1 phases of the cell cycle. (D) Intrachromosomal colocalization of downregulated genes occurred at a significantly high level in the M→G1 and G2→M phase transitions. Venn-diagrams were modified to remove the interaction subsets that were not tested during specific cell cycle phase transitions. Individual P-values are presented in Supplementary Table S12. The expected FDR for (A–D) is 10%.
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Figure 5: Differentially regulated genes colocalize in a cell cycle-specific manner. Genes that had a ≥2-fold change in transcript level during each cell cycle transition were identified (Supplementary File 5). We then determined whether genes with up- or downregulated transcript levels colocalized at a frequency significantly different from randomly selected genomic regions. A significantly high level of (A) inter- and (B) intrachromosomal colocalization was detected between genes that were upregulated during the G1→G2 transition. (C) Interchromosomal colocalization of downregulated genes occurred at a significantly high level in captured interactions that were shared by M and G1 phases of the cell cycle. (D) Intrachromosomal colocalization of downregulated genes occurred at a significantly high level in the M→G1 and G2→M phase transitions. Venn-diagrams were modified to remove the interaction subsets that were not tested during specific cell cycle phase transitions. Individual P-values are presented in Supplementary Table S12. The expected FDR for (A–D) is 10%.

Mentions: Alterations in gene transcription have been associated with changes in the 3D position of a gene(s) (43,44) and the formation or breakage of DNA contacts (8). As for the high and low transcript level genes (Figure 4), we determined the colocalization frequency between genes that showed a ≥2-fold change in transcript level during cell cycle transitions (Figure 5, Supplementary Table S5 and Supplementary File 5). There was no detectable colocalization for many of the differentially regulated gene sets (Figure 5). However, genes that were upregulated during the G1→G2 cell cycle transition had high levels of interchromosomal colocalization in interactions specific to the G1 phase and shared between the G1 and G2 cell cycle phases (Figure 5A). These genes were also highly colocalized in intrachromosomal interaction subsets shared between G1 and G2, and in the subset specific to G2 (Figure 5B). Comparisons of the proportions of inter- and intrachromosomal colocalization for the differentially expressed (Supplementary Figure S10), high and low transcript gene sets revealed a reduction in intrachromosomal colocalization of differentially expressed genes involving elements separated by >50 kb (Supplementary Table S10). This was especially noticeable for genes that were upregulated on entry into M phase or downregulated upon entry into the M or G1 phases (Supplementary Table S10). Thus the genes that are differentially regulated as they enter and exit the M phase are typically involved in short range intrachromosomal connections that are less likely to be affected by M phase chromosome condensation.


Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure.

Grand RS, Pichugina T, Gehlen LR, Jones MB, Tsai P, Allison JR, Martienssen R, O'Sullivan JM - Nucleic Acids Res. (2014)

Differentially regulated genes colocalize in a cell cycle-specific manner. Genes that had a ≥2-fold change in transcript level during each cell cycle transition were identified (Supplementary File 5). We then determined whether genes with up- or downregulated transcript levels colocalized at a frequency significantly different from randomly selected genomic regions. A significantly high level of (A) inter- and (B) intrachromosomal colocalization was detected between genes that were upregulated during the G1→G2 transition. (C) Interchromosomal colocalization of downregulated genes occurred at a significantly high level in captured interactions that were shared by M and G1 phases of the cell cycle. (D) Intrachromosomal colocalization of downregulated genes occurred at a significantly high level in the M→G1 and G2→M phase transitions. Venn-diagrams were modified to remove the interaction subsets that were not tested during specific cell cycle phase transitions. Individual P-values are presented in Supplementary Table S12. The expected FDR for (A–D) is 10%.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4227791&req=5

Figure 5: Differentially regulated genes colocalize in a cell cycle-specific manner. Genes that had a ≥2-fold change in transcript level during each cell cycle transition were identified (Supplementary File 5). We then determined whether genes with up- or downregulated transcript levels colocalized at a frequency significantly different from randomly selected genomic regions. A significantly high level of (A) inter- and (B) intrachromosomal colocalization was detected between genes that were upregulated during the G1→G2 transition. (C) Interchromosomal colocalization of downregulated genes occurred at a significantly high level in captured interactions that were shared by M and G1 phases of the cell cycle. (D) Intrachromosomal colocalization of downregulated genes occurred at a significantly high level in the M→G1 and G2→M phase transitions. Venn-diagrams were modified to remove the interaction subsets that were not tested during specific cell cycle phase transitions. Individual P-values are presented in Supplementary Table S12. The expected FDR for (A–D) is 10%.
Mentions: Alterations in gene transcription have been associated with changes in the 3D position of a gene(s) (43,44) and the formation or breakage of DNA contacts (8). As for the high and low transcript level genes (Figure 4), we determined the colocalization frequency between genes that showed a ≥2-fold change in transcript level during cell cycle transitions (Figure 5, Supplementary Table S5 and Supplementary File 5). There was no detectable colocalization for many of the differentially regulated gene sets (Figure 5). However, genes that were upregulated during the G1→G2 cell cycle transition had high levels of interchromosomal colocalization in interactions specific to the G1 phase and shared between the G1 and G2 cell cycle phases (Figure 5A). These genes were also highly colocalized in intrachromosomal interaction subsets shared between G1 and G2, and in the subset specific to G2 (Figure 5B). Comparisons of the proportions of inter- and intrachromosomal colocalization for the differentially expressed (Supplementary Figure S10), high and low transcript gene sets revealed a reduction in intrachromosomal colocalization of differentially expressed genes involving elements separated by >50 kb (Supplementary Table S10). This was especially noticeable for genes that were upregulated on entry into M phase or downregulated upon entry into the M or G1 phases (Supplementary Table S10). Thus the genes that are differentially regulated as they enter and exit the M phase are typically involved in short range intrachromosomal connections that are less likely to be affected by M phase chromosome condensation.

Bottom Line: These models suggest that groups of genes with high and low, or differentially regulated transcript levels have preferred positions within the S. pombe nucleus.We conclude that the S. pombe nucleus is spatially divided into functional sub-nuclear domains that correlate with gene activity.The observation that chromosomal interactions are maintained even when chromosomes are fully condensed in M phase implicates genome organization in epigenetic inheritance and bookmarking.

View Article: PubMed Central - PubMed

Affiliation: Liggins institute, University of Auckland, Grafton Auckland 1032, NZ Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0745, NZ.

Show MeSH
Related in: MedlinePlus