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Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes.

Schotanus K, Soyer JL, Connolly LR, Grandaubert J, Happel P, Smith KM, Freitag M, Stukenbrock EH - Epigenetics Chromatin (2015)

Bottom Line: Supernumerary chromosomes have been found in many organisms.By fluorescence microscopy, we showed that centromeres of Z. tritici do not cluster into a single chromocenter during interphase.We found dramatically higher enrichment of H3K9me3 and H3K27me3 on the accessory chromosomes, consistent with the twofold higher proportion of repetitive DNA and poorly transcribed genes.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany ; Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7303 USA ; Christian-Albrechts University of Kiel, Environmental Genomics, Am Botanischen Garten 9-11, 24118 Kiel, Germany ; Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany.

ABSTRACT

Background: Supernumerary chromosomes have been found in many organisms. In fungi, these "accessory" or "dispensable" chromosomes are present at different frequencies in populations and are usually characterized by higher repetitive DNA content and lower gene density when compared to the core chromosomes. In the reference strain of the wheat pathogen, Zymoseptoria tritici, eight discrete accessory chromosomes have been found. So far, no functional role has been assigned to these chromosomes; however, they have existed as separate entities in the karyotypes of Zymoseptoria species over evolutionary time. In this study, we addressed what-if anything-distinguishes the chromatin of accessory chromosomes from core chromosomes. We used chromatin immunoprecipitation combined with high-throughput sequencing ("ChIP-seq") of DNA associated with the centromere-specific histone H3, CENP-A (CenH3), to identify centromeric DNA, and ChIP-seq with antibodies against dimethylated H3K4, trimethylated H3K9 and trimethylated H3K27 to determine the relative distribution and proportion of euchromatin, obligate and facultative heterochromatin, respectively.

Results: Centromeres of the eight accessory chromosomes have the same sequence composition and structure as centromeres of the 13 core chromosomes and they are of similar length. Unlike those of most other fungi, Z. tritici centromeres are not composed entirely of repetitive DNA; some centromeres contain only unique DNA sequences, and bona fide expressed genes are located in regions enriched with CenH3. By fluorescence microscopy, we showed that centromeres of Z. tritici do not cluster into a single chromocenter during interphase. We found dramatically higher enrichment of H3K9me3 and H3K27me3 on the accessory chromosomes, consistent with the twofold higher proportion of repetitive DNA and poorly transcribed genes. In contrast, no single histone modification tested here correlated with the distribution of centromeric nucleosomes.

Conclusions: All centromeres are similar in length and composed of a mixture of unique and repeat DNA, and most contain actively transcribed genes. Centromeres, subtelomeric regions or telomere repeat length cannot account for the differences in transfer fidelity between core and accessory chromosomes, but accessory chromosomes are greatly enriched in nucleosomes with H3K27 trimethylation. Genes on accessory chromosomes appear to be silenced by trimethylation of H3K9 and H3K27.

No MeSH data available.


Related in: MedlinePlus

A large segment on the right arm of chromosome 7 shows similarities to an accessory chromosome. The left arm (Cen at 0.259–0.266 Mb) and most of the right arm (up to 1.8 Mb) of chromosome 7 are enriched for H3K4me2 (green) with H3K9me3 (red) and H3K27me3 (orange) found only in the Chr 7L subtelomeric region and TEs. A segment of ~865 kb beginning at 1.8 Mb is enriched with H3K27me3 and lacks gene expression. For each histone modification regions with statistically significant enrichment (see “Methods” for details) are depicted by rectangles in the same color. The apparent second centromeric peak and the strong H3K9me3 peak at position 1.69 Mb are explained by the presence of two rDNA repeats (see “Results” for detail). The ruler indicates chromosome coordinates (Coor, in Mb), and GC-content (%GC, red), centromere position determined by GFP–CenH3 enrichment (Cen, black), location of coding sequences (CDS, blue) and active or inactive transposable elements (TE, marine) are shown
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Fig6: A large segment on the right arm of chromosome 7 shows similarities to an accessory chromosome. The left arm (Cen at 0.259–0.266 Mb) and most of the right arm (up to 1.8 Mb) of chromosome 7 are enriched for H3K4me2 (green) with H3K9me3 (red) and H3K27me3 (orange) found only in the Chr 7L subtelomeric region and TEs. A segment of ~865 kb beginning at 1.8 Mb is enriched with H3K27me3 and lacks gene expression. For each histone modification regions with statistically significant enrichment (see “Methods” for details) are depicted by rectangles in the same color. The apparent second centromeric peak and the strong H3K9me3 peak at position 1.69 Mb are explained by the presence of two rDNA repeats (see “Results” for detail). The ruler indicates chromosome coordinates (Coor, in Mb), and GC-content (%GC, red), centromere position determined by GFP–CenH3 enrichment (Cen, black), location of coding sequences (CDS, blue) and active or inactive transposable elements (TE, marine) are shown

Mentions: Centromeres are not located in the longest AT-rich region. All 21 chromosomes are drawn to scale and the ruler indicates the length of the chromosomes (Core chromosomes in Mb, accessory chromosomes in kb). For each chromosome, the GC-content (%GC, red), centromere position as determined by GFP–CenH3 enrichment (Cen, black), coding sequences (CDS, blue) and active or inactive transposable elements (TE, marine) are shown. Centromeres in Z. tritici are small, ranging from 5.57 kb (Cen13) to 13.55 kb (Cen8). Regions with low GC % are enriched with TEs. Centromeres are not located in the longest AT-rich regions for both core (Chr 1-13) and accessory (Chr 14-21) chromosomes. The apparent second, smaller peak on Chr 7 coincides with two rDNA repeats (positions 1,676,706-1,682,207 and 1,684,968–1,690,469, interrupted by a 2.76 kb intergenic spacer). Of ~50 actual repeats only two are included in the current genome assembly, thus identical reads stack at these positions to yield a false CenH3 peak (for details see also Fig. 6)


Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes.

Schotanus K, Soyer JL, Connolly LR, Grandaubert J, Happel P, Smith KM, Freitag M, Stukenbrock EH - Epigenetics Chromatin (2015)

A large segment on the right arm of chromosome 7 shows similarities to an accessory chromosome. The left arm (Cen at 0.259–0.266 Mb) and most of the right arm (up to 1.8 Mb) of chromosome 7 are enriched for H3K4me2 (green) with H3K9me3 (red) and H3K27me3 (orange) found only in the Chr 7L subtelomeric region and TEs. A segment of ~865 kb beginning at 1.8 Mb is enriched with H3K27me3 and lacks gene expression. For each histone modification regions with statistically significant enrichment (see “Methods” for details) are depicted by rectangles in the same color. The apparent second centromeric peak and the strong H3K9me3 peak at position 1.69 Mb are explained by the presence of two rDNA repeats (see “Results” for detail). The ruler indicates chromosome coordinates (Coor, in Mb), and GC-content (%GC, red), centromere position determined by GFP–CenH3 enrichment (Cen, black), location of coding sequences (CDS, blue) and active or inactive transposable elements (TE, marine) are shown
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig6: A large segment on the right arm of chromosome 7 shows similarities to an accessory chromosome. The left arm (Cen at 0.259–0.266 Mb) and most of the right arm (up to 1.8 Mb) of chromosome 7 are enriched for H3K4me2 (green) with H3K9me3 (red) and H3K27me3 (orange) found only in the Chr 7L subtelomeric region and TEs. A segment of ~865 kb beginning at 1.8 Mb is enriched with H3K27me3 and lacks gene expression. For each histone modification regions with statistically significant enrichment (see “Methods” for details) are depicted by rectangles in the same color. The apparent second centromeric peak and the strong H3K9me3 peak at position 1.69 Mb are explained by the presence of two rDNA repeats (see “Results” for detail). The ruler indicates chromosome coordinates (Coor, in Mb), and GC-content (%GC, red), centromere position determined by GFP–CenH3 enrichment (Cen, black), location of coding sequences (CDS, blue) and active or inactive transposable elements (TE, marine) are shown
Mentions: Centromeres are not located in the longest AT-rich region. All 21 chromosomes are drawn to scale and the ruler indicates the length of the chromosomes (Core chromosomes in Mb, accessory chromosomes in kb). For each chromosome, the GC-content (%GC, red), centromere position as determined by GFP–CenH3 enrichment (Cen, black), coding sequences (CDS, blue) and active or inactive transposable elements (TE, marine) are shown. Centromeres in Z. tritici are small, ranging from 5.57 kb (Cen13) to 13.55 kb (Cen8). Regions with low GC % are enriched with TEs. Centromeres are not located in the longest AT-rich regions for both core (Chr 1-13) and accessory (Chr 14-21) chromosomes. The apparent second, smaller peak on Chr 7 coincides with two rDNA repeats (positions 1,676,706-1,682,207 and 1,684,968–1,690,469, interrupted by a 2.76 kb intergenic spacer). Of ~50 actual repeats only two are included in the current genome assembly, thus identical reads stack at these positions to yield a false CenH3 peak (for details see also Fig. 6)

Bottom Line: Supernumerary chromosomes have been found in many organisms.By fluorescence microscopy, we showed that centromeres of Z. tritici do not cluster into a single chromocenter during interphase.We found dramatically higher enrichment of H3K9me3 and H3K27me3 on the accessory chromosomes, consistent with the twofold higher proportion of repetitive DNA and poorly transcribed genes.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany ; Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7303 USA ; Christian-Albrechts University of Kiel, Environmental Genomics, Am Botanischen Garten 9-11, 24118 Kiel, Germany ; Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany.

ABSTRACT

Background: Supernumerary chromosomes have been found in many organisms. In fungi, these "accessory" or "dispensable" chromosomes are present at different frequencies in populations and are usually characterized by higher repetitive DNA content and lower gene density when compared to the core chromosomes. In the reference strain of the wheat pathogen, Zymoseptoria tritici, eight discrete accessory chromosomes have been found. So far, no functional role has been assigned to these chromosomes; however, they have existed as separate entities in the karyotypes of Zymoseptoria species over evolutionary time. In this study, we addressed what-if anything-distinguishes the chromatin of accessory chromosomes from core chromosomes. We used chromatin immunoprecipitation combined with high-throughput sequencing ("ChIP-seq") of DNA associated with the centromere-specific histone H3, CENP-A (CenH3), to identify centromeric DNA, and ChIP-seq with antibodies against dimethylated H3K4, trimethylated H3K9 and trimethylated H3K27 to determine the relative distribution and proportion of euchromatin, obligate and facultative heterochromatin, respectively.

Results: Centromeres of the eight accessory chromosomes have the same sequence composition and structure as centromeres of the 13 core chromosomes and they are of similar length. Unlike those of most other fungi, Z. tritici centromeres are not composed entirely of repetitive DNA; some centromeres contain only unique DNA sequences, and bona fide expressed genes are located in regions enriched with CenH3. By fluorescence microscopy, we showed that centromeres of Z. tritici do not cluster into a single chromocenter during interphase. We found dramatically higher enrichment of H3K9me3 and H3K27me3 on the accessory chromosomes, consistent with the twofold higher proportion of repetitive DNA and poorly transcribed genes. In contrast, no single histone modification tested here correlated with the distribution of centromeric nucleosomes.

Conclusions: All centromeres are similar in length and composed of a mixture of unique and repeat DNA, and most contain actively transcribed genes. Centromeres, subtelomeric regions or telomere repeat length cannot account for the differences in transfer fidelity between core and accessory chromosomes, but accessory chromosomes are greatly enriched in nucleosomes with H3K27 trimethylation. Genes on accessory chromosomes appear to be silenced by trimethylation of H3K9 and H3K27.

No MeSH data available.


Related in: MedlinePlus