Dataset Information

The genetic and epigenetic landscape of the Arabidopsis centromeres.

ABSTRACT: Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used long-read sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support CENTROMERE SPECIFIC HISTONE H3 (CENH3) occupancy and are densely DNA methylated, with satellite variants private to each chromosome. CENH3 preferentially occupies satellites that show the least amount of divergence and occur in higher-order repeats. The centromeres are invaded by ATHILA retrotransposons, which disrupt genetic and epigenetic organization. Centromeric crossover recombination is suppressed, yet low levels of meiotic DNA double-strand breaks occur that are regulated by DNA methylation. We propose that Arabidopsis centromeres are evolving through cycles of satellite homogenization and retrotransposon-driven diversification.

SUBMITTER: Naish M

PROVIDER: S-EPMC10164409 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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The genetic and epigenetic landscape of the <i>Arabidopsis</i> centromeres.

Naish Matthew M Alonge Michael M Wlodzimierz Piotr P Tock Andrew J AJ Abramson Bradley W BW Schmücker Anna A Mandáková Terezie T Jamge Bhagyshree B Lambing Christophe C Kuo Pallas P Yelina Natasha N Hartwick Nolan N Colt Kelly K Smith Lisa M LM Ton Jurriaan J Kakutani Tetsuji T Martienssen Robert A RA Schneeberger Korbinian K Lysak Martin A MA Berger Frédéric F Bousios Alexandros A Michael Todd P TP Schatz Michael C MC Henderson Ian R IR

Science (New York, N.Y.) 20211112 6569

Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used long-read sequencing to generate the Col-CEN <i>Arabidopsis thaliana</i> genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support CENTROMERE SPECIFIC HISTONE H3 (CENH3) occupancy and are densely DNA methylated, with satelli ...[more]

PMID: 34762468

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Project description:Deletion of native centromeres in the human fungal pathogen Cryptococcus deuterogattii leads to neocentromere formation. Native centromeres span truncated transposable elements, while neocentromeres do not and instead span actively expressed genes. To explore the epigenetic organization of neocentromeres, we analyzed the distribution of the heterochromatic histone modification H3K9me2, 5mC DNA methylation and the euchromatin mark H3K4me2. Native centromeres are enriched for both H3K9me2 and 5mC DNA methylation marks and are devoid of H3K4me2, while neocentromeres do not exhibit any of these features. Neocentromeres in cen10Δ mutants are unstable and chromosome-chromosome fusions occur. After chromosome fusion, the neocentromere is inactivated and the native centromere of the chromosome fusion partner remains as the sole, active centromere. In the present study, the active centromere of a fused chromosome was deleted to investigate if epigenetic memory promoted the re-activation of the inactive neocentromere. Our results show that the inactive neocentromere is not re-activated and instead a novel neocentromere forms directly adjacent to the deleted centromere of the fused chromosome. To study the impact of transcription on centromere stability, the actively expressed URA5 gene was introduced into the CENP-A bound regions of a native centromere. The introduction of the URA5 gene led to a loss of CENP-A from the native centromere, and a neocentromere formed adjacent to the native centromere location. Remarkably, the inactive, native centromere remained enriched for heterochromatin, yet the integrated gene was expressed and devoid of H3K9me2. A cumulative analysis of multiple CENP-A distribution profiles revealed centromere drift in C. deuterogattii, a previously unreported phenomenon in fungi. The CENP-A-binding shifted within the ORF-free regions and showed a possible association with a truncated transposable element. Taken together, our findings reveal that neocentromeres in C. deuterogattii are highly unstable and are not marked with an epigenetic memory, distinguishing them from native centromeres.

Dataset Information

The genetic and epigenetic landscape of the Arabidopsis centromeres.

Publications

The genetic and epigenetic landscape of the <i>Arabidopsis</i> centromeres.

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Dataset Information

The genetic and epigenetic landscape of the Arabidopsis centromeres.

Publications

The genetic and epigenetic landscape of the &lt;i&gt;Arabidopsis&lt;/i&gt; centromeres.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

The genetic and epigenetic landscape of the <i>Arabidopsis</i> centromeres.