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Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis

ABSTRACT: Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis

PROVIDER: PRJNA832333 | ENA |

REPOSITORIES: ENA

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Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis

Project description:This study investigated the mechanisms and novel engineering strategy of locus- specific transgenerational epigenetic inheritance by depositing centromere repeats

2023-05-31 | GSE201629 | GEO

Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis.

Project description:Stable transmission of non-DNA-sequence-based epigenetic information contributes to heritable phenotypic variants and thus to biological diversity. While studies on spontaneous natural epigenome variants have revealed an association of epialleles with a wide range of biological traits in both plants and animals, the function, transmission mechanism, and stability of an epiallele over generations in a locus-specific manner remain poorly investigated. Here, we invented a DNA sequence deposition strategy to generate a locus-specific epiallele by depositing CEN180 satellite repeats into a euchromatic target locus in Arabidopsis. Using CRISPR/Cas9-mediated knock-in system, we demonstrated that depositing CEN180 repeats can induce heterochromatin nucleation accompanied by DNA methylation, H3K9me2, and changes in the nucleosome occupancy at the insertion sites. Interestingly, both DNA methylation and H3K9me2 are restricted within the depositing sites and depletion of an H3K9me2 demethylase IBM1 enables the outward heterochromatin propagation into the neighboring regions, leading to inheritable target gene silencing to persist for at least five generations. Together, these results demonstrate the promise of employing a cis-engineering system for the creation of stable and site-specific epialleles and provide important insights into functional epigenome studies and locus-specific transgenerational epigenetic inheritance.

| S-EPMC10325890 | biostudies-literature

Intragenic DNA inversions expand bacterial coding capacity

Project description:Bacteria can generate heterogeneity through phase variation, including enzyme-mediated inversion of specific intergenic regions of genomic DNA. We developed a computation tool that identifies invertible elements using long-read datasets, PhaVa. We identified over 300 ‘intragenic invertons,’ a new class of invertible elements entirely within genes, in both bacteria and archaea. In the gut commensal Bacteroides thetaiotaomicron, we experimentally characterized an intragenic inverton in the thiamine biosynthesis protein thiC. We used mass spectrometry in data-independent acquisition mode to identify and quantify B. theta proteins, including thiC inverton expression at the protein level.

2024-08-06 | PXD054577 | Pride

Genome-wide maps of chromatin state (H3K9me2 or CENP-A/Cnp1) in wt strains carrying the inactivated Centromere 1 or 2 or Cnp1 spreading with ura4 inserted into the right side of the repetitive sequences of Chromosome 1 (designated as otr1R::ura4)

Project description:We report the high-throughput profiling of histone modification (H3K9me2) or histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 or CENP-A/Cnp1 maps of wild type strains carrying the inactivated Centromere 1 or Centromere 2 or Cnp1 spreading in fission yeast with a reporter gene ura4 cassette inserted into the right side of the repetitive sequences of Chromosome 1 . We find that neocemtromeres are formed preferably at pericentromeric regions ubiquitously and asymmetrically in all three centromeres of these indicated strains.

2019-09-28 | GSE131225 | GEO

The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3

Project description:Centromere is the chromosomal locus at which kinetochore is assembled to direct chromosome segregation. Histone H3 variant CENP-A epigenetically marks active centromeres; however, the mechanism by which CENP-A propagates at the centromere, replacing histone H3, remains poorly understood. Using fission yeast, we find that CENP-ACnp1 chromatin assembly at the centromere requires the Ino80 ATP-dependent chromatin remodeling complex which removes histone H3-containing nucleosomes from associated chromatin. CENP-ACnp1 chromatin actively recruits the Ino80 complex to centromeres to elicit eviction of histone H3-containing nucleosomes. Artificial targeting of Ino80 subunits to a non-centromeric DNA placed in a native centromere enhances the spreading of CENP-ACnp1 chromatin into the non-centromeric DNA. Based on these results, we propose that CENP-ACnp1 chromatin employs the Ino80 complex to mediate replacement of histone H3 with CENP-ACnp1, and thereby reinforces itself.

2017-07-14 | GSE99589 | GEO

DNA replication-mediated error correction of ectopic CENP-A deposition maintains centromere identity

Project description:Chromatin assembled with histone H3 variant CENP-A is the heritable epigenetic determinant of human centromere identity. Using genome-wide mapping and reference models for 23 human centromeres, CENP-A is shown in early G1 to be assembled into nucleosomes within megabase, repetitive a-satellite DNAs at each centromere and onto 11,390 sites on the chromosome arms. Centromere-bound CENP-A is found to be quantitatively maintained during DNA replication by coordinated action of the MCM2 helicase, CAF1, HJURP, and the CCAN network of constitutive centromere components. CCAN serves to tether CENP-A removed by MCM2, thereby enabling local reassembly onto both daughter centromeres with identical DNA sequence preferences and nucleosome phasing as the loading in G1 and independent of CENP-B. Conversely, without CCAN-mediated tethering, DNA replication removes CENP-A from sites on the chromosome arms. Our data identify an MCM2/CAF1/HJURP- and CCAN-dependent error correction mechanism that acts in S-phase to maintain CENP-A-dependent centromere identity.

2019-03-20 | GSE111381 | GEO

Centromere misdivision promotes centromeric sequence changes, de novo centromere formation, and centromere expansion

Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids.

2016-04-02 | GSE63752 | GEO

Genome-wide maps of histone H3 variant CENP-A/Cnp1 in the meiotic haploid progeny of wip1∆/+, mhf1∆/+ and mhf2∆/+ and genome-wide maps of histone H3 variant CENP-A/Cnp1 in mhf2+ (or mhf2∆) carrying the inactivated Centromere 1 or Centromere 2.

Project description:We report the high-throughput profiling of histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide CENP-A/Cnp1 maps of the wild type meiotic haploid progeny of heterozygous deletion diploid wip1∆/+, mhf1∆/+ and mhf2∆/+ and CENP-A/Cnp1 maps of mhf2+ carrying the inactivated Centromere 1 or Centromere 2. We find that CENP-A/Cnp1 spreading into the pericentromeric regions in wild type meiotic progeny of heterozygous deletion diploid wip1∆/+, mhf1∆/+ and mhf2∆/+.

2019-09-28 | GSE131223 | GEO

Centromere misdivision promotes centromeric sequence changes, de novo centromere formation, and centromere expansion

2016-04-02 | E-GEOD-63752 | biostudies-arrayexpress

cotton centromere study

Project description:cotton centromere study using ChIP-seq

| PRJEB14368 | ENA