Project description:In organisms ranging from vertebrates to plants, major components of centromeres are rapidly-evolving repeat sequences, such as tandem repeats (TRs) and transposable elements (TEs). These repeats harbor centromere-specific histone H3 (CENH3), which also evolves rapidly. Complete centromere structures recently determined in human and Arabidopsis suggest frequent integration and purging of retrotransposons within the TR regions of centromeres. Despite the high impact of “centrophilic” retrotransposons on the paradox of rapid centromere evolution, the mechanisms involved in centromere targeting remain poorly understood in any organism. Here we show that both Ty3 and Ty1/Copia LTR elements rapidly turnover within the centromeric TRs of Arabidopsis species. We demonstrate that the Ty1/Copia element Tal1 (Transposon of Arabidopsis lyrata 1) integrates de novo into regions occupied by CENH3 in A. thaliana, and that ectopic expansion of the CENH3 region results in spread of Tal1 integration regions. The integration spectra of chimeric TEs revealed the key structural variations responsible for the contrasting chromatin targeting specificities to centromeres versus gene-rich regions, which have recurrently converted during the evolution of these TEs. Our findings reveal the impact of centromeric chromatin on TE-mediated rapid centromere evolution, with relevance across eukaryotic genomes.
Project description:In organisms ranging from vertebrates to plants, major components of centromeres are rapidly-evolving repeat sequences, such as tandem repeats (TRs) and transposable elements (TEs). These repeats harbor centromere-specific histone H3 (CENH3), which also evolves rapidly. Complete centromere structures recently determined in human and Arabidopsis suggest frequent integration and purging of retrotransposons within the TR regions of centromeres. Despite the high impact of “centrophilic” retrotransposons on the paradox of rapid centromere evolution, the mechanisms involved in centromere targeting remain poorly understood in any organism. Here we show that both Ty3 and Ty1/Copia LTR elements rapidly turnover within the centromeric TRs of Arabidopsis species. We demonstrate that the Ty1/Copia element Tal1 (Transposon of Arabidopsis lyrata 1) integrates de novo into regions occupied by CENH3 in A. thaliana, and that ectopic expansion of the CENH3 region results in spread of Tal1 integration regions. The integration spectra of chimeric TEs revealed the key structural variations responsible for the contrasting chromatin targeting specificities to centromeres versus gene-rich regions, which have recurrently converted during the evolution of these TEs. Our findings reveal the impact of centromeric chromatin on TE-mediated rapid centromere evolution, with relevance across eukaryotic genomes.
Project description:Chromatin immunoprecipitation analysis of CENH3 in the Arabidopsis thaliana accessions Col-0, Ler-0, Cvi-0 and Tanz-1 was performed in order to align reads to PacBio HiFi genome assemblies which contain complete centromere repeat arrays.
Project description:The intent of the experiment was to infer from transcriptome data the differential activation of LTR retrotransposon family members from Onsen/COPIA78, an Arabidopsis thaliana's heat-activated retrotransposon. For this, we performed Illumina 150 bp pair-end RNA-seq, in both wild-type Col-0 and RdDM mutant nrpd1-3 under control and heat stress.
Project description:The intent of the experiment was to infer from DNA sequencing the occurrence of extra-chromosomal DNA from Arabidopsis thaliana's heat-activated LTR retrotransposon Onsen/COPIA78. For this, we performed Illumina 150 bp pair-end PCR-free DNA genome re-sequencing, in both wild-type Col-0 and RdDM mutant nrpd1-3 under control and heat stress.