Biology subjects

Axelsson, E.

Publications and source records attributed to Axelsson, E..

5 recordsLinked to original sources

bioRxiv2023

Histone variants shape the chromatin states in Arabidopsis

How different intrinsic sequence variation or regulatory modifications of histones regulate nucleosome interactions with transcription remain unclear. By contrast with H3 and H2B variants, H2A variants occupy specific domains of chromatin in Arabidopsis thaliana. Broad domains of chromatin are affected by the loss of remodelers that affect the deposition or the exchange of H2A variants. Notably, the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) is required to maintain enrichment in all markers of constitutive heterochromatin including DNA methylation, H3K9me1/2 and the variant H2A.W. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome and showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.

genomics↗

bioRxiv2022

Transposons repressed by H3K27me3 were co-opted as cis-regulatory elements of H3K27me3 controlled protein coding genes during evolution of plants

The mobility of transposable elements (TEs) contributes to evolution of genomes 1,2. Meanwhile, their uncontrolled activity causes genomic instability and therefore expression of TEs is silenced by host genomes 3,4. TEs are marked with DNA and H3K9 methylation that are associated with silencing in flowering plants 5, animals, and fungi 6. Yet, in distantly related eukaryotes TEs are instead marked by H3K27me3 deposited by the Polycomb Repressive Complex 2 (PRC2) 7-11, an epigenetic mark associated with gene silencing in multicellular eukaryotes 12-15. It was therefore proposed that the ancestral activity of PRC2 was the deposition of H3K27me3 to silence TEs 16. To test this hypothesis we obtained mutants deprived of PRC2 activity and used genomics to analyze the role of PRC2 in extant species along the lineage of Archaeplastida. While in the red alga Cyanidioschyzon merolae more TEs than genes were repressed by PRC2, an opposite trend was observed in bryophytes Marchantia polymorpha and Anthoceros agrestis. In the red alga, TEs silenced by H3K27me3 are in subtelomeres but in bryophytes, TEs and genes marked by H3K27me3 form coregulated transcriptional units. The latter trend was also observed in the flowering plant Arabidopsis thaliana, and we identified cis-elements recognised by transcription factors in TEs flanking genes repressed by PRC2. Together with the silencing of TEs by PRC2 in ciliates that diverged early from an ancestor common with Archaeplastida, our findings support the hypothesis that PRC2 deposited H3K27me3 to silence TEs in early lineages of eukaryotes. During evolution, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation that control networks of genes regulated by PRC2. HighlightsH3K27me3 marks a decreasing proportion of TEs during evolution of plants The polycomb repressive complex 2 represses TEs in red algae and bryophytes H3K27me3-marked TEs in flowering plants contain transcription factor binding sites Transcription factors bind TEs and regulate networks of genes controlled by PRC2

evolutionary biology↗

bioRxiv2022

The chromatin landscape of bryophytes

BackgroundIn animals and flowering plants specific chromatin modifications define three chromosomal domains: euchromatin comprising transcribed genes, facultative heterochromatin comprising repressed genes, and constitutive heterochromatin comprising transposons. However, recent studies have shown that the correlation between chromatin modifications and transcription vary among different eukaryotic organisms including mosses and liverworts that differ from one another. Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with all land plants. We aimed to obtain chromatin landscapes in hornworts to establish synapomorphies across bryophytes. ResultsWe mapped the chromatin landscape of the model hornwort Anthoceros agrestis. By comparing chromatin landscapes across bryophytes we defined the common chromatin landscape of the ancestor of extant bryophytes. In this group, constitutive heterochromatin was characterized by a scattered distribution across autosomes, which contrasted with the dense compartments of heterochromatin surrounding the centromeres in flowering plants. Topologically associated domains were primarily occupied by transposons with genes at their boundaries and nearly half of the hornwort transposons were associated with facultative heterochromatin and euchromatin. ConclusionsMost of the features observed in hornworts are also present in liverworts but are distinct from flowering plants. Hence, the ancestral genome of bryophytes was likely a patchwork of units of euchromatin interspersed within facultative and constitutive heterochromatin and each unit contained both transposons and genes sharing the same chromatin state. We propose this genome organization was ancestral to land plants and prevented transposons from being segregated as constitutive heterochromatin around point centromeres as in flowering plants.

genomics↗

bioRxiv2022

Transcriptional activity is shaped by the chromatin landscapes in Arabidopsis

SummaryHow histone variants and histone modifications shape nucleosome-mediated transcriptional repression, and how transcriptional activity shapes the enrichment of histone modifications and variants remain unclear. To clarify these relationships, we examined chromatin organization in the Arabidopsis thaliana genome, identifying a limited number of chromatin landscapes that distinguish transposon families and distinct groups of genes based on their transcriptional regulation. Unexpectedly, H2A variants are strong determinants of the landscape architecture. Combinations of H2A.W and four histone modifications define six domains that are occupied by specific transposon families and organized concentrically around the centromere. Moreover, H2A.Z defines transcriptional gene repression in specific domains. Expressed genes occupy four chromatin landscapes with specific RNA Polymerase II profiles. Although the composition of each chromatin landscape is invariant, they cover genes with a wide range of expression levels. Therefore, chromatin landscapes control the range of transcriptional activity, but transcriptional activity has little effect on chromatin composition. One Sentence SummaryHistone variants and histone modifications build a limited number of distinct chromatin landscapes that instruct the transcriptional regulation of genes and transposons in Arabidopsis.

genomics↗

bioRxiv2022

Viviparity is sufficient for the evolution of genomic imprinting

Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.

molecular biology↗