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Doctoral thesis, 2019

Epigenomic landscape of Arabidopsis thaliana

Minerva, Trejo

Abstract

The basal unit of information storage in the cell is at the level of the DNA sequence. Dynamic packaging of DNA into chromatin allows additional regulatory layers. Two pairs of each histones H3, H4, H2A and H2B constitute an octamer around which about 146 base pairs of DNA are wrapped to build the basic unit of chromatin: the nucleosome. Furthermore, DNA nucleotides can be methylated and the amino-termini of histones tails can be covalently modified by a range of post-transcriptional modifications (PTMs), impacting on DNA accessibility and gene activity. Compared to yeast and animals, the repertoire of histone PTMs in plants is less comprehensive. We identified two novel modifications on histone H3 that were not previously described in plants, but are evolutionarily conserved in high eukaryotes. Acetylation of lysine 36 (H3K36ac), which is enriched in euchromatin and seems to act as a binary indicator of transcription; and monomethylation of lysine 23 (H3K23me1) preferentially found in heterochromatin and along coding genes where it coexists with gene body CG DNA methylation. The spatiotemporal combination of histone modifications and DNA methylation comprises another layer of epigenetic control. Throughout development, changes in the epigenome are programmed to surpass developmental barriers. To address the configuration of the methylome during late stages of plant development, we profiled the DNA methylation landscape of darkness-induced senescent leaves of Arabidopsis thaliana and found modest methylation changes mainly localizing to transposable elements (TEs). Transcriptome changes revealed impairment of a module regulating chromatin conformation, suggesting that the observed changes in DNA methylation are a consequence of global chromatin rearrangements. Similarly, we observed DNA methylation changes localized to pericentromeric TEs in Arabidopsis plants lacking the Chromatin Assembly Factor 1 (CAF-1), a chromatin maintainer during replication and DNA repair. Therefore, disturbed chromatin packaging allows access of the DNA methylation machinery to regions of the genome otherwise inaccessible, highlighting the importance of chromatin structure to prevent faulty DNA modifications. Together, this thesis expanded our knowledge of the epigenetic landscape in Arabidopsis and integrated it into the regulatory networks that drive cell-fate decisions in plants.

Keywords

Epigenetics; chromatin; DNA methylation; histone modification; transcriptomics; ChIP-seq; Bisulphite sequencing

Published in

Acta Universitatis Agriculturae Sueciae
2019, number: 2019:9
ISBN: 978-91-7760-336-8, eISBN: 978-91-7760-337-5
Publisher: Department of Plant Biology, Swedish University of Agricultural Sciences

Authors' information

Minerva, Trejo
Swedish University of Agricultural Sciences, Department of Plant Biology

UKÄ Subject classification

Biochemistry and Molecular Biology
Bioinformatics and Systems Biology
Genetics

URI (permanent link to this page)

https://res.slu.se/id/publ/98440