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Epigenomic landscape of Arabidopsis thaliana

Trejo-Arellano, Minerva S. (2019). Epigenomic landscape of Arabidopsis thaliana. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880
ISBN 978-91-7760-336-8
eISBN 978-91-7760-337-5
[Doctoral thesis]

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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.

Authors/Creators:Trejo-Arellano, Minerva S.
Title:Epigenomic landscape of Arabidopsis thaliana
Alternative abstract:
LanguageAbstract
Spanish

La secuencia de ADN representa el primernivelde almacenamiento de información en la célula. El empaquetamiento dinámico del ADN en lacromatina permite la existencia de niveles de regulación adicionales. Dos pares de cada una de las histonas H3, H4, H2A y H2B forman un complejo octamérico alrededor del cual se empaquetan146 pares de basesde ADN para conformar la unidad básica de la cromatina: el nucleosoma. Además de que los nucleótidosdel ADN pueden sermetilados, las colas amino-terminales de las histonas pueden ser blanco de modificaciones postranscripcionales (MPTs), impactando la accesibilidad del ADN y,en consecuencia,la expresión génica.

El repertorio de MPTs conocidas en histonas de plantas es aún limitado comparado con el de animales y levadura. En este trabajo identificamos dos modificaciones en la cola de la histona H3queno habían sidodescritas enplantas,peroestán conservadas en eucariota. La acetilación en la lisina 36 (H3K36ac) está presente en la eucromatinadonde actúa como marcador binario de la transcripción; ylamonometilación de la lisina 23 (H3K23me1) se encuentra de manera preferente en la heterocromatina. La combinación espaciotemporal entre las MPT de histonas y la metilación del ADN constituyen otra capa decontrol epigenético. A lo largo del desarrollo, el epigenoma es modificado en el contexto deladiferenciación celular. En este trabajo se reporta el perfil de metilación de hojas senescentes de Arabidopsisthaliana. Los cambios de metilación en dicha condición avanzada del desarrollo son modestos y se encuentran localizados a lo largo de transposones. Descubrimos,además,la desregulación de un conjunto de genes involucrados enel mantenimiento de la cromatina, sugiriendo que las alteraciones observadas en el perfil de metilación son consecuencia de una reestructuración global de la cromatina. De manera similar, reportamos cambios localizados en el perfil de metilación de transposones y regiones pericentroméricas en el genomadeArabidopsiscarentesde una versión funcional deChromatin Assembly Factor1(CAF-1), una chaperona de la cromatina durante la replicación y reparación del ADN. Estos resultados apuntan aque alteraciones en la cromatina permitenacceso ala maquinaria de metilación del ADN a regiones del genoma normalmenteocluidas, haciendo evidente la importancia de la correcta conformación de la cromatina. En conjunto, esta tesis contribuye a la descripción de la configuración epigenética del genoma de Arabidopsisy su impacto en las redes de regulación que controlan las transiciones de desarrollo en plantas

Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2019
Number:2019:9
Number of Pages:95
Papers/manuscripts:
NumberReferences
IMinerva S. Trejo-Arellano★, Saher Mehdi, Jennifer the Jonge, Eva Dvorák Tomastíková, Claudia Köhler and Lars Hennig. Senescence causes localized changes in DNA methylation in Arabidopsis (manuscript)
IIIva Mozgová, Thomas Wildhaber, Minerva S. Trejo-Arellano, Jiri Fajkus, Pawel Roszak, Claudia Köhler and Lars Hennig★ (2018). Transgenerational phenotype aggravation in CAF-1 mutants reveals parent-of-origin specific epigenetic inheritance. New Phytologist, 220(3), 908-921.
IIITrejo-Arellano MS, Mahrez W, Nakamura M, Moreno-Romero J, Nanni P, Köhler C, Hennig L★ (2017). H3K23me1 is an evolutionarily conserved histone modification associated with CG DNA methylation in Arabidopsis. Plant Journal, 90(2):293-303.
IVMuñoz-Viana R, Wildhaber T, Trejo-Arellano MS, Mozgová I, Hennig L★ (2017). Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes. Plant Journal, 92(3), 363-374.
VWalid Mahrez, Minerva Susana Trejo Arellano, Jordi Moreno-Romero, Miyuki Nakamura,Huan Shu, Paolo Nanni, Claudia Köhler, Wilhelm Gruissem and Lars Hennig★ (2016). H3K36ac Is an Evolutionary Conserved Plant Histone Modification That Marks Active Genes. Plant Physiol, 170(3), 1566-1577.
Place of Publication:Uppsala
Publisher:Department of Plant Biology, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-7760-336-8
ISBN for electronic version:978-91-7760-337-5
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Article category:Other scientific
Full Text Status:Public
Agris subject categories.:F Plant production > F30 Plant genetics and breeding
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biochemistry and Molecular Biology
Keywords:epigenetics, chromatin, DNA methylation, histone modification, transcriptomics, ChIP-seq, Bisulphite sequencing
URN:NBN:urn:nbn:se:slu:epsilon-e-5233
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-5233
ID Code:15928
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Plant Biology (from 140101)
Deposited By: SLUpub Connector
Deposited On:21 Feb 2019 12:24
Metadata Last Modified:06 Mar 2019 19:25

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