A DEK Domain-Containing Protein Modulates Chromatin Structure and Function in<i>Arabidopsis</i>

Waidmann, Sascha; Kusenda, Branislav; Mayerhofer, Juliane; Mechtler, Karl; Jonak, Claudia

doi:10.1105/tpc.114.129254

Cited by 61 publications

(76 citation statements)

References 83 publications

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“…It is likely that alternative histone chaperone complexes are also implicated in deposition of replacement variants. While no DAXX ortholog has been identified in plants (Zhu et al ., ), Arabidopsis encodes several DEK proteins (Waidmann et al ., ), and other as yet unidentified histone chaperones may play a role in histone variant dynamics (Otero et al ., ).…”

Section: Discussionmentioning

confidence: 99%

The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF‐1 complex mutants

et al. 2015

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SUMMARYChromatin organization is essential for coordinated gene expression, genome stability, and inheritance of epigenetic information. The main components involved in chromatin assembly are specific complexes such as Chromatin Assembly Factor 1 (CAF-1) and Histone Regulator (HIR), which deposit histones in a DNA synthesis-dependent or -independent manner, respectively. Here, we characterize the role of the plant orthologs Histone Regulator A (HIRA), Ubinuclein (UBN) and Calcineurin Binding protein 1 (CABIN1), which constitute the HIR complex. Arabidopsis loss-of-function mutants for the various subunits of the complex are viable, but hira mutants show reduced fertility. We show that loss of HIRA reduces extractable histone H3 protein levels and decreases nucleosome occupancy at both actively transcribed genes and heterochromatic regions. Concomitantly, HIRA contributes to maintenance of silencing of pericentromeric repeats and certain transposons. A genetic analysis based on crosses between mutants deficient in subunits of the CAF-1 and HIR complexes showed that simultaneous loss of both the CAF-1 and HIR histone H3 chaperone complexes severely affects plant survival, growth and reproductive development. Our results suggest that HIRA partially rescues impaired histone deposition in fas mutants to preserve nucleosome occupancy, implying plasticity in histone variant interaction and deposition.

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Section: Discussionmentioning

confidence: 99%

The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF‐1 complex mutants

et al. 2015

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“…Levels of Arabidopsis DEK3 define salinity tolerance, and the protein appears to work in collaboration with DNA topoisomerase 1a. DEK3 is a member of the conserved DEK domain-containing protein family and interacts with H3 and H4, determines nucleosome occupancy, and associates with chromatin at specific loci [85 ]. Rice plants under drought stress express a nuclear-localized protein that, based on sequence homology, is a member of the Alba (acetylation lowers binding affinity) family, but a chromatin connection in plants is not yet evident [86].…”

Section: New Non-histone Nuclear Proteins Associated With Stress Respmentioning

confidence: 99%

Stress-induced structural changes in plant chromatin

Probst

Scheid

2015

Current Opinion in Plant Biology

161

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Stress defense in plants is elaborated at the level of protection and adaptation. Dynamic changes in sophisticated chromatin substructures and concomitant transcriptional changes play an important role in response to stress, as illustrated by the transient rearrangement of compact heterochromatin structures or the modulation of chromatin composition and modification upon stress exposure. To connect cytological, developmental, and molecular data around stress and chromatin is currently an interesting, multifaceted, and sometimes controversial field of research. This review highlights some of the most recent findings on nuclear reorganization, histone variants, histone chaperones, DNA- and histone modifications, and somatic and meiotic heritability in connection with stress.

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“…Some of them, e.g. putative ATRX (Alpha thalasemia/mental retardation/syndrome X–linked) and DEK proteins (Otero et al ., ; Waidmann et al ., ), are present in Arabidopsis. Recently, experimental data on DEK3 was reported showing that it is important to modulate the expression of downstream target genes relevant for the stress response (Waidmann et al ., ).…”

Section: Chromatin Replicationmentioning

confidence: 99%

“…putative ATRX (Alpha thalasemia/mental retardation/syndrome X–linked) and DEK proteins (Otero et al ., ; Waidmann et al ., ), are present in Arabidopsis. Recently, experimental data on DEK3 was reported showing that it is important to modulate the expression of downstream target genes relevant for the stress response (Waidmann et al ., ). Although it is considered within the chaperone class, ASF1 (ANTI‐SILENCING FACTOR 1) actually functions as a stock of H3–H4 dimers (Zhu + ) before transferring them to either CAF1 or HIRA, depending on whether it is formed with H3.1 or H3.3, respectively.…”

Section: Chromatin Replicationmentioning

confidence: 99%

Links between genome replication and chromatin landscapes

Sequeira-Mendes

Gutiérrez

2015

The Plant Journal

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SUMMARYPost-embryonic organogenesis in plants requires the continuous production of cells in the organ primordia, their expansion and a coordinated exit to differentiation. Genome replication is one of the most important processes that occur during the cell cycle, as the maintenance of genomic integrity is of primary relevance for development. As it is chromatin that must be duplicated, a strict coordination occurs between DNA replication, the deposition of new histones, and the introduction of histone modifications and variants. In turn, the chromatin landscape affects several stages during genome replication. Thus, chromatin accessibility is crucial for the initial stages and to specify the location of DNA replication origins with different chromatin signatures. The chromatin landscape also determines the timing of activation during the S phase. Genome replication must occur fully, but only once during each cell cycle. The re-replication avoidance mechanisms rely primarily on restricting the availability of certain replication factors; however, the presence of specific histone modifications are also revealed as contributing to the mechanisms that avoid re-replication, in particular for heterochromatin replication. We provide here an update of genome replication mostly focused on data from Arabidopsis, and the advances that genomic approaches are likely to provide in the coming years. The data available, both in plants and animals, point to the relevance of the chromatin landscape in genome replication, and require a critical evaluation of the existing views about the nature of replication origins, the mechanisms of origin specification and the relevance of epigenetic modifications for genome replication.

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A DEK Domain-Containing Protein Modulates Chromatin Structure and Function inArabidopsis

Cited by 61 publications

References 83 publications

The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF‐1 complex mutants

The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF‐1 complex mutants

Stress-induced structural changes in plant chromatin

Links between genome replication and chromatin landscapes

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