scholarly journals HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion

2019 ◽  
Vol 116 (50) ◽  
pp. 25343-25354 ◽  
Author(s):  
Lennard C. van der Woude ◽  
Giorgio Perrella ◽  
Basten L. Snoek ◽  
Mark van Hoogdalem ◽  
Ondřej Novák ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
High Temperature ◽  
Histone Deacetylase ◽  
Transcriptional Activation ◽  
Histone Deacetylation ◽  
Shade Avoidance ◽  
Ambient Temperatures ◽  
Histone Deacetylase 9 ◽  
Rate Limiting ◽  
Auxin Accumulation

Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the YUCCA8 locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with YUCCA8, allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.

scholarly journals The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation

2020 ◽  
Vol 71 (20) ◽  
pp. 6211-6225
Author(s):  
Peter G H de Rooij ◽  
Giorgio Perrella ◽  
Eirini Kaiserli ◽  
Martijn van Zanten
Keyword(s):  
Histone Deacetylase ◽  
Plant Development ◽  
Transcriptional Activation ◽  
Plant Traits ◽  
Feedback Regulation ◽  
Molecular Networks ◽  
Environmental Biology ◽  
Negative Feedback Regulation ◽  
Lysine Residues ◽  
Histone Deacetylase 9

Abstract Plants tightly control gene transcription to adapt to environmental conditions and steer growth and development. Different types of epigenetic modifications are instrumental in these processes. In recent years, an important role for the chromatin-modifying RPD3/HDA1 class I HDAC HISTONE DEACETYLASE 9 (HDA9) emerged in the regulation of a multitude of plant traits and responses. HDACs are widely considered transcriptional repressors and are typically part of multiprotein complexes containing co-repressors, DNA, and histone-binding proteins. By catalyzing the removal of acetyl groups from lysine residues of histone protein tails, HDA9 negatively controls gene expression in many cases, in concert with interacting proteins such as POWERDRESS (PWR), HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15), WRKY53, ELONGATED HYPOCOTYL 5 (HY5), ABA INSENSITIVE 4 (ABI4), and EARLY FLOWERING 3 (ELF3). However, HDA9 activity has also been directly linked to transcriptional activation. In addition, following the recent breakthrough discovery of mutual negative feedback regulation between HDA9 and its interacting WRKY-domain transcription factor WRKY53, swift progress in gaining understanding of the biology of HDA9 is expected. In this review, we summarize knowledge on this intriguing versatile—and long under-rated—protein and propose novel leads to further unravel HDA9-governed molecular networks underlying plant development and environmental biology.

scholarly journals Histone Deacetylase 9 Activates IKK to Regulate Atherosclerotic Plaque Vulnerability

2020 ◽  
Vol 127 (6) ◽  
pp. 811-823 ◽  
Author(s):  
Yaw Asare ◽  
Thomas A. Campbell-James ◽  
Yury Bokov ◽  
Lydia Luya Yu ◽  
Matthias Prestel ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Atherosclerotic Plaque ◽  
Association Studies ◽  
Endothelial Activation ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Plaque Vulnerability ◽  
Plaque Stability ◽  
Genome Wide ◽  
Histone Deacetylase 9

Rationale: Arterial inflammation manifested as atherosclerosis is the leading cause of mortality worldwide. Genome-wide association studies have identified a prominent role of HDAC (histone deacetylase)-9 in atherosclerosis and its clinical complications including stroke and myocardial infarction. Objective: To determine the mechanisms linking HDAC9 to these vascular pathologies and explore its therapeutic potential for atheroprotection. Methods and Results: We studied the effects of Hdac9 on features of plaque vulnerability using bone marrow reconstitution experiments and pharmacological targeting with a small molecule inhibitor in hyperlipidemic mice. We further used 2-photon and intravital microscopy to study endothelial activation and leukocyte-endothelial interactions. We show that hematopoietic Hdac9 deficiency reduces lesional macrophage content while increasing fibrous cap thickness thus conferring plaque stability. We demonstrate that HDAC9 binds to IKK (inhibitory kappa B kinase)-α and β, resulting in their deacetylation and subsequent activation, which drives inflammatory responses in both macrophages and endothelial cells. Pharmacological inhibition of HDAC9 with the class IIa HDAC inhibitor TMP195 attenuates lesion formation by reducing endothelial activation and leukocyte recruitment along with limiting proinflammatory responses in macrophages. Transcriptional profiling using RNA sequencing revealed that TMP195 downregulates key inflammatory pathways consistent with inhibitory effects on IKKβ. TMP195 mitigates the progression of established lesions and inhibits the infiltration of inflammatory cells. Moreover, TMP195 diminishes features of plaque vulnerability and thereby enhances plaque stability in advanced lesions. Ex vivo treatment of monocytes from patients with established atherosclerosis reduced the production of inflammatory cytokines including IL (interleukin)-1β and IL-6. Conclusions: Our findings identify HDAC9 as a regulator of atherosclerotic plaque stability and IKK activation thus providing a mechanistic explanation for the prominence of HDAC9 as a vascular risk locus in genome-wide association studies. Its therapeutic inhibition may provide a potent lever to alleviate vascular inflammation. Graphical Abstract: A graphical abstract is available for this article.

scholarly journals Histone H4 acetylation and transcription in amphibian chromatin.

1993 ◽  
Vol 120 (2) ◽  
pp. 277-290 ◽  
Author(s):  
J Sommerville ◽  
J Baird ◽  
B M Turner
Keyword(s):  
Transcriptional Activation ◽  
Histone Deacetylation ◽  
Dense Matrix ◽  
Lampbrush Chromosomes ◽  
Loop Formation ◽  
Triturus Cristatus ◽  
Immature Oocytes ◽  
Intense Fluorescence ◽  
Histone H4 Acetylation ◽  
Lysine Residues

Lampbrush chromosomes from oocytes of the amphibian Triturus cristatus have been used to examine the role of histone acetylation in transcription by indirect immunofluorescence with antisera to H4 acetylated at specific lysine residues. Electrophoresis on acid-urea-Triton gels and Western blotting have confirmed the specificity of these antisera and defined the order in which particular lysine residues are acetylated in amphibian cells. As in mammals, lysine 16 is acetylated first, followed by 8 and/or 12 and then 5. With lampbrush chromosomes from immature (previtellogenic) oocytes, antisera to H4 acetylated at lysines 8, 12, and 16 labeled fluorescent foci at the bases of transcription loops. Antisera to H4 acetylated at lysine 5 labeled weakly (i.e., the tri- and tetraacetylated isoforms must be rare). Loops showed weak labeling of the chromatin axis but intense fluorescence at particular points, which probably represent incompletely decondensed chromatin. The RNP matrix of loops, including the RNP-rich sphere bodies and the dense matrix of "marker" loops, was not labeled. Treatment of immature oocytes with butyrate for 12 h to inhibit histone deacetylation did not affect immunolabeling, suggesting that turnover of H4 acetates is slow. In contrast, in chromosomes from mature oocytes, in which loops have retracted and transcription is low, butyrate caused an increase in labeling with all antisera, followed by the appearance of vestigial loops, weakly labeled, but with regions of intense fluorescence. These loops contain RNP and are presumably transcriptionally active. We conclude that H4 acetates turn over more rapidly in mature than immature oocytes and that histone hyperacetylation precedes, and possibly induces, loop formation and transcriptional activation.

scholarly journals The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae

2004 ◽  
Vol 24 (11) ◽  
pp. 4769-4780 ◽  
Author(s):  
Jennifer G. Aparicio ◽  
Christopher J. Viggiani ◽  
Daniel G. Gibson ◽  
Oscar M. Aparicio
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Histone Deacetylase ◽  
Transcriptional Repression ◽  
Replication Timing ◽  
Histone Deacetylation ◽  
Origin Firing ◽  
Replication Checkpoint ◽  
Genome Transcription ◽  
Late Origin

ABSTRACT The replication of eukaryotic genomes follows a temporally staged program, in which late origin firing often occurs within domains of altered chromatin structure(s) and silenced genes. Histone deacetylation functions in gene silencing in some late-replicating regions, prompting an investigation of the role of histone deacetylation in replication timing control in Saccharomyces cerevisiae. Deletion of the histone deacetylase Rpd3 or its interacting partner Sin3 caused early activation of late origins at internal chromosomal loci but did not alter the initiation timing of early origins or a late-firing, telomere-proximal origin. By delaying initiation relative to the earliest origins, Rpd3 enables regulation of late origins by the intra-S replication checkpoint. RPD3 deletion suppresses the slow S phase of clb5Δ cells by enabling late origins to fire earlier, suggesting that Rpd3 modulates the initiation timing of many origins throughout the genome. Examination of factors such as Ume6 that function together with Rpd3 in transcriptional repression indicates that Rpd3 regulates origin initiation timing independently of its role in transcriptional repression. This supports growing evidence that for much of the S. cerevisiae genome transcription and replication timing are not linked.

scholarly journals Transcriptome and translatome changes in germinated pollen under heat stress uncover roles of transporter genes involved in pollen tube growth

2020 ◽  
Author(s):  
Laetitia Poidevin ◽  
Javier Forment ◽  
Dilek Unal ◽  
Alejandro Ferrando
Keyword(s):  
Arabidopsis Thaliana ◽  
Heat Stress ◽  
High Temperature ◽  
Heat Shock ◽  
Pollen Tube ◽  
Pollen Tube Growth ◽  
Tube Growth ◽  
Heat Shock Genes ◽  
Germinated Pollen

ABSTRACTPlant reproduction is one key biological process very sensitive to heat stress and, as a consequence, enhanced global warming poses serious threats to food security worldwide. In this work we have used a high-resolution ribosome profiling technology to study how heat affects both the transcriptome and the translatome of Arabidopsis thaliana pollen germinated in vitro. Overall, a high correlation between transcriptional and translational responses to high temperature was found, but specific regulations at the translational level were also present. We show that bona fide heat shock genes are induced by high temperature indicating that in vitro germinated pollen is a suitable system to understand the molecular basis of heat responses. Concurrently heat induced significant down-regulation of key membrane transporters required for pollen tube growth, thus uncovering heat-sensitive targets. We also found that a large subset of the heat-repressed transporters is specifically up-regulated, in a coordinated manner, with canonical heat-shock genes in pollen tubes grown in vitro and semi in vivo, based on published transcriptomes from Arabidopsis thaliana. Ribosome footprints were also detected in gene sequences annotated as non-coding, highlighting the potential for novel translatable genes and translational dynamics.

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