Histone H2A.Z Regulates the Expression of Several Classes of Phosphate Starvation Response Genes But Not as a Transcriptional Activator

Smith, Aaron P.; Jain, Ajay; Deal, Roger B.; Nagarajan, Vinay K.; Poling, Michael D.; Raghothama, Kashchandra G.; Meagher, Richard B.

doi:10.1104/pp.109.145532

Cited by 169 publications

(172 citation statements)

References 48 publications

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“…In rice, SPX1 is partly involved in regulating the induction of some Pi transporters (Wang et al 2009b). Histone H4 (Os04t0583600) and histone H2B (Os05t0574300) were upregulated in shoot during early -P stress whereas histone H1 (Os03t0799000) and histone H2B (Os01t0152900) were downregulated in shoot during late -P stress thereby supporting the chromatin-level regulation of response to Pi starvation (Smith et al 2010). Under ++P stress treatments, OsIPS1 and OsIPS2 did not show any specific pattern of expression in either root or shoot.…”

Section: Characterization Of Pi Stress-responsive Transcriptsmentioning

confidence: 99%

mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress

Oono

Kawahara

Kanamori

et al. 2011

Rice

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Plants have developed several morphological and physiological strategies to adapt to phosphate stress. We analyzed the inducible transcripts associated with phosphate starvation and over-abundant phosphate supply to characterize the transcriptome in rice seedlings using the mRNA-Seq strategy. Fifty-three million reads obtained from 16 libraries under various phosphate stress and recovery treatments were uniquely mapped to the rice genome. Transcripts identified specifically tagged to 40,574 (root) and 39,748 (shoot) Rice Annotation Project (RAP) transcripts. Additionally, we detected uniquely 10,388 transcripts with no match to any RAP transcript. These transcripts that showed specific response to Pi stress include those without ORFs that may act as non-protein coding transcripts. With an accompanying browser of the transcriptome under Pi stress, a deeper understanding of the structural and functional features of both annotated and unannotated Pi stress-responsive transcripts can provide useful information in improving Pi acquisition and utilization in rice and other cereal crops.

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Section: Characterization Of Pi Stress-responsive Transcriptsmentioning

confidence: 99%

mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress

Oono

Kawahara

Kanamori

et al. 2011

Rice

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“…In Arabidopsis, it has also been implicated in both positive and negative transcriptional regulation. Mutations in the components of SWR1-C cause the derepression of biotic and abiotic plant response genes, such as plant disease resistance genes, heat shock-induced genes, and phosphate starvation response genes, supporting the negative role of H2A.Z (MarchDíaz et al, 2008;Kumar and Wigge, 2010;Smith et al, 2010). By contrast, the mutations cause the suppression of the developmentally regulated FLC gene, supporting the positive role of H2A.…”

Section: Recruitment Of Chromatin Modification Factors and General Trmentioning

confidence: 99%

The FRIGIDA Complex Activates Transcription of FLC, a Strong Flowering Repressor in Arabidopsis, by Recruiting Chromatin Modification Factors

et al. 2011

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The flowering of Arabidopsis thaliana winter annuals is delayed until the subsequent spring by the strong floral repressor FLOWERING LOCUS C (FLC). FRIGIDA (FRI) activates the transcription of FLC, but the molecular mechanism remains elusive. The fri mutation causes early flowering with reduced FLC expression similar to frl1, fes1, suf4, and flx, which are mutants of FLC-specific regulators. Here, we report that FRI acts as a scaffold protein interacting with FRL1, FES1, SUF4, and FLX to form a transcription activator complex (FRI-C). Each component of FRI-C has a specialized function. SUF4 binds to a cis-element of the FLC promoter, FLX and FES1 have transcriptional activation potential, and FRL1 and FES1 stabilize the complex. FRI-C recruits a general transcription factor, a TAF14 homolog, and chromatin modification factors, the SWR1 complex and SET2 homolog. Complex formation was confirmed by the immunoprecipitation of FRI-associated proteins followed by mass spectrometric analysis. Our results provide insight into how a specific transcription activator recruits chromatin modifiers to regulate a key flowering gene.

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“…For example, it has been reported that modifications in chromatin structure through the deposition of the histone variant H2A.Z are involved in the activation of numerous genes associated with Pi deficiency. These findings suggest that chromatin remodeling could play an important role in modulating the transcriptional activation or repression of PSR genes (26). However, to what extent and which epigenetic marks modulate the Pi starvation response remains largely unknown.…”

mentioning

confidence: 96%

Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation

Yong-Villalobos

González-Morales

Wróbel

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

172

181

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Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avoid nutrient starvation. In the past decade, these responses have been studied in detail at the level of gene expression; however, the possible epigenetic components modulating plant Pi starvation responses have not been thoroughly investigated. Here, we report that an extensive remodeling of global DNA methylation occurs in Arabidopsis plants exposed to low Pi availability, and in many instances, this effect is related to changes in gene expression. Modifications in methylation patterns within genic regions were often associated with transcriptional activation or repression, revealing the important role of dynamic methylation changes in modulating the expression of genes in response to Pi starvation. Moreover, Arabidopsis mutants affected in DNA methylation showed that changes in DNA methylation patterns are required for the accurate regulation of a number of Pi-starvation-responsive genes and that DNA methylation is necessary to establish proper morphological and physiological phosphate starvation responses.phosphate | epigenetics | abiotic stress | DNA methylation | methylome D uring evolution, plants have acquired a series of adaptive strategies that allow them to survive and complete their life cycles under adverse environmental conditions. Consequently, plants have evolved a myriad of physiological, cellular, and molecular mechanisms to cope with challenging environments. Plant responses to environmental stress include modifications in postembryonic development and metabolic reprogramming, which are highly dependent on the regulation of gene expression. It is well documented that gene regulation at the transcriptional and posttranscriptional levels plays an important role in plant stress responses; however, more recent evidence suggests that epigenetic mechanisms also play an important role in reprogramming gene expression in response to environmental cues and that epigenetic marks can serve as a priming mechanism to prepare future generations to better withstand biotic and abiotic stresses (1-3). These epigenetic marks include, but are not restricted to, posttranslational histone modifications and DNA methylation, a mechanism by which cytosine DNA methylation regulates the silencing and control of transposable elements (TEs) and repetitive sequences, genomic imprinting, and gene silencing. In plants, this DNA methylation modification is applied in three different sequence contexts (CG, CHG, and CHH, where H = A, C, or T), and the involvement of different pathways is necessary for the establishment, maintenance, and modification of DNA methylation patterns in these contexts (4, 5). These epigenetic processes can interact to orchestrate new heterochromatin states that modify gene expression [for re...

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Histone H2A.Z Regulates the Expression of Several Classes of Phosphate Starvation Response Genes But Not as a Transcriptional Activator

Cited by 169 publications

References 48 publications

mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress

mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress

The FRIGIDA Complex Activates Transcription of FLC, a Strong Flowering Repressor in Arabidopsis, by Recruiting Chromatin Modification Factors

Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation

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