Ordered Histone Modifications Are Associated with Transcriptional Poising and Activation of the <i>phaseolin</i> Promoter

Ng, David C.; Chandrasekharan, Mahesh B.; Hall, Timothy C.

doi:10.1105/tpc.105.037010

Cited by 82 publications

(104 citation statements)

References 75 publications

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“…Hall, unpublished data) and PvALF (Phaseolus vulgaris ABI3-like factor) [77][78][79]. In addition, an increase in H3K4me 3 at the phas chromatin was detected within one hour upon phas activation, illustrating the dynamic aspects of chromatin remodeling in mediating the activation of this seed-specific promoter [79].…”

Section: Class Iii: the Trithorax Homologs And Related Proteins (H3k4)mentioning

confidence: 91%

Plant SET domain-containing proteins: Structure, function and regulation

Wang

Chandrasekharan

et al. 2007

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expres

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176

195

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Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/ interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein-protein interactions through both intra-and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread. An exciting and tantalizing question is whether, or how, this alternative splicing affects gene function. For example, it is conceivable that one isoform may debilitate methyltransferase function whereas the other may enhance it, providing an opportunity for differential regulation. The review concludes with the speculation that modulation of SET protein function is mediated by antisense or sense-antisense RNA.

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Section: Class Iii: the Trithorax Homologs And Related Proteins (H3k4)mentioning

confidence: 91%

Plant SET domain-containing proteins: Structure, function and regulation

Wang

Chandrasekharan

et al. 2007

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expres

Self Cite

176

195

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“…For example, a histone methyltransferase equipped with a CW domain has recently been shown to regulate flowering in Arabidopsis . Intriguingly, chromatin remodeling has been implicated in gene regulation mediated by other B3 domain factors, including ABI3 (Li et al, 1999;Levy et al, 2002;Fukaki et al, 2006;Ng et al, 2006), with association of PKL function (Fukaki et al, 2006). Hence, VAL B3 factors may associate with general chromatin factors, perhaps as part of the protein complex, to repress expression of a specific set of genes.…”

Section: Discussionmentioning

confidence: 99%

Repression of theLEAFY COTYLEDON 1/B3Regulatory Network in Plant Embryo Development byVP1/ABSCISIC ACID INSENSITIVE 3-LIKEB3 Genes

2006

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Plant embryo development is regulated by a network of transcription factors that include LEAFY COTYLEDON 1 (LEC1), LEC1-LIKE (L1L), and B3 domain factors, LEAFY COTYLEDON 2 (LEC2), FUSCA3 (FUS3), and ABSCISIC ACID INSENSITIVE 3 (ABI3) of Arabidopsis (Arabidopsis thaliana). Interactions of these genes result in temporal progression of overlapping B3 gene expression culminating in maturation and desiccation of the seed. Three VP1/ABI3-LIKE (VAL) genes encode B3 proteins that include plant homeodomain-like and CW domains associated with chromatin factors. Whereas val monogenic mutants have phenotypes similar to wild type, val1 val2 double-mutant seedlings form no leaves and develop embryo-like proliferations in root and apical meristem regions. In a val1 background, val2 and val3 condition a dominant variegated leaf phenotype revealing a VAL function in vegetative development. Reminiscent of the pickle (pkl) mutant, inhibition of gibberellin biosynthesis during germination induces embryonic phenotypes in val1 seedlings. Consistent with the embryonic seedling phenotype, LEC1, L1L, ABI3, and FUS3 are up-regulated in val1 val2 seedlings in association with a global shift in gene expression to a profile resembling late-torpedo-stage embryogenesis. Hence, VAL factors function as global repressors of the LEC1/B3 gene system. The consensus binding site of the ABI3/FUS3/LEC2 B3 DNA-binding domain (Sph/RY) is strongly enriched in the promoters and first introns of VAL-repressed genes, including the early acting LEC1 and L1L genes. We suggest that VAL targets Sph/RY-containing genes in the network for chromatin-mediated repression in conjunction with the PKLrelated CHD3 chromatin-remodeling factors.

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“…7). Both modification states are positively correlated with transcriptional activation in Arabidopsis (40,41), and the levels of both modifications have previously been demonstrated to be decreased by mutation of a histone acetyltransferase (GCN5) or increased by mutation of a histone deacetylase (HD1) at light-responsive promoters (42). In contrast to our analysis of H3K27me3 levels, we observed a much more modest and sporadic effect on acetylation of H3 and H4 in response to loss of PKL (Fig.…”

Section: ϫ4mentioning

confidence: 99%

The CHD3 Remodeler PICKLE Promotes Trimethylation of Histone H3 Lysine 27

Zhang

Rider

Henderson

et al. 2008

Journal of Biological Chemistry

131

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CHD3 proteins are ATP-dependent chromatin remodelers that contribute to repression of developmentally regulated genes in both animal and plant systems. In animals, this repression has been linked to a multiple subunit complex, Mi-2/NuRD, whose constituents include a CHD3 protein, a histone deacetylase, and a methylCpG-binding domain protein. In Arabidopsis, PICKLE (PKL) codes for a CHD3 protein that acts during germination to repress expression of seed-associated genes. Repression of seed-associated traits is promoted in pkl seedlings by the plant growth regulator gibberellin (GA). We undertook a microarray analysis to determine how PKL and GA act to promote the transition from seed to seedling. We found that PKL and GA act in separate pathways to repress expression of seed-specific genes. Comparison of genomic datasets revealed that PKL-dependent genes are enriched for trimethylation of histone H3 lysine 27 (H3K27me3), a repressive epigenetic mark. Chromatin immunoprecipitation studies demonstrate that PKL promotes H3K27me3 in both germinating seedlings and in adult plants but do not identify a connection between PKLdependent expression and acetylation levels. Taken together, our analyses illuminate a new pathway by which CHD3 remodelers contribute to repression in eukaryotes.The transition from inert seed to growing seedling marks the culmination of a remarkable transformation in developmental identity and transcriptional programs. During seed formation, numerous genes are expressed that contribute to establishment of the body plan, laying down of storage reserves, and desiccation tolerance (1, 2). Many of these genes are widely expressed in the developing seed only to be silenced by the time the seed germinates, often for the remainder of the life cycle of the plant (3). Although several key regulators have been identified that activate various seed transcriptional programs, such as the LEAFY COTY-LEDON (LEC) genes and ABSCISIC ACID-INSENSITIVE3 (ABI3) (4, 5), relatively little is known about the mechanisms that ensure that these programs are restricted to developing seeds. This repression is critical for subsequent stages of plant development. In particular, continued expression of LEC genes leads to continued expression of seed-specific programs and substantial alteration of seedling development (6 -8).PICKLE (PKL) has previously been shown to play a significant role in repression of seed-associated genes. In pkl plants, many seed-associated traits continue to be expressed after germination, including accumulation of seed storage reserves and the ability to undergo somatic embryogenesis (9, 10). Primary roots of pkl seedlings that continue to express seed-associated developmental programs stop elongating and adopt a green tuberous phenotype referred to as the "pickle root" phenotype. PKL codes for a predicted ATP-dependent chromatin remodeling factor in the CHD3 family (11,12). In animal systems, CHD3 proteins are a component of the Mi-2/NuRD complex (13-16). This complex includes several other proteins, in...

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Ordered Histone Modifications Are Associated with Transcriptional Poising and Activation of the phaseolin Promoter

Cited by 82 publications

References 75 publications

Plant SET domain-containing proteins: Structure, function and regulation

Plant SET domain-containing proteins: Structure, function and regulation

Repression of theLEAFY COTYLEDON 1/B3Regulatory Network in Plant Embryo Development byVP1/ABSCISIC ACID INSENSITIVE 3-LIKEB3 Genes

The CHD3 Remodeler PICKLE Promotes Trimethylation of Histone H3 Lysine 27

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