Ethylene gas is essential for developmental processes and stress responses in plants. Although the membrane-bound protein EIN2 is critical for ethylene signaling, the mechanism by which the ethylene signal is transduced remains largely unknown. Here we show the levels of H3K14Ac and H3K23Ac are correlated with the levels of EIN2 protein and demonstrate EIN2 C terminus (EIN2-C) is sufficient to rescue the levels of H3K14/23Ac of ein2-5 at the target loci, using CRISPR/dCas9-EIN2-C. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and ChIP-reChIP-seq analyses revealed that EIN2-C associates with histone partially through an interaction with EIN2 nuclear-associated protein1 (ENAP1), which preferentially binds to the genome regions that are associated with actively expressed genes both with and without ethylene treatments. Specifically, in the presence of ethylene, ENAP1-binding regions are more accessible upon the interaction with EIN2, and more EIN3 proteins bind to the loci where ENAP1 is enriched for a quick response. Together, these results reveal EIN2-C is the key factor regulating H3K14Ac and H3K23Ac in response to ethylene and uncover a unique mechanism by which ENAP1 interacts with chromatin, potentially preserving the open chromatin regions in the absence of ethylene; in the presence of ethylene, EIN2 interacts with ENAP1, elevating the levels of H3K14Ac and H3K23Ac, promoting more EIN3 binding to the targets shared with ENAP1 and resulting in a rapid transcriptional regulation.T he plant hormone ethylene is essential for a myriad of physiological and developmental processes. It is important in responses to stress, such as drought, cold, flooding, and pathogen infection (1, 2), and modulates stem cell division (3). The common aquatic ancestor of plants possessed the ethylene signaling pathway and the mechanism has been elucidated by analysis of Arabidopsis (4). Ethylene is perceived by a family of receptors bound to the membrane of the endoplasmic reticulum (ER) that are similar in sequence and structure to bacterial two-component histidine kinases (5-9). Each ethylene receptor has an N-terminal transmembrane domain, and the receptors form dimers that bind ethylene via a copper cofactor RAN1 (10, 11). Signaling from one of the receptors, ETR1, induces its physical association with the ER-localized protein RTE1 (12). The ethylene receptors function redundantly to negatively regulate ethylene responses (5) via a downstream Raf-like protein kinase called CTR1 (13,14).In the absence of ethylene, both the ethylene receptors and CTR1 are active, and CTR1 is associated with the ER membrane through a direct interaction with ETR1 (13). The CTR1 downstream factor, EIN2, is localized to the ER membrane, where it interacts with ETR1 (15). The protein stability of EIN2 is regulated by two F-box proteins, ETP1 and ETP2, which mediated its degradation by the ubiquitin-proteasome pathway (16). In the absence of ethylene, the CTR1-mediated phosphorylation at the C-terminal end of EIN2 (EIN2-C) leads to ...

BackgroundHistone acetylation and deacetylation are essential for gene regulation and have been implicated in the regulation of plant hormone responses. Many studies have indicated the role of histone acetylation in ethylene signaling; however, few studies have investigated how ethylene signaling regulates the genomic landscape of chromatin states. Recently, we found that ethylene can specifically elevate histone H3K14 acetylation and the non-canonical histone H3K23 acetylation in etiolated seedlings and the gene activation is positively associated with the elevation of H3K14Ac and H3K23Ac in response to ethylene. To assess the role of H3K9, H3K14, and H3K23 histone modifications in the ethylene response, we examined how ethylene regulates histone acetylation and the transcriptome at global level and in ethylene regulated genes both in wild type (Col-0) and ein2-5 seedlings.ResultsOur results revealed that H3K9Ac, H3K14Ac, and H3K23Ac are preferentially enriched around the transcription start sites and are positively correlated with gene expression levels in Col-0 and ein2-5 seedlings both with and without ethylene treatment. In the absence of ethylene, no combinatorial effect of H3K9Ac, H3K14Ac, and H3K23Ac on gene expression was detected. In the presence of ethylene, however, combined enrichment of the three histone acetylation marks was associated with high gene expression levels, and this ethylene-induced change was EIN2 dependent. In addition, we found that ethylene-regulated genes are expressed at medium or high levels, and a group of ethylene regulated genes are marked by either one of H3K9Ac, H3K14Ac or H3K23Ac. In this group of genes, the levels of H3K9Ac were altered by ethylene, but in the absence of ethylene the levels of H3K9Ac and peak breadths are distinguished in up- and down- regulated genes. In the presence of ethylene, the changes in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expressions.ConclusionsOur study reveals that the plant hormone ethylene induces combinatorial effects of H3K9Ac, K14Ac and K23Ac histone acetylation in gene expression genome widely. Further, for a group of ethylene regulated genes, in the absence of ethylene the levels and the covered breadths of H3K9Ac are the preexist markers for distinguishing up- and down- regulated genes, the change in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expression in the presence of ethylene.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3929-6) contains supplementary material, which is available to authorized users.

The paradigm of activation via ordered recruitment has evolved into a complicated picture as the influence of coactivators and chromatin structures on gene regulation becomes understood. We present here a comprehensive study of many elements of activation of ADH2 and FBP1, two glucose-regulated genes. We identify SWI/SNF as the major chromatin-remodeling complex at these genes, whereas SAGA (Spt-AdaGcn5-acetyltransferase complex) is required for stable recruitment of other coactivators. Mediator plays a crucial role in expression of both genes but does not affect chromatin remodeling. We found that Adr1 bound unaided by coactivators to ADH2, but Cat8 binding depended on coactivators at FBP1. Taken together, our results suggest that commonly regulated genes share many aspects of activation, but that gene-specific regulators or elements of promoter architecture may account for small differences in the mechanism of activation. Finally, we found that activator overexpression can compensate for the loss of SWI/SNF but not for the loss of SAGA.The paradigm of eukaryotic gene activation centers on activators recognizing and binding to unique sequences of DNA and then recruiting coactivators and the transcription machinery (1). The order of recruitment events has been determined for several yeast genes, including HO (2), PHO5 (3-6), and the GAL genes (7-9). Based on these and other studies, the idea of activation has evolved beyond simple ordered recruitment.One of the reasons for this evolving picture of activation is the finding that many coactivator complexes can play multiple roles. For example SAGA 4 functions as a histone-acetyltransferase (HAT) at the HO promoter (10), but it is required for a non-HAT function at the GAL1 promoter (7). In cases such as these, knowing the order in which SAGA arrives at a promoter is insufficient for understanding its role in activation. The dual nature of coactivators emphasizes the need to look not only at their recruitment to the promoter, but also at the functional consequences of this recruitment. Glucose-regulated genes, under the control of Snf1, the homolog of the mammalian AMP-activated kinase, provide a model for such comprehensive studies. In response to glucose starvation, ϳ200 genes are activated by Snf1, many of which depend on the transcription factors Adr1 and Cat8 (11). Previous work in our laboratory has established that SAGA, SWI/SNF, and Mediator are recruited by these two activators upon derepression (12). However, the specific roles of these coactivators and their interactions at these genes remain undetermined.This subset of genes allowed us to address several factors that may influence the mechanisms of activation. First, we focused on two genes, ADH2 and FBP1, which have differential dependences on both the activators Adr1 and Cat8 (13), and on the repressor Mig1 (14), allowing us to determine if trends were regulator-specific. Second, these promoters have established chromatin structures providing a basis for examining the impact of promoter architecture o...

Solutions to the nonlinear Poisson-Boltzmann equation were used to obtain the electrostatic potentials of RNA molecules that have known three-dimensional structures. The results are described in terms of isopotential contours and surface electrostatic potential maps. Both representations have unexpected features: 'cavities' within isopotential contours and areas of enhanced negative potential on molecular surfaces. Intriguingly, the sites of unusual electrostatic features correspond to functionally important regions, suggesting that electrostatic properties play a key role in RNA recognition and stabilization. These calculations reveal that the electrostatic potentials generated by RNA molecules have a variety of functionally important characteristics that cannot be discerned by simple visual inspection of the molecular structure.

The lambda cI lysogenic transcript is unusual in having no leader. Expression of a cI-lacZ protein fusion was relatively resistant to kasugamycin and pactamycin, which inhibit translation initiation on transcripts with leaders. Our data imply that there are distinct differences in translation initiation between the two classes of transcripts.