Transcriptional Repression by Histone Deacetylases in Plants

Reversible histone acetylation and deacetylation at the N-terminus of histone tails play crucial roles in regulation of eukaryotic gene activity. Acetylation of core histones usually induces an ＇open＇ chromatin structure and is associated with gene activation, whereas deacetylation of histone is often correlated with ＇closed＇ chromatin and gene repression. Histone deacetylation is catalyzed by histone deacetylases （HDACs）. A growing number of studies have demonstrated the importance of histone deacetylation/acetylation on genome stability, transcriptional regulation, and development in plants. Furthermore, HDACs were shown to interact with various chromatin remolding factors and transcription factors involved in transcriptional repression in multiple developmental processes. In this review, we summarized recent findings on the transcriptional repression mediated by HDACs in plants.

Transcriptional repression of hDaxx enhanced by adenovirus 12 E1B 55-kDa oncoprotein interacting with hDaxx

Background Daxx has been identified as a nuclear protein that involves in apoptosis and transcriptional repression. Daxx co-localizes with the promyelocytic leukemia (PML) protein and regulates transcription. Human Daxx (hDaxx) is a protein that functions as a transcriptional regulation through its interaction with some DNA-associated proteins. The aim of this study was to explore the transcriptional regulatory effect of hDaxx interacting with adenovirus (Ad) 12 E1B (Ad12E1B) 55-kDa oncoprotein Methods The co-localization of hDaxx-Ad12E1B or hDaxx-PML protein in the nucleus was observed under a confocal microscope Interaction of hDaxx and Ad12E1B was analyzed by yeast two-hybrid assay Direct binding of hDaxx and Ad12E1B was analyzed using coimmunoprecipitation and Western blot in vivo and in vitro The activity of a luciferase reporter gene, which was regulated by an hDaxx modulated thymidine kinase (TK) promoter, was detected in an automat luminometer Results Ad12E1B, which co-localized with hDaxx in the nuclei of G401-CC3 cells, disrupted the co-localization of hDaxx and PML in the PML oncogenic domains (PODs) hDaxx bound directly to Ad12E1B in vivo and in vitro hDaxx interacted with Ad12E1B along its full length Ad12E1B enhanced transcriptional repression activity of hDaxx Conclusion Ad12E1B disrupts the co-localization of hDaxx with PML in PODs and enhances transcriptional repression activity of hDaxx

Chromatin remodeling regulated by steroid and nuclearreceptors

Coactivators and corepressors regulate transcriptionby controlling interactions between sequence-specific transcription factors, the basal transcriptional machinery andthe chromatin environment. This review consider the access of nuclear and steroid receptors to chromatin, theiruse of corepressors and coactivators to modify chromatinstructure and the implications for transcriptional control.The assembly of specific nucleoprotein architectures andtargeted histone modification emerge as central controlling elements for gene expression.

Strategies that regulate LSD1 for novel therapeutics

Histone methylation plays crucial roles in regulating chromatin structure and gene transcrip-tion in epigenetic modifications.Lysine-specific demethylase 1(LSD1),the first identified histone de-methylase,is universally overexpressed in various diseases.LSD1 dysregulation is closely associated with cancer,viral infections,and neurodegenerative diseases,etc.,making it a promising therapeutic target.Several LSD1 inhibitors and two small-molecule degraders(UM171 and BEA-17)have entered the clinical stage.LSD1 can remove methyl groups from histone 3 at lysine 4 or lysine 9(H3K4 or H3K9),resulting in either transcription repression or activation.While the roles of LSD1 in transcrip-tional regulation are well-established,studies have revealed that LSDl can also be dynamically regulated by other factors.For example,the expression or activity of LSD1 can be regulated by many proteins that form transcriptional corepressor complexes with LSD1.Moreover,some post-transcriptional modifica-tions and cellular metabolites can also regulate LSD1 expression or its demethylase activity.Therefore,in this review,we will systematically summarize how proteins involved in the transcriptional corepressor complex,various post-translational modifications,and metabolites act as regulatory factors for LSD1 ac-tivity.

Distinct gene expression pattern of RUNX1 mutations coordinated by target repression and promoter hypermethylation in acute myeloid leukemia

Runt-related transcription factor 1(RUNX1)is an essential regulator of normal hematopoiesis.Its dysfunction,caused by either fusions or mutations,is frequently reported in acute myeloid leukemia(AML).However,RUNX1 mutations have been largely under-explored compared with RUNX1 fusions mainly due to their elusive genetic characteristics.Here,based on 1741 patients with AML,we report a unique expression pattern associated with RUNX1 mutations in AML.This expression pattern was coordinated by target repression and promoter hypermethylation.We first reanalyzed a joint AML cohort that consisted of three public cohorts and found that RUNX1 mutations were mainly distributed in the Runt domain and almost mutually exclusive with NPM1 mutations.Then,based on RNA-seq data from The Cancer Genome Atlas AML cohort,we developed a 300-gene signature that significantly distinguished the patients with RUNX1 mutations from those with other AML subtypes.Furthermore,we explored the mechanisms underlying this signature from the transcriptional and epigenetic levels.Using chromatin immunoprecipitation sequencing data,we found that RUNX1 target genes tended to be repressed in patients with RUNX1 mutations.Through the integration of DNA methylation array data,we illustrated that hypermethylation on the promoter regions of RUNX1-regulated genes also contributed to dysregulation in RUNX1-mutated AML.This study revealed the distinct gene expression pattern of RUNX1 mutations and the underlying mechanisms in AML development.

Phf15-a novel transcriptional repressor regulating inflammation in a mouse microglial cell line

Aim: Excessive microglial inflammation has emerged as a key player in mediating the effects of aging and neurodegeneration on brain dysfunction. Thus, there is great interest in discovering transcriptional repressors that can control this process. We aimed to examine whether Phf15 - one of the top differentially expressed genes in microglia during aging in humans - could regulate transcription of proinflammatory mediators in microglia. Methods: Real-time quantitative PCR was used to assess Phf15 mRNA expression in mouse brain during aging. Loss-of-function [short hairpin RNA (shRNA) -mediated knockdown (KD) and CRISPR/Cas9-mediated knockout (KO) of Phf15] and gain-of-function [retroviral overexpression (OE) of murine Phf15 cDNA] studies in a murine microglial cell line (SIM-A9) followed by immune activation with lipopolysaccharide were used to determine the effect of Phf15 on proinflammatory factor (Tnfα , IL-1β , and Nos2) mRNA expression. RNA sequencing was used to determine global transcriptional changes afterPhf15 knockout under basal conditions and after lipopolysaccharide stimulation. Results:Phf15 expression increases in mouse brain during aging, similar to humans. KD, KO, and OE studies determined that Phf15 represses mRNA expression levels of proinflammatory mediators such as Tnfα , IL-1β , and Nos2 . Global transcriptional changes after Phf15 KO showed that Phf15 specifically represses genes related to the antiviral (type I interferon) response and cytokine production in microglia. Conclusion: We provide the first evidence thatPhf15 is an important transcriptional repressor of microglial inflammation, regulating the antiviral response and proinflammatory cytokine production. Importantly, Phf15 regulates both basal and signal-dependent activation and controls the magnitude and duration of the microglial inflammatory response.

Epigenetic regulation of N-hydroxypipecolic acid biosynthesis by the AIPP3-PHD2-CPL2 complex

N-Hydroxypipecolic acid(NHP)is a signaling molecule crucial for systemic acquired resistance(SAR),a systemic immune response in plants that provides long-lasting and broad-spectrum protection against secondary pathogen infections.To identify negative regulators of NHP biosynthesis,we performed a forward genetic screen to search for mutants with elevated expression of the NHP biosynthesis gene FLAVIN-DEPENDENT MONOOXYGENASE 1(FMO1).Analysis of two constitutive expression of FMO1(cef)and one induced expression of FMO1(ief)mutants revealed that the AIPP3–PHD2–CPL2 protein complex,which is involved in the recognition of the histone modification H3K27me3 and transcriptional repression,contributes to the negative regulation of FMO1 expression and NHP biosynthesis.Our study suggests that epigenetic regulation plays a crucial role in controlling FMO1 expression and NHP levels in plants.

Regulation of jasmonate signaling by reversible acetylation of TOPLESS in Arabidopsis

The plant hormone jasmonate(JA)regulates plant immunity and adaptive growth by orchestrating a genome-wide transcriptional program.Key regulators of JA-responsive gene expression include the master transcription factor MYc2,which is repressed by the conserved Groucho/Tup1-like corepressor TOPLESS(TPL)in the resting state.However,the mechanisms underlying TPL-mediated transcriptional repression of MYc2 activity and hormone-dependent switching between repression and de-repression remainenigmatic.Here,we report the regulation of TPLactivity and JAsignaling byreversibleacetylation of TPL.We found that the histone acetyltransferase GCN5 could mediate TPL acetylation,which enhances its interaction with the NOVEL-INTERACTOR-OF-JAZ(NINJA)adaptor and promotes its recruitment to MYc2 target promoters,facilitating transcriptional repression.Conversely,TPL deacetylation by the histonedeacetylase HDA6 weakens TPL-NINJA interaction and inhibitsTPL recruitmentto MYC2 target promoters,facilitating transcriptional activation.In the resting state,the opposing activities of GCN5 and HDA6 maintain TPL acetylation homeostasis,promoting transcriptional repression activity of TPL.In response to JA elicitation,HDA6 expression is transiently induced,resulted in decreased TPL acetylation and repressor activity,thereby transcriptional activation of MYC2 target genes.Thus,the GCN5-TPL-HDA6 module main tains the homeostasis of acetylated TPL,thereby determining the transcriptional state of JA-responsive genes.Our findings uncovered a mechanism by which the TPL corepressor activity in JA signaling is activelytuned inarapidandreversiblemanner.

A histone H3K27me3 reader cooperates with a family of PHD finger-containing proteins to regulate flowering time in Arabidopsis

Trimethylated histone H3 lysine 27(H3 K27 me3)is a repressive histone marker that regulates a variety of developmental processes,including those that determine flowering time.However,relatively little is known about the mechanism of how H3 K27 me3 is recognized to regulate transcription.Here,we identified BAH domain-containing transcriptional regulator 1(BDT1)as an H3 K27 me3 reader.BDT1 is responsible for preventing flowering by suppressing the expression of flowering genes.Mutation of the H3 K27 me3 recognition sites in the BAH domain disrupted the binding of BDT1 to H3 K27 me3,leading to de-repression of H3 K27 me3-enriched flowering genes and an earlyflowering phenotype.We also found that BDT1 interacts with a family of PHD finger-containing proteins,which we named PHD1–6,and with CPL2,a Pol II carboxyl terminal domain(CTD)phosphatase responsible for transcriptional repression.Pull-down assays showed that the PHD finger-containing proteins can enhance the binding of BDT1 to the H3 K27 me3 peptide.Mutations in all of the PHD genes caused increased expression of flowering genes and an earlyflowering phenotype.This study suggests that the binding of BDT1 to the H3 K27 me3 peptide,which is enhanced by PHD proteins,is critical for preventing early flowering.

The transcription factor ZEB1 promotes an aggressive phenotype in prostate cancer cell lines

It has been reported that one of the factors that promotes tumoral progression is the abnormal activation of the epithelial-mesenchymal transition program. This process is associated with tumoral cells acquiring invasive and malignant properties and has the transcription factor zinc finger E-box-binding homeobox 1 （ZEB1） as one of its main activators. However, the role of ZEB1 in promoting malignancy in prostate cancer （PC, a） is still unclear. Here, we report that ZEB1 expression correlates with Gleason score in PCa samples and that expression of ZEB1 regulates epithelial-mesenchymal transition and malignant characteristics in PCa cell lines. The results showed that ZEB1 expression is higher in samples of higher malignancy and that overexpression of ZEB1 was able to induce epithelial-mesenchymal transition by upregulating the mesenchymal marker Vimentin and downregulating the epithelial marker E-Cadherin. On the contrary, ZEB 1 silencing repressed Vimentin expression and upregulated E-Cadherin. ZEB1 expression conferred enhanced motility and invasiveness and a higher colony formation capacity to 22Rvl cells whereas DU145 cells with ZEB1 silencing showed a decrease in those same properties. The results showed that ZEB1 could be a key promoter of tumoral progression toward advanced stages of PC, a.

CUL4B negatively regulates Toll-like receptor-triggered proinflammatory responses by repressing Pten transcription

Toll-like receptors (TLRs) play critical roles in innate immunity and inflammation. The molecular mechanisms by which TLR signaling is fine-tuned remain to be completely elucidated. Cullin 4B (CUL4B), which assembles the CUL4B-RING E3 ligase complex (CRL4B), has been shown to regulate diverse developmental and physiological processes by catalyzing monoubiquitination for histone modification or polyubiquitination for proteasomal degradation. Here, we identified the role of CUL4B as an intrinsic negative regulator of the TLR-triggered inflammatory response. Deletion of CUL4B in macrophages increased the production of proinflammatory cytokines and decreased anti-inflammatory cytokine IL-10 production in response to pathogens that activate TLR3, TLR4, or TLR2. Myeloid cell-specific Cul4b knockout mice were more susceptible to septic shock when challenged with lipopolysaccharide, polyinosinic-polycytidylic acid or Salmonella typhimurium infection. We further demonstrated that enhanced TLR-induced inflammatory responses in the absence of CUL4B were mediated by increased GSK3β activity. Suppression of GSK3β activity efficiently blocked the TLR-triggered increase in proinflammatory cytokine production and attenuated TLR-triggered death in Cul4b mutant mice. Mechanistically, CUL4B was found to negatively regulate TLR-triggered signaling by epigenetically repressing the transcription of Pten, thus maintaining the anti-inflammatory PI3K-AKT-GSK3β pathway. The upregulation of PTEN caused by CUL4B deletion led to uncontrolled GSK3β activity and excessive inflammatory immune responses. Thus, our findings indicate that CUL4B functions to restrict TLR-triggered inflammatory responses through regulating the AKT-GSK3β pathway.