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Chen, D.-H.

Publications and source records attributed to Chen, D.-H..

5 recordsLinked to original sources

Reconstitution of +1 nucleosome transcription reveals coordinated functions of SAGA, Mediator, and TFIIH

The +1 nucleosome has emerged as a key regulator of eukaryotic transcription, but how it controls transcription initiation remains poorly understood. Here we reconstitute transcription through the +1 nucleosome using eleven purified yeast factors: RNA polymerase II (Pol II), the six general transcription factors (GTFs), TFIIS, the activator Pho4, and the SAGA and Mediator complexes. The system recapitulates key features of regulation observed in vivo. SAGA, acting with Pho4, directs pre-initiation complex (PIC) assembly to the correct position through its TBP-loading activity. Mediator stimulates transcription when the +1 nucleosome imposes a barrier to PIC formation, consistent with stabilization of productive TFIIH-DNA engagement. Contrary to the prevailing model, SAGA remains bound to the PIC after TBP loading and acetylates the +1 nucleosome within the assembled complex. The isolated PIC-Mediator-SAGA-nucleosome complex is transcriptionally active, and the repressive effect of the nucleosome is relieved by the DNA translocase activity of Ssl2, the TFIIH subunit that opens promoter DNA. TFIIH thus couples promoter melting to remodeling of the +1 nucleosome.

biochemistry↗

SUMO2 Deletion Changes Chromatin Accessibility and Enhances Cytotoxic T Cell Activation and Tumor Infiltration

Cytotoxic T cells (CTL) are crucial for adaptive immunity that leads to prolonged survival and potential cures for cancer. Recent clinical data has shown that pharmacological inhibition of SUMOylation (SUMOi) profoundly modifies tumor microenvironment (TME) and activates CTL, although the mechanism is not well described. In this study, we found that T cell specific knock out (KO) of the most dominant SUMO paralog, Sumo2/SUMO2, in both mouse and human CD8+ T cells significantly enhanced CD8+ T cell activation that is independent of the known mechanism - inducing type I IFN (IFN-I) expression by myeloid cells. Sumo2/SUMO2 KO in CD8+ T cells increased chromatin accessibility for transcription factors BATF, JunB, ATF3, FRA1, FRA2, and AP1 that are known to promote T cell activation and proliferation. Using antigen-specific T cell models, OT1 and Chimeric Antigen Receptor (CAR)-T cells, we found that Sumo2 KO CD8+ T cells had significantly higher tumor infiltration as revealed by flow cytometry, immuno-fluorescence (IF) staining, and single nuclei RNA-sequencing (snRNA-seq) and conferred greater tumor growth inhibition than wildtype (WT) control T cells. snRNA-seq also revealed Sumo2 KO CD8+ T cells increased the expression of Tumor Necrosis Factor-Related Apoptosis-inducing Ligand (TRAIL), induced apoptosis genes in tumor cells and activated IFN-I and IFN-{gamma} responsive genes in all cell types in the TME. These findings elucidate a novel mechanism regarding how SUMOylation can directly control CTL activation and tumor infiltration that activate anti-tumor immunity in the TME. SUMO2 KO can also be a potential strategy to enhance adoptive T cell therapies of solid tumors by enhancing their activity, tumor infiltration and their ability to after the TME.

immunology↗

The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion.

Abstract.Varicella-zoster virus (VZV) is a medically important alphaherpesvirus that induces fusion of the virion envelope and the cell membrane during entry, and between cells to form polykaryocytes within infected tissues during pathogenesis. All members of the Herpesviridae, including VZV, have a conserved core fusion complex composed of glycoproteins, gB, gH and gL. The ectodomain of the primary fusogen, gB, has five domains, DI-V, of which DI contains the fusion loops needed for fusion function. We recently demonstrated that DIV is critical for fusion initiation, which was revealed by a 2.8[A] structure of a VZV neutralizing mAb, 93k, bound to gB and mutagenesis of the gB-93k interface. To further assess the mechanism of mAb 93k neutralization, the binding site of a non-neutralizing mAb to gB, SG2, was compared to mAb 93k using single particle cryogenic electron microscopy (cryo-EM). The gB-SG2 interface partially overlapped with that of gB-93k but, unlike mAb 93k, mAb SG2 did not interact with the gB N-terminus, suggesting a potential role for the gB N-terminus in membrane fusion. The gB ectodomain structure in the absence of antibody was defined at near atomic resolution by single particle cryo-EM (3.9[A]) of native full-length gB purified from infected cells and by X-ray crystallography (2.4[A]) of the transiently expressed ectodomain. Both structures revealed that the VZV gB N-terminus (aa72-114) was flexible based on the absence of visible structures in the cryo-EM or X-ray crystallography data but the presence of gB N-terminal peptides were confirmed by mass spectrometry. Notably, N-terminal residues 109KSQD112 were predicted to form a small -helix and alanine substitution of these residues abolished cell-cell fusion in a virus-free assay. Importantly, transferring the 109AAAA112 mutation into the VZV genome significantly impaired viral propagation. These data establish a functional role for the gB N-terminus in membrane fusion broadly relevant to the Herpesviridae. Author SummaryHerpesviruses are ubiquitous infectious agents of medical and economic importance, including varicella-zoster virus (VZV), which causes chicken pox and shingles. A unifying theme of herpesviruses is their mechanism of entry into host cells, membrane fusion, via a core complex of virally expressed envelope glycoproteins gB, gH and gL. Of these, the primary fusogen, gB, is activated by the heterodimer gH-gL through an unknown mechanism and enables the virus envelope to merge with cell membranes to release the DNA containing capsid into the cytoplasm to initiate infection. By using a human antibody that neutralizes VZV we have recently demonstrated that the initiation of membrane fusion is associated with the crown region of gB. Here, we use cryogenic electron microscopy to compare the structure of this human neutralizing antibody, 93k, to a non-neutralizing antibody SG2. Surprisingly, both antibodies bind to the crown of gB with considerable overlap of their footprints on gB with one important exception, SG2 does not bind to a flexible region in the gB N-terminus. Mutations incorporated into this flexible region disrupts gB mediated membrane fusion and significantly impairs VZV propagation, identifying an Achilles heel in viral replication.

microbiology↗

Limited Dishevelled/Axin oligomerization determines efficiency of Wnt/β-catenin signal transduction

In Wnt/{beta}-catenin signaling, the transcriptional coactivator {beta}-catenin is regulated by its phosphorylation in a complex that includes the scaffold protein Axin and associated kinases. Wnt binding to its coreceptors activates the cytosolic effector Dishevelled (Dvl), leading to the recruitment of Axin and the inhibition of {beta}-catenin phosphorylation. This process requires interaction of homologous DIX domains present in Dvl and Axin, but is mechanistically undefined. We show that Dvl DIX forms antiparallel, double-stranded oligomers in vitro, and that Dvl in cells forms oligomers typically <10 molecules at endogenous expression levels. Axin DIX (DAX) forms small single-stranded oligomers, but its self-association is stronger than that of DIX. DAX caps the ends of DIX oligomers, such that a DIX oligomer has at most four DAX binding sites. The relative affinities and stoichiometry of the DIX-DAX interaction provide a mechanism for efficient inhibition of {beta}-catenin phosphorylation upon Axin recruitment to the Wnt receptor complex.

biochemistry↗

eIF5B gates the transition from translation initiation to elongation

Translation initiation determines both the quantity and identity of the protein product by establishing the reading frame for protein synthesis. In eukaryotic cells, numerous translation initiation factors (eIFs) prepare ribosomes for polypeptide elongation, yet the underlying dynamics of this process remain enigmatic1-4. A central question is how eukaryotic ribosomes transition from translation initiation to elongation. Here, we applied in vitro single-molecule fluorescence microscopy approaches to monitor directly in real time the pathways of late translation initiation and the transition to elongation using a purified yeast Saccharomyces cerevisiae translation system. This transition was remarkably slower in our eukaryotic system than that reported for Escherichia coli5-7. The slow entry to elongation was defined by a long residence time of eIF5B on the 80S ribosome after joining of individual ribosomal subunits, which is catalyzed by this universally conserved initiation factor. Inhibition of eIF5B GTPase activity following subunit joining prevented eIF5B dissociation from the 80S complex, thereby preventing elongation. Our findings illustrate how eIF5B dissociation serves as a kinetic checkpoint for the transition from initiation to elongation, and its release may be governed by a conformation of the ribosome complex that triggers GTP hydrolysis.

biochemistry↗