scholarly journals Ubp8p, a Histone Deubiquitinase Whose Association with SAGA Is Mediated by Sgf11p, Differentially Regulates Lysine 4 Methylation of Histone H3 In Vivo

2006 ◽  
Vol 26 (9) ◽  
pp. 3339-3352 ◽  
Author(s):  
Abhijit Shukla ◽  
Nadia Stanojevic ◽  
Zhen Duan ◽  
Payel Sen ◽  
Sukesh R. Bhaumik
Keyword(s):  
Core Promoter ◽  
Histone H3 ◽  
Chip Assay ◽  
General Role ◽  
Reading Frame ◽  
Core Promoters ◽  
Yeast Genes ◽  
Complex Regulatory Network

ABSTRACT Despite recent advances in characterizing the regulation of histone H3 lysine 4 (H3-K4) methylation at the GAL1 gene by the H2B-K123-specific deubiquitinase activity of Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-acetyltransferase)-associated Ubp8p, our knowledge on the general role of Ubp8p at the SAGA-dependent genes is lacking. For this study, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation (ChIP) assay, we have analyzed the role of Ubp8p in the regulation of H3-K4 methylation at three other SAGA-dependent yeast genes, namely, PHO84, ADH1, and CUP1. Like that at GAL1, H3-K4 methylation is increased at the PHO84 core promoter in the UBP8 deletion mutant. We also show that H3-K4 methylation remains invariant at the PHO84 open reading frame in the Δubp8 mutant, demonstrating a highly localized role of Upb8p in regulation of H3-K4 methylation at the promoter in vivo. However, unlike that at PHO84, H3-K4 methylation at the two other SAGA-dependent genes is not controlled by Ubp8p. Interestingly, Ubp8p and H3-K4 methylation are dispensable for preinitiation complex assembly at the core promoters of these genes. Our ChIP assay further demonstrates that the association of Ubp8p with SAGA is mediated by Sgf11p, consistent with recent biochemical data. Collectively, the data show that Ubp8p differentially controls H3-K4 methylation at the SAGA-dependent promoters, revealing a complex regulatory network of histone methylation in vivo.

scholarly journals Embryonic Poly(A)-Binding Protein Stimulates Translation in Germ Cells

2005 ◽  
Vol 25 (5) ◽  
pp. 2060-2071 ◽  
Author(s):  
Gavin S. Wilkie ◽  
Philippe Gautier ◽  
Diane Lawson ◽  
Nicola K. Gray
Keyword(s):  
Xenopus Laevis ◽  
Oocyte Maturation ◽  
Germ Cells ◽  
Binding Protein ◽  
Expression Patterns ◽  
General Role ◽  
Early Embryos ◽  
Relative Divergence

ABSTRACT The function of poly(A)-binding protein 1 (PABP1) in poly(A)-mediated translation has been extensively characterized. Recently, Xenopus laevis oocytes and early embryos were shown to contain a novel poly(A)-binding protein, ePABP, which has not been described in other organisms. ePABP was identified as a protein that binds AU-rich sequences and prevents shortening of poly(A) tails. Here, we show that ePABP is also expressed in X. laevis testis, suggesting a more general role for ePABP in gametogenesis. We find that ePABP is conserved throughout vertebrates and that mouse and X. laevis cells have similar tissue-specific ePABP expression patterns. Furthermore, we directly assess the role of ePABP in translation. We show that ePABP is associated with polysomes and can activate the translation of reporter mRNAs in vivo. Despite its relative divergence from PABP1, we find that ePABP has similar functional domains and can bind to several PABP1 partners, suggesting that they may use similar mechanisms to activate translation. In addition, we find that PABP1 and ePABP can interact, suggesting that these proteins may be bound simultaneously to the same mRNA. Finally, we show that the activity of both PABP1 and ePABP increases during oocyte maturation, when many mRNAs undergo polyadenylation.

scholarly journals A Role for Gcn5-Mediated Global Histone Acetylation in Transcriptional Regulation

2006 ◽  
Vol 26 (5) ◽  
pp. 1610-1616 ◽  
Author(s):  
Rachel Maria Imoberdorf ◽  
Irini Topalidou ◽  
Michel Strubin
Keyword(s):  
Histone Acetylation ◽  
Core Promoter ◽  
Histone Acetyltransferases ◽  
Gene Promoters ◽  
Core Promoters ◽  
The Core ◽  
Strength Of Interaction ◽  
Genome Wide ◽  
The Common

ABSTRACT Transcriptional activators often require histone acetyltransferases (HATs) for full activity. The common explanation is that activators directly recruit HATs to gene promoters to locally hyperacetylate histones and thereby facilitate transcription complex formation. However, in addition to being targeted to specific loci, HATs such as Gcn5 also modify histones genome-wide. Here we provide evidence for a role of this global HAT activity in regulated transcription. We show that activation by direct recruitment of the transcriptional machinery neither recruits Gcn5 nor induces changes in histone acetylation yet can strongly depend on Gcn5 at promoters showing a high basal state of Gcn5-mediated histone acetylation. We also show that Gcn5 dependency varies among core promoters and is influenced by the strength of interaction used to recruit the machinery and by the affinity of the latter for the core promoter. These data support a role for global Gcn5 HAT activity in modulating transcription independently of its known coactivator function.

scholarly journals MAZ-LINC00645-GP73 Axis Promotes Hepatocellular Carcinoma Proliferation and Metastasis

2020 ◽  
Author(s):  
Yang Chen ◽  
Huiyan Li ◽  
Chunxun Liu ◽  
Yongmei Han ◽  
Yubao Zhang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Mechanisms ◽  
Tumor Promoter ◽  
Transcriptional Analysis ◽  
Luciferase Reporter ◽  
Chip Assay ◽  
Bioinformatics Analyses

Abstract BACKGROUND: Long non-coding RNAs (lncRNA) have been shown to play important roles in the development and progression of hepatocellular carcinoma (HCC). In this report, we examined the role of lncRNA LINC00645 in HCC. MATERIAL AND METHODS: Based on public databases and integrating bioinformatics analyses, the over-expression of LINC00645 in HCC tissues was detected and further validated in a cohort of liver tissues. A series of in vitro and in vivo functional experiments were executed to investigate the role of LINC00645 in the carcinogenesis and development of HCC. Comprehensive transcriptional analysis, chromatin immunoprecipitation (ChIP) assay, dual-luciferase reporter assay and western blot etc. were performed to explore the molecular mechanisms underlying the functions of LINC00645. RESULTS: LINC00645 was significantly upregulated in HCC cell lines and HCC tissues, which was correlated with poor prognosis in HCC patients. LINC00645 knockdown remarkably suppressed tumor growth in vitro and in vivo. Mechanistically, LINC00645 could competitively bind with miR-141-3p to prevent the degradation of its target gene GP73, which acts as a tumor-promoter in HCC. Furthermore, the ChIP assay showed that the transcription factor MAZ could bind to the LINC00645 promoter and increase its transcription. CONCLUSIONS: Collectively, this study demonstrated that LINC00645 plays a critical regulatory role in hepatocellular carcinoma cells and LINC00645 may serve as a potential diagnostic biomarker and therapeutic target of HCC. Thus, targeting MAZ/LINC00645/miR-141-3p/GP73 signaling axis may prevent the progression of HCC.

scholarly journals N-terminal sumoylation of centromeric histone H3 variant Cse4 regulates its proteolysis to prevent mislocalization to non-centromeric chromatin

2017 ◽  
Author(s):  
Kentaro Ohkuni ◽  
Reuben Levy-Myers ◽  
Jack Warren ◽  
Wei-Chun Au ◽  
Yoshimitsu Takahashi ◽  
...  
Keyword(s):  
Genome Stability ◽  
Histone H3 ◽  
Physiological Role ◽  
Centromeric Chromatin ◽  
E3 Ligases ◽  
Physiological Conditions ◽  
Evolutionarily Conserved ◽  
Histone H3 Variant

AbstractStringent regulation of cellular levels of evolutionarily conserved centromeric histone H3 variant (CENP-A in humans, CID in flies, Cse4 in yeast) prevents its mislocalization to non-centromeric chromatin. Overexpression and mislocalization of CENP-A has been observed in cancers and leads to aneuploidy in yeast, flies, and human cells. Ubiquitin-mediated proteolysis of Cse4 by E3 ligases such as Psh1 and Sumo-Targeted Ubiquitin Ligase (STUbL) Slx5 prevent mislocalization of Cse4. Previously, we identified Siz1 and Siz2 as the major E3 ligases for sumoylation of Cse4. In this study, we identify lysine 65 (K65) in Cse4 as a SUMO site and show that sumoylation of Cse4 K65 regulates its ubiquitin-mediated proteolysis by Slx5. Strains expressing cse4 K65R exhibit reduced levels of sumoylated and ubiquitinated Cse4 in vivo. Furthermore, co-immunoprecipitation experiments reveal reduced interaction of cse4 K65R with Slx5. Defects in sumoylation of cse4 K65R contribute to increased stability and mislocalization of cse4 K65R under normal physiological conditions. Based on the increased stability of cse4 K65R in psh1∆ strains but not in slx5∆ strains, we conclude that Slx5 targets sumoylated Cse4 K65 for ubiquitination-mediated proteolysis independent of Psh1. In summary, we have identified and characterized the physiological role of Cse4 sumoylation and determined that sumoylation of Cse4 K65 regulates ubiquitin-mediated proteolysis and prevents mislocalization of Cse4 which is required for genome stability.

scholarly journals Attenuation of Marek's Disease Virus by Deletion of Open Reading Frame RLORF4 but Not RLORF5a

2005 ◽  
Vol 79 (18) ◽  
pp. 11647-11659 ◽  
Author(s):  
Keith W. Jarosinski ◽  
Nikolaus Osterrieder ◽  
Venugopal K. Nair ◽  
Karel A. Schat
Keyword(s):  
Virus Isolation ◽  
Cultured Cells ◽  
Artificial Chromosome ◽  
Marek's Disease ◽  
Marek’S Disease ◽  
Reading Frame ◽  
Multiple Organs ◽  
Kinetics Of

ABSTRACT Marek's disease (MD) in chickens is caused by the alphaherpesvirus MD virus (MDV) and is characterized by the development of lymphoblastoid tumors in multiple organs. The recent identification and cloning of RLORF4 and the finding that four of six attenuated strains of MDV contained deletions within RLORF4 suggested that it is involved in the attenuation process of MDV. To assess the role of RLORF4 in MD pathogenesis, its coding sequence was deleted in the pRB-1B bacterial artificial chromosome clone. Additionally, RLORF5a was deleted separately to examine its importance for oncogenesis. The sizes of plaques produced by MDV reconstituted from pRB-1BΔRLORF5a (rRB-1BΔRLORF5a) were similar to those produced by the parental pRB-1B virus (rRB-1B). In contrast, virus reconstituted from pRB-1BΔRLORF4 (rRB-1BΔRLORF4) produced significantly larger plaques. Replication of the latter virus in cultured cells was higher than that of rRB-1B or rRB-1BΔRLORF5a using quantitative PCR (qPCR) assays. In vivo, both deletion mutants and rRB-1B replicated at comparable levels at 4, 7, and 10 days postinoculation (p.i.), as determined by virus isolation and qPCR assays. At 14 days p.i., the number of PFU of virus isolated from chickens infected with rRB-1BΔRLORF4 was comparable to that from chickens infected with highly attenuated RB-1B and significantly lower than that from rRB-1B-infected birds. The number of tumors and kinetics of tumor production in chickens infected with rRB-1BΔRLORF5a were similar to those of P2a chickens infected with rRB-1B. In stark contrast, none of the chickens inoculated with rRB-1BΔRLORF4 died up to 13 weeks p.i.; however, two chickens had tumors at the termination of the experiment. The data indicate that RLORF4 is involved in attenuation of MDV, although the function of RLORF4 is still unknown.

scholarly journals The Yng1p Plant Homeodomain Finger Is a Methyl-Histone Binding Module That Recognizes Lysine 4-Methylated Histone H3

2006 ◽  
Vol 26 (21) ◽  
pp. 7871-7879 ◽  
Author(s):  
David G. E. Martin ◽  
Kristin Baetz ◽  
Xiaobing Shi ◽  
Kay L. Walter ◽  
Vicki E. MacDonald ◽  
...  
Keyword(s):  
Histone H3 ◽  
General Role ◽  
Histone Binding ◽  
Phd Finger ◽  
Amino Terminal ◽  
Plant Homeodomain Finger ◽  
Plant Homeodomain ◽  
Insight Into

ABSTRACT The ING (inhibitor of growth) protein family includes a group of homologous nuclear proteins that share a highly conserved plant homeodomain (PHD) finger domain at their carboxyl termini. Members of this family are found in multiprotein complexes that posttranslationally modify histones, suggesting that these proteins serve a general role in permitting various enzymatic activities to interact with nucleosomes. There are three members of the ING family in Saccharomyces cerevisiae: Yng1p, Yng2p, and Pho23p. Yng1p is a component of the NuA3 histone acetyltransferase complex and is required for the interaction of NuA3 with chromatin. To gain insight into the function of the ING proteins, we made use of a genetic strategy to identify genes required for the binding of Yng1p to histones. Using the toxicity of YNG1 overexpression as a tool, we showed that Yng1p interacts with the amino-terminal tail of histone H3 and that this interaction can be disrupted by loss of lysine 4 methylation within this tail. Additionally, we mapped the region of Yng1p required for overexpression of toxicity to the PHD finger, showed that this region capable of binding lysine 4-methylated histone H3 in vitro, and demonstrated that mutations of the PHD finger that abolish binding in vitro are no longer toxic in vivo. These results identify a novel function for the Yng1p PHD finger in promoting stabilization of the NuA3 complex at chromatin through recognition of histone H3 lysine 4 methylation.

scholarly journals Pervasive and Dynamic Transcription Initiation in Saccharomyces cerevisiae

2018 ◽  
Author(s):  
Zhaolian Lu ◽  
Zhenguo Lin
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Model Organism ◽  
Start Codon ◽  
Yeast Genome ◽  
Core Promoters ◽  
Nucleotide Resolution ◽  
Yeast Genes

AbstractTranscription initiation is finely regulated to ensure the proper expression and function of these genes. The regulated transcription initiation in response to various environmental cues in the model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start site (TSS) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions using no-amplification non-tagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. Based on 337 million uniquely mapped CAGE tags, we mapped ~1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact genome of yeast. The comprehensive TSS maps allowed us to identify core promoters for ~96% verified protein-coding genes and to revise the predicted translation start codon for 183 genes. We found that 56% of yeast genes have at least two core promoters and alternative usage of different core promoters in a gene is widespread in response to changing environments. More importantly, most core promoter shifts are coupled with differential gene expression, indicating that core promoter shift might play an important role in controlling transcriptional activity of yeast genes. Based on their dynamic activities, we divided yeast core promoters as constitutive core promoters (55%) and inducible core promoters (45%). The two classes of core promoters exhibit distinctive patterns in transcriptional abundance, chromatin structure, promoter shape, and sequence context. In summary, the quantitative TSS maps generated by this study improved the annotation of yeast genome, and revealed a highly pervasive and dynamic nature of transcription initiation in yeast.

scholarly journals A general role of zinc binding domain revealed by structures of σ28-dependent transcribing complexes

2020 ◽  
Author(s):  
Wei Shi ◽  
Wei Zhou ◽  
Baoyue Zhang ◽  
Shaojia Huang ◽  
Yanan Jiang ◽  
...  
Keyword(s):  
Binding Domain ◽  
Zinc Binding ◽  
General Mechanism ◽  
General Role ◽  
Template Strand ◽  
Promoter Dna ◽  
Zinc Binding Domain

AbstractIn bacteria, σ28 is the flagella-specific sigma factor that controls the expression of flagella-related genes involving bacterial motility and chemotaxis. However, its transcriptional mechanism remains largely unclear. Here we report cryo-EM structures of σ28-dependent transcribing complexes on a complete flagella-specific DNA promoter. The structures reveal how σ28-RNA polymerase (RNAP) recognizes promoter DNA through strong interaction with −10 element but weak contact with −35 element to initiate transcription. In addition, we observed a distinct architecture in which the β′ zinc binding domain (ZBD) of RNAP stretches out from its canonical position to interact with the upstream non-template strand. Further in vitro and in vivo assays demonstrate that this interaction facilitates the isomerization of RNAP-promoter closed to open complex due to compensating the weak interaction between σ4/−35 element, and suggest that ZBD-relocation is a general mechanism employed by the σ70-family factors to enhance transcription from promoters with weak σ4/−35 element interactions.

scholarly journals Role of rpoS in Stress Survival and Virulence of Vibrio cholerae

1998 ◽  
Vol 180 (4) ◽  
pp. 773-784 ◽  
Author(s):  
Fitnat H. Yildiz ◽  
Gary K. Schoolnik
Keyword(s):  
Vibrio Cholerae ◽  
Genomic Library ◽  
Bacterial Species ◽  
Wild Type ◽  
Reading Frame ◽  
Infant Mouse ◽  
Acid Protein ◽  
Amino Acid Protein

ABSTRACT Vibrio cholerae is known to persist in aquatic environments under nutrient-limiting conditions. To analyze the possible involvement of the alternative sigma factor encoded byrpoS, which is shown to be important for survival during nutrient deprivation in several other bacterial species, a V. cholerae rpoS homolog was cloned by functional complementation of an Escherichia coli mutant by using a wild-type genomic library. Sequence analysis of the complementing clone revealed an 1.008-bp open reading frame which is predicted to encode a 336-amino-acid protein with 71 to 63% overall identity to other reported rpoS gene products. To determine the functional role of rpoS in V. cholerae, we inactivatedrpoS by homologous recombination. V. choleraestrains lacking rpoS are impaired in the ability to survive diverse environmental stresses, including exposure to hydrogen peroxide, hyperosmolarity, and carbon starvation. These results suggest that rpoS may be required for the persistence of V. cholerae in aquatic habitats. In addition, the rpoSmutation led to reduced production or secretion of hemagglutinin/protease. However, rpoS is not critical for in vivo survival, as determined by an infant mouse intestinal competition assay.

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