scholarly journals Independent Recruitment of the Mediator Tail Module to the HO Promoter Suggests Mediator Core Limits Coactivator Recruitment in Saccharomyces cerevisiae

2019 ◽  
Author(s):  
Robert M. Yarrington ◽  
Yaxin Yu ◽  
Chao Yan ◽  
Lu Bai ◽  
David J. Stillman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Gene Transcription ◽  
Gene Activation ◽  
Kinase Domain ◽  
Mediator Complex ◽  
Transcriptional Coactivator ◽  
The Core ◽  
Eukaryotic Organisms

ABSTRACTMediator is an essential, multisubunit complex that functions as a transcriptional coactivator in yeast and other eukaryotic organisms. Mediator has four conserved modules, Head, Middle, Tail, and Kinase, and has been implicated in nearly all aspects of gene regulation. The Tail module has been shown to recruit the Mediator complex to the enhancer or UAS regions of genes via interactions with transcription factors, and the Kinase domain facilitates the transition of Mediator from the UAS/enhancer to the preinitiation complex via protein phosphorylation. Here we analyze expression of the Saccharomyces cerevisiae HO gene using a sin4 Mediator Tail mutation that separates the Tail module from the rest of the complex; the sin4 mutation permits independent recruitment of the Tail module to promoters without the rest of Mediator. Significant increases in recruitment of the SWI/SNF and SAGA coactivators to the HO promoter UAS were observed in a sin4 mutant, along with increased gene activation. These results are consistent with recent studies that have suggested the Kinase module functions negatively to inhibit activation by the Tail. However, we found that Kinase module mutations did not mimic the effect of a sin4 mutation on HO expression. This suggests that at HO the core Mediator complex (Middle and Head modules) must play a role in limiting Tail binding to the promoter UAS and gene activation. We propose that the core Mediator complex helps modulate Mediator binding to the UAS regions of genes to limit coactivator recruitment and ensure proper regulation of gene transcription.

scholarly journals A Role for Mediator Core in Limiting Coactivator Recruitment in Saccharomyces cerevisiae

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 407-420 ◽  
Author(s):  
Robert M. Yarrington ◽  
Yaxin Yu ◽  
Chao Yan ◽  
Lu Bai ◽  
David J. Stillman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Gene Activation ◽  
Mediator Complex ◽  
Transcriptional Coactivator ◽  
The Core ◽  
Link Type ◽  
Upstream Activating Sequence ◽  
Eukaryotic Organisms

Mediator is an essential, multisubunit complex that functions as a transcriptional coactivator in yeast and other eukaryotic organisms. Mediator has four conserved modules, Head, Middle, Tail, and Kinase, and has been implicated in nearly all aspects of gene regulation. The Tail module has been shown to recruit the Mediator complex to the enhancer or upstream activating sequence (UAS) regions of genes via interactions with transcription factors, and the Kinase module facilitates the transition of Mediator from the UAS/enhancer to the preinitiation complex via protein phosphorylation. Here, we analyze expression of the Saccharomyces cerevisiae HO gene using a sin4 Mediator Tail mutation that separates the Tail module from the rest of the complex; the sin4 mutation permits independent recruitment of the Tail module to promoters without the rest of Mediator. Significant increases in recruitment of the SWI/SNF and SAGA coactivators to the HO promoter UAS were observed in a sin4 mutant, along with increased gene activation. These results are consistent with recent studies that have suggested that the Kinase module functions negatively to inhibit activation by the Tail. However, we found that Kinase module mutations did not mimic the effect of a sin4 mutation on HO expression. This suggests that at HO the core Mediator complex (Middle and Head modules) must play a role in limiting Tail binding to the promoter UAS and gene activation. We propose that the core Mediator complex helps modulate Mediator binding to the UAS regions of genes to limit coactivator recruitment and ensure proper regulation of gene transcription.

scholarly journals Cohesin Irr1/Scc3 is likely to influence transcription in Saccharomyces cerevisiae via interaction with Mediator complex.

2013 ◽  
Vol 60 (2) ◽  
Author(s):  
Agata Cena ◽  
Marek Skoneczny ◽  
Anna Chełstowska ◽  
Piotr Kowalec ◽  
Renata Natorff ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Mediator Complex ◽  
Regulation Of Transcription ◽  
Transcriptional Coactivator ◽  
Diploid Strain ◽  
The Core ◽  
Chromatid Cohesion ◽  
Evolutionarily Conserved

The evolutionarily conserved proteins forming sister chromatid cohesion complex are also involved in the regulation of gene transcription. The participation of SA2p (mammalian ortholog of yeast Irr1p, associated with the core of the complex) in the regulation of transcription is already described. Here we analyzed microarray profiles of gene expression of a Saccharomyces cerevisiae irr1-1/IRR1 heterozygous diploid strain. We report that expression of 33 genes is affected by the presence of the mutated Irr1-1p and identify those genes. This supports the suggested role of Irr1p in the regulation of transcription. We also indicate that Irr1p may interact with elements of transcriptional coactivator Mediator.

scholarly journals Bacterium-Enabled Transient Gene Activation by Artificial Transcription Factor for Resolving Gene Regulation in Maize

2021 ◽  
Author(s):  
Mingxia Zhao ◽  
Zhao Peng ◽  
Yang Qin ◽  
Ling Zhang ◽  
Bin Tian ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Protein Delivery ◽  
Graphical Model ◽  
Gene Activation ◽  
Cuticular Wax ◽  
Host Cells ◽  
Myb Transcription Factor ◽  
Leaf Phenotype

ABSTRACTCellular functions are diversified through intricate transcription regulations, and an understanding gene regulation networks is essential to elucidating many developmental processes and environmental responses. Here, we employed the Transcriptional-Activator Like effectors (TALes), which represent a family of transcription factors that are synthesized by members of the γ-proteobacterium genus Xanthomonas and secreted to host cells for activation of targeted host genes. Through delivery by the maize pathogen, Xanthomonas vasicola pv. vasculorum, designer TALes (dTALes), which are synthetic TALes, were used to induce the expression of the maize gene glossy3 (gl3), a MYB transcription factor gene involved in the cuticular wax biosynthesis. RNA-Seq analysis of leaf samples identified 146 gl3 downstream genes. Eight of the nine known genes known to be involved in the cuticular wax biosynthesis were up-regulated by at least one dTALe. A top-down Gaussian graphical model predicted that 68 gl3 downstream genes were directly regulated by GL3. A chemically induced mutant of the gene Zm00001d017418 from the gl3 downstream gene, encoding aldehyde dehydrogenase, exhibited a typical glossy leaf phenotype and reduced epicuticular waxes. The bacterial protein delivery of artificial transcription factors, dTALes, proved to be a straightforward and powerful approach for the revelation of gene regulation in plants.

scholarly journals Groucho/TLE/R-esp proteins associate with the nuclear matrix and repress RUNX (CBF(alpha)/AML/PEBP2(alpha)) dependent activation of tissue-specific gene transcription

2000 ◽  
Vol 113 (12) ◽  
pp. 2221-2231 ◽  
Author(s):  
A. Javed ◽  
B. Guo ◽  
S. Hiebert ◽  
J.Y. Choi ◽  
J. Green ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Transcription ◽  
Nuclear Matrix ◽  
Gene Activation ◽  
Multi Drug Resistance ◽  
Specific Gene ◽  
Dependent Manner ◽  
Subnuclear Localization ◽  
Rous Sarcoma ◽  
C Terminus

The Runt related transcription factors RUNX (AML/CBF(alpha)/PEBP2(alpha)) are key regulators of hematopoiesis and osteogenesis. Using co-transfection experiments with four natural promoters, including those of the osteocalcin (OC), multi drug resistance (MDR), Rous Sarcoma Virus long terminal repeat (LTR), and bone sialoprotein (BSP) genes, we show that each of these promoters responds differently to the forced expression of RUNX proteins. However, the three RUNX subtypes (i.e. AML1, AML2, and AML3) regulate each promoter in a similar manner. Although the OC promoter is activated in a C terminus dependent manner, the MDR, LTR and BSP promoters are repressed by three distinct mechanisms, either independent of or involving the AML C terminus, or requiring only the conserved C-terminal pentapeptide VWRPY. Using yeast two hybrid assays we find that the C terminus of AML1 interacts with a Groucho/TLE/R-esp repressor protein. Co-expression assays reveal that TLE proteins repress AML dependent activation of OC gene transcription. Western and northern blot analyses suggest that TLE expression is regulated reciprocally with the levels of OC gene expression during osteoblast differentiation. Digital immunofluorescence microscopy results show that TLE1 and TLE2 are both associated with the nuclear matrix, and that a significant subset of each colocalizes with AML transcription factors. This co-localization of TLE and AML proteins is lost upon removing the C terminus of AML family members. Our findings indicate that suppression of AML-dependent gene activation by TLE proteins involves functional interactions with the C terminus of AML at the nuclear matrix in situ. Our data are consistent with the concept that the C termini of AML proteins support activation or repression of cell-type specific genes depending on the regulatory organization of the target promoter and subnuclear localization.

scholarly journals Peptones Stimulate Intestinal Cholecystokinin Gene Transcription via Cyclic Adenosine Monophosphate Response Element-Binding Factors

Endocrinology ◽  
2001 ◽  
Vol 142 (2) ◽  
pp. 721-729 ◽  
Author(s):  
Christine Bernard ◽  
Anne Sutter ◽  
Charles Vinson ◽  
Christelle Ratineau ◽  
Jean-Alain Chayvialle ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Transcription ◽  
Molecular Mechanisms ◽  
Adenosine Monophosphate ◽  
Dominant Negative ◽  
Site Directed Mutagenesis ◽  
Intestinal Lumen ◽  
Response Element ◽  
The Core ◽  
Transcriptional Stimulation

Abstract Cholecystokinin (CCK) is a potent intestinal hormone that regulates several digestive functions. Despite the physiological importance of CCK, the cellular and molecular mechanisms that govern its synthesis and secretion are not completely identified. Peptones, which are fair counterparts of the protein fraction in the intestinal lumen, are good stimulants of CCK secretion. We have previously shown that peptones activate CCK gene transcription in STC-1 enteroendocrine cells. The DNA element(s) necessary to induce the transcriptional stimulation was preliminary, localized in the first 800 bp of the CCK gene promoter. In the present study, we identify a DNA element [peptone-response element (PepRE)] essential to confer peptone-responsiveness to the CCK promoter, and we characterize the transcription factors implicated. Localization of the PepRE between −93 and −70 bp of the promoter was established using serial 5′-3′deletions. Systematic site-directed mutagenesis demonstrated that the core PepRE sequence, spanning from nucleotide −72 to −83, overlapped with the putative AP-1/CRE site. Mutations in the core sequence dramatically decreased peptone-responsiveness of CCK promoter fragments. The PepRE functioned as a low-affinity CRE consensus site, binding only transcription factors of the CREB family. Overexpression, in STC-1 cells, of a dominant-negative protein (A-CREB), that prevented the binding of CREB factors to DNA, completely abolished the peptone-induced transcriptional stimulation. Peptone treatment did not modify the nature and the abundance of proteins bound to the PepRE but led to increased phosphorylation of the CREB factors. In conclusion, the present study first demonstrates that CCK gene expression is under the control of protein-derived nutrients in the STC-1 enteroendocrine cell line.

scholarly journals H2B Ubiquitin Protease Ubp8 and Sgf11 Constitute a Discrete Functional Module within the Saccharomyces cerevisiae SAGA Complex

2005 ◽  
Vol 25 (3) ◽  
pp. 1162-1172 ◽  
Author(s):  
Kristin Ingvarsdottir ◽  
Nevan J. Krogan ◽  
N. C. Tolga Emre ◽  
Anastasia Wyce ◽  
Natalie J. Thompson ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Regulation ◽  
Transcriptional Activation ◽  
Functional Module ◽  
Gene Activation ◽  
Tata Binding Protein ◽  
Binding Domain ◽  
Genetic Interactions ◽  
Saga Complex ◽  
Microarray Analyses

ABSTRACT The SAGA complex is a multisubunit protein complex involved in transcriptional regulation in Saccharomyces cerevisiae. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation (Gcn5) and histone deubiquitylation (Ubp8). We recently showed that H2B ubiquitylation and Ubp8-mediated deubiquitylation are both required for transcriptional activation. For this study, we investigated the interaction of Ubp8 with SAGA. Using mutagenesis, we identified a putative zinc (Zn) binding domain within Ubp8 as being critical for the association with SAGA. The Zn binding domain is required for H2B deubiquitylation and for growth on media requiring Ubp8's function in gene activation. Furthermore, we identified an 11-kDa subunit of SAGA, Sgf11, and showed that it is required for the Ubp8 association with SAGA and for H2B deubiquitylation. Different approaches indicated that the functions of Ubp8 and Sgf11 are related and separable from those of other components of SAGA. In particular, the profiles of Ubp8 and Sgf11 deletions were remarkably similar in microarray analyses and synthetic genetic interactions and were distinct from those of the Spt3 and Spt8 subunits of SAGA, which are involved in TBP regulation. These data indicate that Ubp8 and Sgf11 likely represent a new functional module within SAGA that is involved in gene regulation through H2B deubiquitylation.

scholarly journals Repression by the Arabidopsis TOPLESS corepressor requires association with the core Mediator complex

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alexander R Leydon ◽  
Wei Wang ◽  
Hardik P Gala ◽  
Sabrina Gilmour ◽  
Samuel Juarez-Solis ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Structure And Function ◽  
Mediator Complex ◽  
Environmental Cues ◽  
Auxin Response ◽  
The Core ◽  
N Terminus ◽  
And Function ◽  
The Relationship ◽  
Repression Domain

The plant corepressor TOPLESS (TPL) is recruited to a large number of loci that are selectively induced in response to developmental or environmental cues, yet the mechanisms by which it inhibits expression in the absence of these stimuli is poorly understood. Previously, we had used the N-terminus of Arabidopsis thaliana TPL to enable repression of a synthetic auxin response circuit in Saccharomyces cerevisiae (yeast). Here, we leveraged the yeast system to interrogate the relationship between TPL structure and function, specifically scanning for repression domains. We identified a potent repression domain in Helix 8 located within the CRA domain, which directly interacted with the Mediator middle module subunits Med21 and Med10. Interactions between TPL and Mediator were required to fully repress transcription in both yeast and plants. In contrast, we found that multimer formation, a conserved feature of many corepressors, had minimal influence on the repression strength of TPL.

scholarly journals Modeling Cooperative Gene Regulation Using Fast Orthogonal Search

2008 ◽  
Vol 2 (1) ◽  
pp. 80-89 ◽  
Author(s):  
Ian Minz ◽  
Michael J. Korenberg
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Gene Regulation ◽  
Transcription Factor ◽  
Gene Transcription ◽  
Binding Motifs ◽  
Final Model ◽  
Orthogonal Search ◽  
Fast Orthogonal Search

Gene regulation is a complex and relatively poorly understood process. While a number of methods have suggested means by which gene transcription is activated, there are factors at work that no model has been able to fully explain. In eukaryotes, gene regulation is quite complex, so models have primarily focused on a relatively simple species, Saccharomyces cerevisiae. Because of the inherent complexity in higher species, and even in yeast, a method of identifying transcription factor (TF) binding motifs must be efficient and thorough in its analysis. Here we propose a method using the very efficient Fast Orthogonal Search (FOS) algorithm in order to uncover motifs as well as cooperatively binding groups of motifs that can explain variations in gene expression. The algorithm is very fast, exploring a motif list and constructing a final model within seconds or a few minutes, produces model terms that are consistent with known motifs while also revealing new motifs and interactions, and causes impressive reduction in variance with relatively few model terms over the cell cycle.

scholarly journals The MSN1 and NHP6A Genes Suppress SWI6 Defects in Saccharomyces cerevisiae

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 45-55
Author(s):  
Julia Sidorova ◽  
Linda Breeden
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Gene Transcription ◽  
Chromatin Structure ◽  
Transcriptional Activator ◽  
Temperature Sensitive ◽  
Gene Products ◽  
Protein Association

Abstract Ankyrin (ANK) repeats were first found in the Swi6 transcription factor of Saccharomyces cerevisiae and since then were identified in many proteins of eukaryotes and prokaryotes. These repeats are thought to serve as protein association domains. In Swi6, ANK repeats affect DNA binding of both the Swi4/Swi6 and Mbp1/Swi6 complexes. We have previously described generation of random mutations within the ANK repeats of Swi6 that render the protein temperature sensitive in its ability to activate HO transcription. Two of these SWI6 mutants were used in a screen for high copy suppressors of this phenotype. We found that MSN1, which encodes a transcriptional activator, and NHP6A, which encodes an HMG-like protein, are able to suppress defective Swi6 function. Both of these gene products are involved in HO transcription, and Nhp6A may also be involved in CLN1 transcription. Moreover, because overexpression of NHP6A can suppress caffeine sensitivity of one of the SWI6 ANK mutants, swi6-405, other SWI6-dependent genes may also be affected by Nhp6A. We hypothesize that Nhp6A and Msn1 modulate Swi6-dependent gene transcription indirectly, through effects on chromatin structure or other transcription factors, because we have not been able to demonstrate that either Msn1 or Nhp6A interact with the Swi4/Swi6 complex.

GENE ACTIVATION IN MAMMARY CELLS

1972 ◽  
Vol 71 (2_Suppla) ◽  
pp. S346-S368 ◽  
Author(s):  
Roger W. Turkington ◽  
Nobuyuki Kadohama
Keyword(s):  
Cell Differentiation ◽  
Gene Transcription ◽  
Hormonal Regulation ◽  
Gene Activation ◽  
Milk Proteins ◽  
Mouse Mammary Gland ◽  
Nuclear Proteins ◽  
Mammary Cells ◽  
Alveolar Cells ◽  
Mammary Cell

ABSTRACT Hormonal activation of gene transcription has been studied in a model system, the mouse mammary gland in organ culture. Transcriptive activity is stimulated in mammary stem cells by insulin, and in mammary alveolar cells by prolactin and insulin. Studies on the template requirement for expression of the genes for milk proteins demonstrate that DNA methylation has an obligatory dependence upon DNA synthesis, but is otherwise independent from hormonal regulation of mammary cell differentiation. Incorporation of 5-bromo-2′deoxyuridine into DNA selectively inhibits expression of the genes for specific milk proteins. Undifferentiated mammary cells activate the synthesis of specific acidic nuclear proteins when stimulated by insulin. Several of these induced acidic nuclear proteins are undetectable in unstimulated undifferentiated cells, but appear to be characteristic components of the nuclei of differentiated cells. These results indicate that mammary cell differentiation is associated with a change in acidic nuclear proteins, and they provide evidence to support the concept that acidic nuclear proteins may be involved in the regulation of gene transcription and of mammary cell differentiation.

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