Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

ABSTRACT: Activation: A pooled screen for protein fragments that induce transcriptional activation of a reporter GFP gene. A pooled pull-down experiment for protein fragments, expressed with mRNA display, that bind Mediator Med15 or TFIID subcomplex. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): synthetic construct Saccharomyces cerevisiae

PROVIDER: GSE173156 | GEO | 2021/04/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Pulldown)

Project description:A pooled pull-down experiment for protein fragments, expressed with mRNA display, that bind Med15 or TFIID subcomplex

2021-04-26 | GSE173152 | GEO

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Activation)

Project description:A pooled screen for protein fragments that induce transcriptional activation of a reporter GFP gene.

2021-04-26 | GSE173149 | GEO

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator.

Project description:Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity ('fuzzy' binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.

| S-EPMC8137143 | biostudies-literature

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

Project description:Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

| PRJNA723885 | ENA

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Activation)

Project description:Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Activation)

| PRJNA723892 | ENA

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Pulldown)

Project description:Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Pulldown)

| PRJNA723893 | ENA

A Med15 - Hrp1 complex associates with fission yeast Mediator

Project description:The multiprotein Mediator complex is an important regulator of RNA polymerase II-dependent genes in eukaryotic cell. In contrast to the situation in many other eukaryotes, the conserved Med15 protein is not a stable component of Mediator isolated from fission yeast. We now demonstrate that Med15 exists in a protein complex together with Hrp1, an ATP-dependent chromatin remodeling protein. The Med15/Hrp1 subcomplex is not a component of the core Mediator complex, but can interact with the repressive L-Mediator conformation. Deletion of MED15 and HRP1 cause similar effects on global steady-state levels of mRNA, but only MED15 is required for galactose-dependent activation of the inv1 gene. Hrp1 has been found in complex with other proteins and genome-wide analysis demonstrates that Med15 only associates with a distinct subset of Hrp1-bound gene promoters. Global analysis reveals that Hrp1-binding normally is associated with increased histone H3 density, but at promoters also bound by Med15, histone H3 density is instead increased. Our findings reveal that Med15 functions as a separate entity in fission yeast and indicate that the function and organization of the Mediator complex may differ significantly between eukaryotes. Keywords: ChIP-chip

2010-09-21 | GSE10079 | GEO

Combinational reasoning of quantitative fuzzy topological relations for simple fuzzy regions.

Project description:In recent years, formalization and reasoning of topological relations have become a hot topic as a means to generate knowledge about the relations between spatial objects at the conceptual and geometrical levels. These mechanisms have been widely used in spatial data query, spatial data mining, evaluation of equivalence and similarity in a spatial scene, as well as for consistency assessment of the topological relations of multi-resolution spatial databases. The concept of computational fuzzy topological space is applied to simple fuzzy regions to efficiently and more accurately solve fuzzy topological relations. Thus, extending the existing research and improving upon the previous work, this paper presents a new method to describe fuzzy topological relations between simple spatial regions in Geographic Information Sciences (GIS) and Artificial Intelligence (AI). Firstly, we propose a new definition for simple fuzzy line segments and simple fuzzy regions based on the computational fuzzy topology. And then, based on the new definitions, we also propose a new combinational reasoning method to compute the topological relations between simple fuzzy regions, moreover, this study has discovered that there are (1) 23 different topological relations between a simple crisp region and a simple fuzzy region; (2) 152 different topological relations between two simple fuzzy regions. In the end, we have discussed some examples to demonstrate the validity of the new method, through comparisons with existing fuzzy models, we showed that the proposed method can compute more than the existing models, as it is more expressive than the existing fuzzy models.

| S-EPMC4361350 | biostudies-literature

The polymorphic PolyQ tail protein of the Mediator Complex, Med15, regulates variable response to stress

Project description:The Mediator is composed of multiple of proteins in the head, body, tail and CDK subunits conserved from yeast to humans. However, not all the components are required for transcription. Components of the tail subunit are not essential but to varying degrees are required for changes in transcription to stress. While some stresses are familiar such as heat, desiccation, and starvation, others are exotic yet elicit a physical stress response. MCHM is a hydrotrope that induces growth arrest in yeast. By exploiting genetic variation, specifically in Med15, between yeast strains, we found that Med15 with the polyQ expansion conferred MCHM sensitivity. This sensitivity was not from a loss of function as the reciprocal hemizygous hybrids were all sensitive, suggesting that there is an incompatibility between Mediator complexes from genetic divergent yeast strains. Transcriptomics from yeast expressing the incompatible Med15 changed expression in diverse pathways. Expansion of polyQ tracts in Med15 resulted in multiple isoforms which were mostly from likely post-translational modifications. Stability of Med15 was dependent on Ydj1, a chaperone and the incompatible Med15 allele was expressed at lower levels and less stable than the compatible Med15 allele. Med15 is tethered to the rest of the Mediator complex via Med2 and 3. Deletion of either Med2 or Med3 changes the Med15 isoform patterns in the in a similar manner whereas deletion of Med5, a distal component of the tail did not change the pattern. The med2 and 3 mutants are similarly sensitive to MCHM while med5 mutants are not. Differences between the Med15 alleles extend to responses to different stresses. Whereas the incompatible allele of Med15 improved growth to chemicals that produce free radicals, and the compatible allele of Med15 improved growth to reducing agents, caffeine, and hydroxyurea. This may reflect the positive and negative role that Med15 has in transcription.

2020-04-06 | GSE129898 | GEO

Simple decision rules underlie collaborative hunting in yellow saddle goatfish.

Project description:Collaborative hunting, the coordination of animal behaviour in space and time to capture prey, is reported in several vertebrate species. However, previous studies are observational, hampering our ability to identify individual decision rules that result in collaboration. We experimentally investigated collaborative hunting in yellow saddle goatfish (Parupeneus cyclostomus) by exposing pairs to a mock prey that fled to an artificial shelter with multiple entrances. The first fish to initiate the chase (the 'initiator') was always closest to the prey and pursued it directly in its path. Conversely, the behaviour of the second goatfish (the 'follower') depended on its spatial position relative to the initiator. When the follower was less than one body length behind the initiator, it also accelerated directly towards the prey in over 95% of cases. However, if the two goatfish were separated by a distance of one body length or more, the follower chose a less direct route to reach the prey in 87% of cases. In this scenario, the follower often reached the prey's more distant refuge first, which might increase its hunting success or block the prey's escape path under natural conditions. Our findings suggest that coordinated hunting behaviour can result from simple, self-serving decisions.

| S-EPMC5805943 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data