Eukaryotic transcription: The core of eukaryotic gene activation

AbstractA key functional event in eukaryotic gene activation is the formation of dynamic protein-protein interaction networks between transcriptional activators and transcriptional coactivators. Seemingly incongruent with the tight regulation of transcription, many biochemical and biophysical studies suggest that activators use nonspecific hydrophobic and/or electrostatic interactions to bind to coactivators, with few if any specific contacts. Here a mechanistic dissection of a set of representative dynamic activator•coactivator complexes, comprised of the ETV/PEA3 family of activators and the coactivator Med25, reveals a different molecular recognition model. The data demonstrate that small sequence variations within an activator family significantly redistribute the conformational ensemble of the complex while not affecting overall affinity, and distal residues within the activator—not often considered as contributing to binding—play a key role in mediating conformational redistribution. The ETV/PEA3•Med25 ensembles are directed by specific contacts between the disordered activator and the Med25 interface, which is facilitated by structural shifts of the coactivator binding surface. Taken together, these data highlight the critical role coactivator plasticity plays in recognition of disordered activators, and indicates that molecular recognition models of disordered proteins must consider the ability of the binding partners to mediate specificity.

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

Genetics ◽

10.1534/genetics.120.303254 ◽

2020 ◽

Vol 215 (2) ◽

pp. 407-420 ◽

Cited By ~ 1

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.

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Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

Science ◽

10.1126/science.1172926 ◽

2009 ◽

Vol 325 (5940) ◽

pp. 626-628 ◽

Cited By ~ 243

Author(s):

Courtney Hodges ◽

Lacramioara Bintu ◽

Lucyna Lubkowska ◽

Mikhail Kashlev ◽

Carlos Bustamante

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Optical Tweezers ◽

Direct Evidence ◽

Eukaryotic Transcription ◽

Pol Ii ◽

The Core ◽

Nucleosomal Dna ◽

Dna Loop ◽

Core Histones

RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes during transcription elongation. We have developed an optical tweezers assay to follow individual Pol II complexes as they transcribe nucleosomal DNA. Our results indicate that the nucleosome behaves as a fluctuating barrier that locally increases pause density, slows pause recovery, and reduces the apparent pause-free velocity of Pol II. The polymerase, rather than actively separating DNA from histones, functions instead as a ratchet that rectifies nucleosomal fluctuations. We also obtained direct evidence that transcription through a nucleosome involves transfer of the core histones behind the transcribing polymerase via a transient DNA loop. The interplay between polymerase dynamics and nucleosome fluctuations provides a physical basis for the regulation of eukaryotic transcription.

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Enhanced regulation of prokaryotic gene expression by a eukaryotic transcriptional activator

Nature Communications ◽

10.1038/s41467-021-24434-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

I. Cody MacDonald ◽

Travis R. Seamons ◽

Jonathan C. Emmons ◽

Shwan B. Javdan ◽

Tara L. Deans

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcriptional Activation ◽

Dynamic Range ◽

Current Trend ◽

Medical Science ◽

Genetic Circuits ◽

Eukaryotic Transcription ◽

Complex Functions ◽

Eukaryotic Gene

AbstractExpanding the genetic toolbox for prokaryotic synthetic biology is a promising strategy for enhancing the dynamic range of gene expression and enabling new engineered applications for research and biomedicine. Here, we reverse the current trend of moving genetic parts from prokaryotes to eukaryotes and demonstrate that the activating eukaryotic transcription factor QF and its corresponding DNA-binding sequence can be moved to E. coli to introduce transcriptional activation, in addition to tight off states. We further demonstrate that the QF transcription factor can be used in genetic devices that respond to low input levels with robust and sustained output signals. Collectively, we show that eukaryotic gene regulator elements are functional in prokaryotes and establish a versatile and broadly applicable approach for constructing genetic circuits with complex functions. These genetic tools hold the potential to improve biotechnology applications for medical science and research.

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The MAGOH paralogs - MAGOH, MAGOHB and their multiple isoforms

10.1101/2021.05.07.443087 ◽

2021 ◽

Author(s):

Ayushi Rehman ◽

Pratap Chandra ◽

Kusum Kumari Singh

Keyword(s):

Amino Acid ◽

Splice Variants ◽

Protein Isoforms ◽

Amino Acid Residues ◽

Central Processing ◽

The Core ◽

Eukaryotic Gene ◽

Paralog Pair ◽

Processing Event ◽

Exon Junctions

A central processing event in eukaryotic gene expression is splicing. Concurrent with splicing, the core-EJC proteins, eIF4A3 and RBM8A-MAGOH heterodimer are deposited 24 bases upstream of newly formed exon-exon junctions. One of the core-EJC proteins, MAGOH contains a paralog MAGOHB, and this paralog pair is conserved across vertebrates. Upon analysis of the splice variants of MAGOH-paralogs, we have found the presence of alternate protein isoforms which are also evolutionarily conserved. Further, comparison of the amino acid sequence of the principal and alternate protein isoforms has revealed absence of key amino acid residues in the alternate isoforms. The conservation of principal and alternate isoforms correlates to the importance of MAGOH and MAGOHB across vertebrates.

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Ccr4–Not is at the core of the eukaryotic gene expression circuitry

Biochemical Society Transactions ◽

10.1042/bst20150167 ◽

2015 ◽

Vol 43 (6) ◽

pp. 1253-1258 ◽

Cited By ~ 14

Author(s):

Zoltan Villanyi ◽

Martine A. Collart

Keyword(s):

Gene Expression ◽

Protein Structure ◽

Current Knowledge ◽

The Core ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene ◽

Transcription Regulators ◽

Selection For ◽

Different Levels ◽

Protein Complex Assembly

In this mini-review, we summarize our current knowledge about the cross-talk between the different levels of gene expression. We introduce the Ccr4 (carbon catabolite repressed 4)–Not (negative on TATA-less) complex as a candidate to be a master regulator that orchestrates between the different levels of gene expression. An integrated view of the findings about the Ccr4–Not complex suggests that it is involved in gene expression co-ordination. Since the discovery of the Not proteins in a selection for transcription regulators in yeast [Collart and Struhl (1994) Genes Dev. 8, 525–537], the Ccr4–Not complex has been connected to every step of the mRNA lifecycle. Moreover, it has been found to be relevant for appropriate protein folding and quaternary protein structure by being involved in co-translational protein complex assembly.

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

10.1101/766006 ◽

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.

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Identifying a TFIID interactome via integrated biochemical and high-throughput proteomic studies

10.1101/111682 ◽

2017 ◽

Author(s):

Wei-Li Liu ◽

Lihua Song ◽

Gina Dailey ◽

Anna Piasecka ◽

Robert A. Coleman

Keyword(s):

Transcription Factors ◽

Rna Polymerase Ii ◽

High Throughput ◽

Transcription Initiation ◽

Core Promoter ◽

Regulatory Pathways ◽

The Core ◽

Promoter Recognition ◽

Eukaryotic Gene ◽

Promoter Dna

AbstractThe core promoter recognition TFIID complex acts as a central regulator for eukaryotic gene expression. To direct transcription initiation, TFIID binds the core promoter DNA and aids recruitment of the transcription machinery (e.g., RNA polymerase II) to the transcription start site. Many transcription factors target TFIID to control vital cellular processes. Current studies on finding TFIID interactors have predominantly focused on transcription factors. Yet, a comprehensive interactome of mammalian TFIID has not been established. Therefore, this study sought to reveal potential TFIID-nucleated networks by identifying likely co-regulatory factors that bind TFIID. By using intact native human TFIID complexes, we have exploited three independent approaches including a high-throughput Next Generation DNA sequencing coupled with proteomic analysis. Among these methods, we found some overlapping and new candidates in which we further assessed three putative interactors (i.e., Sox2, H2A and EMSY) by co-immunoprecipitation assays. Notably, in addition to known TFIID interactors, we identified a number of novel factors that participate either in co-regulatory pathways or non-transcription related functions of TFIID. Overal, these results indicate that, in addition to transcription initiation, mammalian TFIID may be involved in broader regulatory pathways than previous studies suggested.

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A mathematical model for synergistic eukaryotic gene activation 1 1Edited by F. E. Cohen

Journal of Molecular Biology ◽

10.1006/jmbi.1998.2489 ◽

1999 ◽

Vol 286 (2) ◽

pp. 315-325 ◽

Cited By ~ 23

Author(s):

Jin Wang ◽

Katharine Ellwood ◽

Alison Lehman ◽

Michael F Carey ◽

Zhen-Su She

Keyword(s):

Mathematical Model ◽

Gene Activation ◽

Eukaryotic Gene

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A Novel Encoded Particle Technology that Enables Simultaneous Interrogation of Multiple Cell Types

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057103260088 ◽

2004 ◽

Vol 9 (3) ◽

pp. 173-185 ◽

Cited By ~ 25

Author(s):

Oren Beske ◽

Jinjiao Guo ◽

Jianren Li ◽

Daniel Bassoni ◽

Kimberly Bland ◽

...

Keyword(s):

Gene Activation ◽

Cell Types ◽

Calcium Flux ◽

Diverse Range ◽

Particle Technology ◽

The Core ◽

Cellular Assays ◽

Cellular Analysis ◽

Multiple Cell ◽

Analysis Platform

The authors have developed a cellular analysis platform, based on encoded microcarriers, that enables the multiplexed analysis of a diverse range of cellular assays. At the core of this technology are classes of microcarriers that have unique, identifiable codes that are deciphered using CCD-based imaging and subsequent image analysis. The platform is compatible with a wide variety of cellular imaging-based assays, including calcium flux, reporter gene activation, cytotoxicity, and proliferation. In addition, the platform is compatible with both colorimetric and fluorescent readouts. Notably, this technology has the unique ability to multiplex different cell lines in a single microplate well, enabling scientists to perform assays and data analysis in novel ways.

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