Genome-Wide Analysis Reveals the Role of Mediator Complex in the Soybean—Phytophthora sojae Interaction

The mediator complex is an essential link between transcription factors and RNA polymerase II, and mainly functions in the transduction of diverse signals to genes involved in different pathways. Limited information is available on the role of soybean mediator subunits in growth and development, and their participation in defense response regulation. Here, we performed genome-wide identification of the 95 soybean mediator subunits, which were unevenly localized on the 20 chromosomes and only segmental duplication events were detected. We focused on GmMED16-1, which is highly expressed in the roots, for further functional analysis. Transcription of GmMED16-1 was induced in response to Phytophthora sojae infection. Agrobacterium rhizogenes mediated soybean hairy root transformation was performed for the silencing of the GmMED16-1 gene. Silencing of GmMED16-1 led to an enhanced susceptibility phenotype and increased accumulation of P. sojae biomass in hairy roots of transformants. The transcript levels of NPR1, PR1a, and PR5 in the salicylic acid defense pathway in roots of GmMED16-1-silenced transformants were lower than those of empty-vector transformants. The results provide evidence that GmMED16-1 may participate in the soybean–P. sojae interaction via a salicylic acid-dependent process.

Download Full-text

Role of the pre-initiation complex in Mediator recruitment and dynamics

eLife ◽

10.7554/elife.39633 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 10

Author(s):

Elisabeth R Knoll ◽

Z Iris Zhu ◽

Debasish Sarkar ◽

David Landsman ◽

Randall H Morse

Keyword(s):

Rna Polymerase Ii ◽

Gene Activation ◽

Mediator Complex ◽

Gene Promoters ◽

Initiation Complex ◽

Yeast Saccharomyces Cerevisiae ◽

Pol Ii ◽

Genome Wide ◽

Cooperative Assembly

The Mediator complex stimulates the cooperative assembly of a pre-initiation complex (PIC) and recruitment of RNA Polymerase II (Pol II) for gene activation. The core Mediator complex is organized into head, middle, and tail modules, and in budding yeast (Saccharomyces cerevisiae), Mediator recruitment has generally been ascribed to sequence-specific activators engaging the tail module triad of Med2-Med3-Med15 at upstream activating sequences (UASs). We show that yeast lacking Med2-Med3-Med15 are viable and that Mediator and PolII are recruited to promoters genome-wide in these cells, albeit at reduced levels. To test whether Mediator might alternatively be recruited via interactions with the PIC, we examined Mediator association genome-wide after depleting PIC components. We found that depletion of Taf1, Rpb3, and TBP profoundly affected Mediator association at active gene promoters, with TBP being critical for transit of Mediator from UAS to promoter, while Pol II and Taf1 stabilize Mediator association at proximal promoters.

Download Full-text

Role of the pre-initiation complex in Mediator recruitment and dynamics

10.1101/207282 ◽

2017 ◽

Cited By ~ 1

Author(s):

Elisabeth R. Knoll ◽

Z. Iris Zhu ◽

David Landsman ◽

Randall H. Morse

Keyword(s):

Rna Polymerase Ii ◽

Gene Activation ◽

Mediator Complex ◽

Gene Promoters ◽

Initiation Complex ◽

Eukaryotic Transcription ◽

Pol Ii ◽

Genome Wide ◽

Complex Functions

AbstractThe Mediator complex functions in eukaryotic transcription by stimulating the cooperative assembly of a pre-initiation complex (PIC) and recruitment of RNA Polymerase II (Pol II) for gene activation. The core Mediator complex is organized into head, middle, and tail modules, and in budding yeast (Saccharomyces cerevisiae), Mediator recruitment has generally been ascribed to sequence-specific activators engaging the tail module triad of Med2-Med3-Med15 at upstream activating sequences (UASs). We show that med2Δ med3Δ med15Δ yeast are viable and that Mediator lacking Med2-Med3-Med15 is associated with active promoters genome-wide. To test whether Mediator might alternatively be recruited via interactions with the PIC, we examined Mediator association genome-wide after depleting PIC components. We found that depletion of Taf1, Rpb3, and TBP profoundly affected Mediator association at active gene promoters, with TBP being critical for transit of Mediator from UAS to promoter, while Pol II and Taf1 stabilize Mediator association at proximal promoters.

Download Full-text

The plant Mediator complex and its role in jasmonate signaling

Journal of Experimental Botany ◽

10.1093/jxb/erz233 ◽

2019 ◽

Vol 70 (13) ◽

pp. 3415-3424 ◽

Cited By ~ 12

Author(s):

Qingzhe Zhai ◽

Chuanyou Li

Keyword(s):

Rna Polymerase Ii ◽

Plant Hormone ◽

Plant Immunity ◽

Mediator Complex ◽

Transcriptional Coactivator ◽

Jasmonate Signaling ◽

Helix Loop Helix ◽

Transcriptional Reprogramming ◽

Genome Wide ◽

Ja Signaling

Abstract The Mediator complex is an essential, multisubunit transcriptional coactivator that is highly conserved in eukaryotes. Mediator interacts with gene-specific transcription factors, the RNA polymerase II transcriptional machinery, as well as several other factors involved in transcription, and acts as an integral hub to regulate various aspects of transcription. Recent studies of the plant Mediator complex have established that it functions in diverse aspects of plant development and fitness. Jasmonate (JA) is an oxylipin-derived plant hormone that regulates plant immunity and development. The basic helix–loop–helix transcription factor MYC2, which is a master regulator of JA signaling, orchestrates genome-wide transcriptional reprogramming of plant cells to coordinate defense- and growth-related processes. Here, we review the function of the plant Mediator complex in regulating JA signaling. We focus on the multifunctional Mediator subunit MED25, which emerges as an integrative hub for the transcriptional regulation of jasmonate signaling.

Download Full-text

Novel critical role of a human Mediator complex for basal RNA polymerase II transcription

EMBO Reports ◽

10.1093/embo-reports/kve186 ◽

2001 ◽

Vol 2 (9) ◽

pp. 808-813 ◽

Cited By ~ 93

Author(s):

Gerhard Mittler ◽

Elisabeth Kremmer ◽

H Th. Marc Timmers ◽

Michael Meisterernst

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Critical Role ◽

Mediator Complex ◽

Rna Polymerase Ii Transcription

Download Full-text

Cyclin C influences the timing of mitosis in fission yeast

Molecular Biology of the Cell ◽

10.1091/mbc.e16-11-0787 ◽

2017 ◽

Vol 28 (13) ◽

pp. 1738-1744 ◽

Cited By ~ 2

Author(s):

Gabor Banyai ◽

Zsolt Szilagyi ◽

Vera Baraznenok ◽

Olga Khorosjutina ◽

Claes M. Gustafsson

Keyword(s):

Cell Cycle ◽

Fission Yeast ◽

Rna Polymerase Ii ◽

Cell Cycle Progression ◽

Cell Cycle Control ◽

Mediator Complex ◽

Cycle Progression ◽

Cyclin C ◽

M Phase

The multiprotein Mediator complex is required for the regulated transcription of nearly all RNA polymerase II–dependent genes. Mediator contains the Cdk8 regulatory subcomplex, which directs periodic transcription and influences cell cycle progression in fission yeast. Here we investigate the role of CycC, the cognate cyclin partner of Cdk8, in cell cycle control. Previous reports suggested that CycC interacts with other cellular Cdks, but a fusion of CycC to Cdk8 reported here did not cause any obvious cell cycle phenotypes. We find that Cdk8 and CycC interactions are stabilized within the Mediator complex and the activity of Cdk8-CycC is regulated by other Mediator components. Analysis of a mutant yeast strain reveals that CycC, together with Cdk8, primarily affects M-phase progression but mutations that release Cdk8 from CycC control also affect timing of entry into S phase.

Download Full-text

Elongin A regulates transcription in vivo through enhanced RNA polymerase processivity

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.015876 ◽

2020 ◽

pp. jbc.RA120.015876

Author(s):

Yating Wang ◽

Liming Hou ◽

M. Behfar Ardehali ◽

Robert E. Kingston ◽

Brian D Dynlacht

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcriptional Elongation ◽

Rna Seq ◽

Transcription Profiles ◽

Genome Wide ◽

The Impact

Elongin is an RNA polymerase II (RNAPII)-associated factor that has been shown to stimulate transcriptional elongation in vitro. The Elongin complex is thought to be required for transcriptional induction in response to cellular stimuli and to ubiquitinate RNAPII in response to DNA damage. Yet the impact of the Elongin complex on transcription in vivo has not been well studied. Here, we performed comprehensive studies of the role of Elongin A, the largest subunit of the Elongin complex, on RNAPII transcription genome-wide. Our results suggest that Elongin A localizes to actively transcribed regions and potential enhancers, and the level of recruitment correlated with transcription levels. We also identified a large group of factors involved in transcription as Elongin A-associated factors. In addition, we found that loss of Elongin A leads to dramatically reduced levels of Ser2-phosphorylated, but not total, RNAPII, and cells depleted of Elongin A show stronger promoter RNAPII pausing, suggesting that Elongin A may be involved in the release of paused RNAPII. Our RNA-seq studies suggest that loss of Elongin A did not alter global transcription, and unlike prior in vitro studies, we did not observe a dramatic impact on RNAPII elongation rates in our cell-based nascent RNA-seq experiments upon Elongin A depletion. Taken together, our studies provide the first comprehensive analysis of the role of Elongin A in regulating transcription in vivo. Our studies also revealed that unlike prior in vitro findings, depletion of Elongin A has little impact on global transcription profiles and transcription elongation in vivo.

Download Full-text

ASXL1 Directs Neutrophilic Differentiation via Modulation of MYC and RNA Polymerase II.

10.1101/2020.09.14.295295 ◽

2020 ◽

Author(s):

Theodore P Braun ◽

Joseph Estabrook ◽

Daniel J Coleman ◽

Zachary Schonrock ◽

Brittany M Smith ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Myeloid Malignancies ◽

Polycomb Repressive Complex 2 ◽

Genome Wide ◽

Sex Combs ◽

Epigenetic Regulator ◽

Additional Sex Combs ◽

Global Increase

Mutations in the gene Additional Sex-Combs Like 1 (ASXL1) are recurrent in myeloid malignancies as well as the pre-malignant condition clonal hematopoiesis, where they are universally associated with poor prognosis. An epigenetic regulator, ASXL1 ca-nonically directs the deposition of H3K27me3 via the polycomb repressive complex 2. However, its precise role in myeloid lineage maturation is incompletely described. We utilized single cell RNA sequencing (scRNA-seq) on a murine model of hematopoietic-specific ASXL1 deletion and identified a specific role for ASXL1 in terminal granulo-cyte maturation. Terminal maturation is accompanied by down regulation of Myc ex-pression and cell cycle exit. ASXL1 deletion leads to hyperactivation of Myc in granu-locyte precursors and a quantitative decrease in neutrophil production. This failure of normal developmentally-associated Myc suppression is not accompanied by signifi-cant changes in the landscape of covalent histone modifications including H3K27me3. Examining the genome-wide localization of ASXL1 in myeloid progenitors revealed strong co-localization with RNA Polymerase II (RNAPII) at the promoters and spread across the gene bodies of transcriptionally active genes. ASXL1 deletion results in a decrease in RNAPII promoter-proximal pausing in granulocyte progenitors, indicative of a global increase in productive transcription, consistent with the known role of ASXL1 as a mediator of RNAPII pause release. These results suggest that ASXL1 in-hibits productive transcription in granulocyte progenitors, identifying a new role for this epigenetic regulator and highlighting a novel potential oncogenic mechanism for ASXL1 mutations in myeloid malignancies.

Download Full-text

RNA Polymerase II Independent Recruitment of SPT6 at Transcription Start Sites in Arabidopsis

10.1101/506063 ◽

2018 ◽

Author(s):

Chen Chen ◽

Jie Shu ◽

Chenlong Li ◽

Raj K. Thapa ◽

Vi Nguyen ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcription Initiation ◽

Potential Role ◽

Elongation Factor ◽

Gene Body ◽

Transcription Start Sites ◽

Genome Wide ◽

Shed Light

SummarySPT6 is a conserved transcription regulator that is generally viewed as an elongation factor. However, emerging evidence show its potential role in the control of transcription initiation at genic and intragenic promoters. Here we first present the genome-wide occupancy of Arabidopsis SPT6-like (SPT6L) and demonstrate its conserved role in facilitating RNA Polymerase II (RNAPII) occupancy across transcribed genes. Further, we show that SPT6L enrichment is shifted, unexpectedly, from gene body to the transcription starting site (TSS) when its association with RNAPII is disrupted. Finally, we demonstrate that recruitment of SPT6L starts at TSS, and then spreads to the gene body during transcription. These findings refine the mechanisms underlying SPT6L recruitment in transcription and shed light on the role of SPT6L in transcription initiation.

Download Full-text

Activator-Specific Requirement of Yeast Mediator Proteins for RNA Polymerase II Transcriptional Activation

Molecular and Cellular Biology ◽

10.1128/mcb.19.2.979 ◽

1999 ◽

Vol 19 (2) ◽

pp. 979-988 ◽

Cited By ~ 58

Author(s):

Sang Jun Han ◽

Young Chul Lee ◽

Byung Soo Gim ◽

Gi-Hyuck Ryu ◽

Soon Jung Park ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcriptional Activation ◽

Mediator Complex ◽

Specific Requirement ◽

Pol Ii ◽

Mediator Protein ◽

Mutant Forms ◽

Mutant Cells

ABSTRACT The multisubunit Mediator complex of Saccharomyces cerevisiae is required for most RNA polymerase II (Pol II) transcription. The Mediator complex is composed of two subcomplexes, the Rgr1 and Srb4 subcomplexes, which appear to function in the reception of activator signals and the subsequent modulation of Pol II activity, respectively. In order to determine the precise composition of the Mediator complex and to explore the specific role of each Mediator protein, our goal was to identify all of the Mediator components. To this end, we cloned three previously unidentified Mediator subunits, Med9/Cse2, Med10/Nut2, and Med11, and isolated mutant forms of each of them to analyze their transcriptional defects. Differential display and Northern analyses of mRNAs from wild-type and Mediator mutant cells demonstrated an activator-specific requirement for each Mediator subunit. Med9/Cse2 and Med10/Nut2 were required, respectively, for Bas1/Bas2- and Gcn4-mediated transcription of amino acid biosynthetic genes. Gal11 was required for Gal4- and Rap1-mediated transcriptional activation. Med11 was also required specifically for MFα1 transcription. On the other hand, Med6 was required for all of these transcriptional activation processes. These results suggest that distinct Mediator proteins in the Rgr1 subcomplex are required for activator-specific transcriptional activation and that the activation signals mediated by these Mediator proteins converge on Med6 (or the Srb4 subcomplex) to modulate Pol II activity.

Download Full-text

Metabolic stress regulates genome-wide transcription in a PTEN-dependent manner

Human Molecular Genetics ◽

10.1093/hmg/ddaa168 ◽

2020 ◽

Vol 29 (16) ◽

pp. 2736-2745

Author(s):

Ata Abbas ◽

Roshan Padmanabhan ◽

Charis Eng

Keyword(s):

Transcriptional Regulation ◽

Rna Polymerase Ii ◽

Cancer Progression ◽

Metabolic Stress ◽

Glucose Deprivation ◽

Regulation Of Transcription ◽

Dependent Manner ◽

Loss Of Function ◽

Genome Wide

Abstract PTEN is implicated in a wide variety of pathophysiological conditions and traditionally studied in the context of the PIK3–AKT–mTOR axis. Recent studies from our group and others have reported a novel role of PTEN in the regulation of transcription at the genome-wide scale. This emerging role of PTEN on global transcriptional regulation is providing a better understanding of various diseases, including cancer. Because cancer progression is an energy-demanding process and PTEN is known to regulate metabolic processes, we sought to understand the role of PTEN in transcriptional regulation under metabolic stress, a condition often developing in the tumor microenvironment. In the present study, we demonstrate that PTEN modulates genome-wide RNA Polymerase II occupancy in cells undergoing glucose deprivation. The glucose-deprived PTEN null cells were found to continue global gene transcription, which may activate a survival mode. However, cells with constitutive PTEN expression slow transcription, an evolutionary mechanism that may save cellular energy and activate programmed cell death pathways, in the absence of glucose. Interestingly, alternative exon usage by PTEN null cells is increased under metabolic stress in contrast to PTEN-expressing cells. Overall, our study demonstrates distinct mechanisms involved in PTEN-dependent genome-wide transcriptional control under metabolic stress. Our findings provide a new insight in understanding tumor pathology and how PTEN loss of function, whether by genetic or non-genetic mechanisms, can contribute to a favorable transcriptional program employed by tumor cells to escape apoptosis, hence developing more aggressive and metastatic phenotypes.

Download Full-text