Selective role of Mediator tail module in the transcription of highly regulated genes in yeast

Article (PDF Available)inTranscription 3(3):110-4 · May 2012with34 Reads
DOI: 10.4161/trns.19840 · Source: PubMed
Abstract
The tail module subunits of Mediator complex are targets of activators both in yeast and metazoans. Here we discuss recent evidence from studies in yeast for tail module specificity for SAGA-dependent, TATA-containing genes including highly regulated stress response genes, and for independent recruitment and function of the tail module.
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Transcription 3:3, 110-114;May/June 2012; © 2012 Landes Bioscience
POINTOFVIEW
110 Transcription Volume 3 Issue 3
Keywords: transcription, mediator,
chromatin, stress response genes, SAGA,
Swi/Snf
Submitted: 02/16/12
Revised: 02/27/12
Accepted: 02/28/12
http://dx.doi.org/10.4161/trns.19840
Correspondence to: Suraiya Ansari and Randall
Morse; Email: sansari@wadsworth.org and
randall.morse@wadsworth.org
T
he tail module subunits of the
Mediator complex are targets of
activators both in yeast and metazoans.
Here we discuss recent evidence from
studies in yeast for tail module specificity
for SAGA-dependent, TATA-containing
genes including highly regulated stress
response genes, and for independent
recruitment and function of the tail
module.
The Mediator complex is a central player
in the transcriptional regulation of protein-
coding genes, being required for nearly
all transcription by RNA polymerase II
(RNAP II), and is highly conserved from
yeast to human.
1
Structural and biochemi-
cal studies, together with yeast genetic
studies showing similar phenotypes result-
ing from deletion of specific non-essential
subunits, indicate that the core Mediator
complex comprises three distinct modules:
head, middle and tail. In addition, a fourth
module that includes a cyclin-CDK pair of
subunits and hence is often referred to as the
kinase module, associates transiently with
the core Mediator complex. Yeast Mediator
comprises 25 subunits, all of which have
homologs in mammals.
2,3
Five additional
metazoan specific subunits make mam-
malian Mediator a 30 subunit complex.
The yeast Mediator tail module comprises
Med2, Med3, Med15/Gal11 and Med16/
Sin4 subunits, and microarray experi-
ments together with biochemical data indi-
cate that Med2, Med3 and Med15/Gal11
belong to a functionally discrete submod-
ule.
4,5
(A new nomenclature for Mediator
subunits was adopted in 2004,
6
so some
subunits have more than one name).
Selective role of Mediator tail module in the transcription of highly
regulated genes in yeast
Suraiya A. Ansari
1
and Randall H. Morse
1,2
1
Laboratory of Molecular Genetics; Wadsworth Center; New York State Department of Health; Albany, NY USA
2
Department of Biomedical Science; University at Albany School of Public Health; Albany, NY USA
Direct interactions between gene-
specific transcriptional activators and
tail module subunits have been reported
in several previous studies. For example,
Gcn4 interacts with Med15/Gal11, Med2
and Med3 tail subunits, and Oaf1 and
Gal4 interact directly with Med15,
7-10
while in mammals, SREBP-1 interacts
wit h Med15.
11
Subunits of the head and
middle modules, on the other hand, inter-
act with general transcription factors and
RNAP II subunits, although interactions
have also been reported with gene-specific
activators, particularly in mammalian sys-
tems.
1,12-14
Based on these studies, the gen-
eral model of Mediator complex function
that emerges is that the tail module sub-
units, by interacting with activators, signal
through the head and middle modules to
the basal transcription machinery to regu-
late transcription initiation (Fig. 1).
Tail Module Specicity for SAGA/
Swi-Snf Dependent Promoters
Several Mediator middle and head mod-
ule subunits are essential, and inactiva-
tion of essential subunits from the head
module affects expression of over 90% of
all RNAP II transcribed genes in yeast.
9
In contrast, the tail module contains only
non-essential subunits and deletion of any
individual tail module subunit affects
the expression of only a fraction of the
genome,
4,5
indicating that the tail module
has a gene selective rather than a general
role in transcription. The question then
arises as to which genes require the tail
module for their expression. To gain new
insight into the role of the tail module in
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www.landesbioscience.com Transcription 111
POINTOFVIEW
POINTOFVIEW
provide transcriptional specificity at par-
ticular promoters.
20
In contrast, TFIID-
dependent genes, many of which may
not require Swi/Snf, could depend on
Mediator subunits other than those in the
tail module to interact with activators or
TFIID components, thus leading to the
interactions with other GTFs and forma-
tion of PIC.
23-25
In summary, although connections
between the Mediator tail, Swi/Snf and
SAGA have been established, the detailed
mechanisms behind these interconnec-
tions likely differ at different promot-
ers, and an understanding of the precise
molecular basis underlying these connec-
tions remains to be achieved.
Antagonism between the Tail
Module and Kinase Module at
Stress Response Genes
Genes that are commonly upregulated
during general environmental stress are
strongly biased toward being SAGA domi-
nated.
15,16
Consistent with the strong cor-
relation that we found between SAGA
dependent and tail module dependent
genes, we observed significant enrichment
of general stress response genes among
genes affected by loss of tail module sub-
units.
5
The tail module therefore seems to
act as a global transcriptional co-activator
of stress response genes. In contrast, dele-
tion of kinase module subunits Cdk8/
Srb10 and Med12/Srb8 causes upregula-
tion of many of these same stress response
genes.
Previous work has pointed to antago-
nistic roles for the tail and kinase modules
in regulating gene expression. Genetic
analysis indicates that this module is
involved in the negative regulation of a
subset of genes in yeast, and these genes are
enriched among those showing decreased
expression upon tail subunit deletion.
4,9
These and our genetic analyses used yeast
grown in rich medium or complete syn-
thetic medium, conditions in which many
genes are expressed at low levels or not at
all. Additional experiments using other
growth conditions have also revealed an
antagonistic relationship between the tail
and kinase modules. For example, osmotic
stress genes are repressed by the Tup1/Ssn6
complex, which appears to function in
as the SAGA complex can modify histone
N-terminal tails, thus altering affinity of
transcriptional regulatory factors to pro-
moter chromatin.
18
It is not difficult to
imagine that chromatin remodeling at
active gene promoters would be required
for Mediator to efficiently and produc-
tively recruit RNAP II and, indeed, pre-
vious studies have established genetic
interactions among Mediator, Swi/Snf
and SAGA. For example, loss of the Spt20
subunit of the SAGA complex leaves yeast
cells inviable if Mediator subunits, includ-
ing tail subunits Med15/Gal11 or Med16/
Sin4, or the Snf2 subunit of Swi/Snf com-
plex, are also absent.
19
Studies on the interrelationships
among Mediator, Swi/Snf and SAGA at
individual active promoters in yeast indi-
cate that there is no single mechanism
for their recruitment.
20
For example, at
the Gcn4 dependent ARG1 and SNZ1
promoters, recruitment of Mediator and
SAGA is interdependent, while recruit-
ment of Mediator and SAGA to promoters
controlled by the activator Met4 occurs
independently.
21,22
These and other dif-
ferences in the requirement of Mediator
for the recruitment of SAGA or Swi/Snf
complex at different promoters suggest
that complex interactions between spe-
cific activators and Mediator tail subunits,
Swi/Snf and SAGA subunits, as well as
between Mediator subunits and Swi/
Snf and SAGA subunits, are required to
genome wide transcription, we assessed
the effect of both single and double tail
subunit deletions.
5
We found that the
tail module subunits Med2, Med3 and
Med15/Gal11 function redundantly at
many target genes.
Yeast genes can be divided into two
principal types: (1) stress regulated, TATA-
containing, SAGA dependent genes (10
15%) and (2) constitutive, TATA-less,
TFIID-dependent genes (85–90%).
15,16
Strikingly, our analysis of genome-wide
expression changes in a med3Δ med15/
gal11Δ mutant revealed that the tail mod-
ule preferentially regulates genes that
depend on SAGA and Swi/Snf, and not
TFIID, for their activation. Many factors
that regulate chromatin, TBP and RNAP
II play a greater role at SAGA dominated
genes than at TFIID dominated genes.
15,16
Our observation that the tail module
preferentially regulates SAGA dominated
genes suggests that the tail module might
function along with specific chromatin
regulators to help pre-initiation complex
(PIC) formation on these highly regulated
genes (Fig. 1).
The remodeling of nucleosomes at the
promoter is an important step in tran-
scriptional activation, and can involve
multiple mechanisms. ATP-dependent
chromatin remodelers such as the yeast
Swi/Snf complex can increase the acces-
sibility of the transcriptional machinery to
nucleosomal DNA,
17
while cofactors such
Figure 1. Mediator bridges activators and the general transcription machinery. At TATA-con-
taining promoters in yeast, sequence-specic transcriptional activators preferentially interact
with Mediator via subunits of the Med2/Med3/Med15 tail triad; these same genes are generally
also regulated by Swi/Snf and the SAGA complex. Genes involved in stress response or meta-
bolic genes are mainly TATA containing and depend on the SAGA and Swi/Snf complexes and,
correspondingly, show a strong requirement for tail module subunits. The kinase module, which
associates transiently with the core Mediator complex (see text), is omitted for clarity. Also not
shown are interactions between the middle module of Mediator and other GTFs.
© 2012 Landes Bioscience.
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112 Transcription Volume 3 Issue 3
transcriptional specicity.
5,8,37
Thus, envi-
ronmental perturbations are perceived by
tail subunits and the information is fur-
ther relayed to the general transcription
machinery to cause the required transcrip-
tional outcomes.
Independent Recruitment and
Function of Med15/Med3/Med2
Tail Subcomplex
Biochemical fractionation and purifica-
tion studies suggest that the head, middle
and tail modules of Mediator are pres-
ent as a single complex.
1
A genome-wide
localization study also shows the pres-
ence of all modules of Mediator together
on promoters.
33
However, several reports
show that under some circumstances,
the Med15/Med3/Med2 triad can be
recruited and may be able to exert some
functions independently of the remainder
of the Mediator complex.
5,8,41
Previous
studies in our lab have shown that the
loss of Mediator head and middle mod-
ules from several constitutive as well as
inducible gene promoters in med17/srb4 ts
mutant yeast leaves the tail module asso-
ciated with these promoters.
23,41
However,
the loss of head and middle modules in
this mutant resulted in greatly reduced
binding of RNAP II, TBP and other
GTFs to all RNAP II transcribed genes
examined,
23
consistent with loss of tran-
scription of almost all RNAP II tran-
scribed genes in this mutant.
9
The tail
module, however, might be able to func-
tion independently in early steps of PIC
formation such as recruitment of SAGA or
Swi/Snf complex and chromatin remod-
eling. In support of this possibility, He
et al. showed that the recruitment of the
Swi/Snf complex and chromatin remod-
eling remains unaffected at the CHA1
promoter in med17/srb4 ts mutant yeast at
the non-permissive temperature, although
CHA1 induction is nearly eliminated
(Fig. 2A).
41
However, although this could
mean that the tail module was able under
these circumstances to contribute to Swi/
Snf recruitment and chromatin remodel-
ing, these events could also have occurred
independently of Mediator.
A related result was observed by
Zhang et al. who reported that the
Med15/Med3/Med2 triad is recruited
genes involved in metabolic pathways such
as drug metabolism and detoxification,
carbohydrate metabolism and amino acid
metabolism are downregulated or upregu-
lated by Mediator tail deletion.
5
Mediator
complex, and particularly the tail module,
has been implicated in the transcription
of specific metabolic pathway genes both
in yeast and metazoans. Although many
metabolic pathway genes are also stress-
regulated, dependence on tail subunits has
been observed for activation of some such
genes via non-stress pathways. For exam-
ple, the Med15 subunit of the tail module
has been shown to regulate the expression
of genes involved in fatty acid metabo-
lism by directly interacting with activator
SREBPα through its KIX-domain, lead-
ing to the transcriptional activation of
target genes in human.
11
Similarly, SBP-1
in C. elegans and Oaf1 in yeast interact
directly with Med15 through the con-
served KIX domain to regulate fatty acid
metabolism.
7,11,35
The Med15 subunit has
also been shown to regulate galactose
and amino acid metabolism in yeast by
directly interacting with activators Gal4
and Gcn4.
10,36-38
The requirement of Med15 in the
metabolism of xenobiotics has also been
reported in yeast and C. elegans. In yeast,
Med15 directly binds to Pdr1 orthologs,
which regulate the expression of genes
involved in drug-efflux pumps.
39
Similarly,
in C. elegans, genome-wide expression
analysis shows that loss of the Med15 sub-
unit causes significant downregulation of
drug metabolic genes and genes required
for energy homeostasis such as glucose
and lipid metabolism.
40
These studies sug-
gest that the tail module might act as co-
sensor in the nutrient/metabolic signaling
pathway: tail subunits could directly or
indirectly interact with upstream signal-
ing components and transfer the signal-
ing information to the promoter by either
binding to activators or by interacting with
chromatin regulators, which will then lead
to chromatin remodeling at the promoter
and PIC assembly. The tail module thus
helps to provide a platform for PIC assem-
bly. Our finding that tail subunits act
redundantly is consistent with the idea,
also proposed by others, that multiple
contacts between tail subunits and vari-
ous transcription regulators contribute to
part via the kinase module;
26,27
these same
genes show diminished activation in tail
subunit deletion mutants.
28
Furthermore,
SAGA and Swi/Snf are required for over-
coming Tup1-mediated repression of
osmotic stress inducible genes,
27
consistent
with these co-activators being preferen-
tially involved in activation of genes that
require the Mediator tail module for their
expression.
5
Similarly, the general stress
response genes, which are activated by
Msn2/Msn4,
29
are upregulated upon loss
of kinase module subunits,
9
and require
Med15/Gal11 for activation.
30
Structural and biochemical studies
have shown that the Med13 subunit of
the kinase module binds the Mediator
tail module, and this interaction blocks
Mediator interaction with RNAP II.
31,32
This suggests a scenario in which, under
inducing conditions, the interaction of
Mediator tail subunits with activators or
co-activators such as SAGA and Swi/Snf
complex causes transcriptional activation,
whereas under non-inducing conditions,
Mediator tail rather interacts with the
kinase module subunit, blocking its asso-
ciation with RNAP II and leading to tran-
scription repression. Consistent with this
scenario, a dynamic interaction between
the core Mediator complex and the kinase
module is suggested by a ChIP-chip
analysis showing that the kinase module
is associated with the core module at all
sites but with lower occupancy.
33
Such a
dynamic interaction could be stabilized
or destabilized by gene-specific repressors
and activators, thereby modulating gene
expression. Alternative mechanisms for
repression by the kinase module are also
possible. For example, Msn2 is targeted
for degradation by phosphorylation by
Srb10/Cdk8,
30,34
suggesting a mechanism
involving activator destruction. Further
experiments are needed to fully under-
stand the mechanistic details of Mediator
tail regulated activation and kinase mod-
ule dependent repression of stress response
genes.
Tail Module Requirement for
Metabolic Pathway Regulation
The specific requirement for the tail mod-
ule also includes the activation of meta-
bolic genes. A significant percentage of
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www.landesbioscience.com Transcription 113
the rest of Mediator. Clearly, we are a long
way from an exhaustive understanding of
this fundamental player in transcriptional
activation, and additional interesting sur-
prises are sure to lie ahead.
Acknowledgments
We thank Joe Wade for a critical reading
of the manuscript. This work was sup-
ported by NSF grant MCB0949722.
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In conclusion, the tail module of Mediator
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  • [Show abstract] [Hide abstract] ABSTRACT: We have earlier demonstrated the involvement of Mediator subunit Srb5/Med18 in the termination of transcription for a subset of genes in yeast. Srb5/Med18 could affect termination either indirectly by modulating CTD-Ser2 phosphorylation near the 3' end of a gene or directly by physically interacting with the cleavage and polyadenylation factor (CPF) or cleavage factor 1 (CF1) complex and facilitating their recruitment to the terminator region. Here we show that the CTD-Ser2 phosphorylation pattern on Srb5/Med18-dependent genes remains unchanged in the absence of Srb5 in cells. Coimmunoprecipitation analysis revealed the physical interaction of Srb5/Med18 with the CF1 complex. No such interaction of Srb5/Med18 with the CPF complex, however, could be detected. The Srb5/Med18-CF1 interaction was not observed in the looping defective sua7-1 strain. Srb5/Med18 crosslinking to the 3' end of genes was also abolished in the sua7-1 strain. Chromosome conformation capture (CCC) analysis revealed that the looped architecture of Srb5/Med18-dependent genes was abrogated in srb5- cells. Furthermore, Srb5-dependent termination of transcription was compromised in the looping defective sua7-1 cells. The overall conclusion of these results is that gene looping plays a crucial role in Srb5/Med18 facilitated termination of transcription, and the looped gene architecture may have a general role in termination of transcription in budding yeast.
    Article · Mar 2013
  • [Show abstract] [Hide abstract] ABSTRACT: The multisubunit eukaryotic Mediator complex integrates diverse positive and negative gene regulatory signals and transmits them to the core transcription machinery. Mutations in individual subunits within the complex can lead to decreased or increased transcription of certain subsets of genes, which are highly specific to the mutated subunit. Recent studies suggest a role for Mediator in epigenetic silencing. Using white-opaque morphological switching in Candida albicans as a model, we have shown that Mediator is required for the stability of both the epigenetic silenced (white) and active (opaque) states of the bistable transcription circuit driven by the master regulator Wor1. Individual deletions of eight C. albicans Mediator subunits have shown that different Mediator subunits have dramatically diverse effects on the directionality, frequency, and environmental induction of epigenetic switching. Among the Mediator deletion mutants analyzed, only Med12 has a steady-state transcriptional effect on the components of the Wor1 circuit that clearly corresponds to its effect on switching. The MED16 and MED9 genes have been found to be among a small subset of genes that are required for the stability of both the white and opaque states. Deletion of the Med3 subunit completely destabilizes the opaque state, even though the Wor1 transcription circuit is intact and can be driven by ectopic expression of Wor1. The highly impaired ability of the med3 deletion mutant to mate, even when Wor1 expression is ectopically induced, reveals that the activation of the Wor1 circuit can be decoupled from the opaque state and one of its primary biological consequences.
    Article · Jul 2013
  • [Show abstract] [Hide abstract] ABSTRACT: Mediator is a large, multisubunit complex that is required for essentially all mRNA transcription in eukaryotes. In spite of the importance of Mediator, the range of its targets and how it is recruited to these is not well understood. Previous work showed that in Saccharomyces cerevisiae, Mediator contributes to transcriptional activation by two distinct mechanisms, one depending on the tail module triad and favoring SAGA-regulated genes, and the second occurring independently of the tail module and favoring TFIID-regulated genes. Here, we use chromatin immunoprecipitation sequencing (ChIP-seq) to show that dependence on tail module subunits for Mediator recruitment and polymerase II (Pol II) association occurs preferentially at SAGA-regulated over TFIID-regulated genes on a genome-wide scale. We also show that recruitment of tail module subunits to active gene promoters continues genome-wide when Mediator integrity is compromised in med17 temperature-sensitive (ts) yeast, demonstrating the modular nature of the Mediator complex in vivo. In addition, our data indicate that promoters exhibiting strong and stable occupancy by Mediator have a wide range of activity and are enriched for targets of the Tup1-Cyc8 repressor complex. We also identify a number of strong Mediator occupancy peaks that overlap dubious open reading frames (ORFs) and are likely to include previously unrecognized upstream activator sequences.
    Full-text · Article · Nov 2014
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