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.

Gene expression buffering

In eukaryotic cells, genes are transcribed in the nucleus and the produced mRNAs are exported for translation and subsequent degradation to the cytoplasm. Despite this separation in time and space for the different stages of gene expression, compelling evidence has accumulated these last years to indicate that the processes are intimately connected. Components of the different cellular machines that participate to production and degradation of mRNAs circulate between the different compartments. For several of these factors, it has now been shown that they exert their major function in one compartment, but can moonlight in the other compartment to oppositely affect gene expression. This serves the purpose of buffering gene expression, namely by inducing compensatory changes in production and degradation of mRNAs to maintain homoeostasis.

Instrumental in revealing the circuitry of gene expression have been studies by Tirosh and colleagues [1] in which they found that mRNAs of a given gene were expressed at a relatively similar level despite very different decay rates in different yeast species. Similar observations could be made by comparing different metazoans [2]. These findings were supported and extended by evidence that mRNA synthesis and decay rates were oppositely affected by mutations in the synthesis or decay machines in Saccharomyces cerevisiae [3].

Coupled changes in synthesis and decay rates of different yeast have been linked in cis to transcription factor-binding sites in gene promoters, suggesting that binding of transcription factors to promoters might co-ordinate transcription and decay rates. Indeed, replacement of an upstream activating sequence in a yeast reporter gene without changing the sequence of the produced transcript alters the kinetics of mRNA degradation [4]. Moreover, single-molecule FISH (fluorescent in situ hybridization) experiments demonstrated that the specificity and timing of decay of two cell cycle-regulated genes in yeast was completely dependent upon their promoter [5]. In fact, at a genomic scale, co-ordination of mRNA synthesis and decay rates is defined by promoter sequences, in yeast and also in human [2]. Interestingly a promoter's function may not only be mediated through transcription factors, but through other promoter-associated factors such as a kinase that can remain associated and be exported with an mRNA [5].

Gene expression buffering requires that communication occurs forward, from mRNA synthesis to degradation, but also in reverse direction, namely from degradation to synthesis. The first evidence for forward buffering from a component of the mRNA synthesis machinery itself was provided in 2005 [6]. A subunit of RNA polymerase II (RNA Pol II), Rpb4 (RNA polymerase B subunit 4), was shown to be required for the decay of a specific class of mRNAs in yeast. Rpb4 shuttles between the nucleus and the cytoplasm and in the cytoplasm associates with components of the major mRNA decay pathway and even localizes to P-bodies, where it is thought that mRNAs are decapped and degraded [79]. Consistently with this role for Rpb4, the most prominent trans mutations that correlate with coupled changes in mRNA synthesis and decay rates in diverse yeast are linked to RPB4 [3].

Rpb4 forms a heterodimeric complex with another subunit of RNA Pol II, Rpb7 and the dimer associates with the largest subunit of RNA Pol II, Rpb1, at a region that is situated near to the transcript exit groove and the C-terminal repeat region of Rpb1 (CTD) known to serve as a platform for assembly of components of post-transcriptional regulatory machines. This dimer tends to dissociate readily from the rest of the polymerase and is dispensable in vitro for stable recruitment of polymerase to active pre-initiation complexes, though it is necessary for promoter-dependent transcription initiation [1017]. Whereas Rpb4 is dispensable for viability in S. cerevisiae, Rpb7 is essential. Rpb7 has also been reported to be important to connect mRNA synthesis and decay rates [8]. The Rpb4–Rpb7 dimer was proposed to associate with transcripts at the completion of transcription in a co-transcriptional manner (mRNA imprinting), be exported with the mRNAs and govern mRNA decay in the cytoplasm [7]. Subsequent work has argued against a cytoplasmic function of Rpb4 because a yeast strain in which Rpb4 was fused to Rpb2 compensated altered synthesis and mRNA decay rates due to the Rpb4 deletion [18]. However, our study published last year has indicated that the presence of Rpb7 in the cytoplasm may be connected to its co-translational assembly into RNA Pol II [19]. We showed that Rpb2 was also present in polysomes for this purpose, such that a fusion of Rpb4 and Rpb2 would similarly be able to localize to polysomes where Rpb4 might be able to exert its cytoplasmic function. It is unlikely that co-transcriptional Rpb4 mRNA imprinting can take place if Rpb4 is fused to Rpb2. However, if the mRNA is imprinted instead by a factor that usually tethers Rpb4, it would still be possible for Rpb4 to have a cytoplasmic effect via it's recruitment to the mRNA by the interacting factor in the cytoplasm. Ccr4 (carbon catabolite repressed 4)–Not (negative on TATA-less) complex is certainly a candidate for such a factor. Indeed, cytoplasmic presence of Rpb4 was shown to be dependent on Not5 [19]. The co-translational assembly of the transcription machinery in the cytoplasm that we reported is likely to participate in the global scheme of gene expression buffering (see below) [19]. In this scheme, cytoplasmic Rpb4 could play a role.

Whereas forward buffering (inducing changes in mRNA decay to compensate for changes in transcription) is very easy to grasp as mRNA can be marked during transcription, reverse buffering (inducing changes in transcription to compensate for changes in mRNA decay) from the cytoplasm to the nucleus is much less intuitive. The Cramer laboratory investigated which components of the mRNA degradation machines were most important for buffering of mRNA levels in yeast [20]. They tested a large number of components of the RNA degradation machines and identified the 5′- to 3′-exonuclease Xrn1 (exoribonuclease 1) as absolutely key for buffering. Cells lacking Xrn1 are unable on a global scale to compensate for reduced mRNA degradation by reduced synthesis. They found that the catalytic function of Xrn1 and the presence of Xrn1 in the nucleus were required for buffering. They argued against a direct repression of transcription by Xrn1 since they found no cross-linking to genes and no effect on in vitro transcription by extracts. Instead, they observed that the synthesis of the mRNA encoding a global repressor, Nrg1 (negative regulator of glucose-repressed genes 1), was increased in xrn1Δ and also in other mRNA degradation mutants (such as caf1Δ or ccr4Δ) indicating that this repressor could be part of the buffering system. Others have argued instead that Xrn1 does directly impact on transcription and is present at promoters and during transcription elongation [21,22].

Ccr4–Not complex in gene expression buffering

After synthesis, mRNAs are translated before they are degraded and hence missing in our knowledge of the buffering of gene expression in eukaryotes is how to integrate translation in the circuitry. It is more than certain that it will play an essential role. For instance comparison of S. cerevisiae and Saccharomyces paradoxus mRNA abundance and ribosome occupancy revealed that translation regulatory divergence often buffers species differences in mRNA abundance [23]. Our recent finding that a subunit of the Ccr4–Not complex, Not5, connects transcription to translation and backwards translation to transcription, playing essential roles in the nucleus and in the cytoplasm, seems to indicate that an important master regulator integrating translation in the buffering circuitry could be the Ccr4–Not complex [19]. Subunits of this complex are present at the sites of transcription [2437] and impact on transcription elongation [36,38,39], the major eukaryotic deadenylases are subunits of this complex [40] and finally Ccr4–Not subunits are present at polysomes during translation and have been implicated in co-translational quality control [4144].

The core Ccr4–Not complex is composed of between nine and 11 identified subunits in different organisms [28,4550]. In yeast, these subunits are the five Not proteins, Caf1 (Ccr4 associated factor 1), Ccr4, Caf40 and Caf130. The large Not1 protein serves as a scaffold for assembly of the different subunits into the complex, but it also serves as a scaffold to bring mRNAs in contact with the major eukaryotic deadenylases, Ccr4 and Caf1 [51,52]. The other Ccr4–Not subunits dock on to the Not1 scaffold and can in certain cases contribute to bring the deadenylases on the Not1 scaffold together with mRNAs, but their primary function does not seem to be deadenylation [46,5356]. The Not4 subunit has an E3 ligase activity and ubiquitylates a variety of substrates [5763]; it is also involved in co-translational quality control [4244,64]. Not4 binds to the C-terminal region of Not1 [65,66].

The Not2 and Not5 subunits function together and form a heterodimer that also binds the C-terminus of Not1 [65,67]. The binding of Not4 and Not2/5 to the Not1 scaffold occur on largely separate surfaces of Not1 [66]. Not2 and Not5 were first described to function in transcription [24,26,45,54,65,68,69]. This idea will need to be revisited with our current knowledge that cells lacking Not5 contain improperly assembled RNA Pol II [19]. Indeed, Not5 is essential during translation for proper interactions of nascent Rpb1, the largest subunit of RNA Pol II, with its chaperone and subsequent functional co-translational assembly of Rpb1 into polymerase complexes [19]. Efficient Pol II assembly hence is connected to translation and this suggests that the status of the translation apparatus, the availability of actively translating ribosomes may feedback to transcription by modulating the quantity of newly assembled Pol II. Hence, Not5 connects translation with transcription. Another interesting finding that connects the Ccr4–Not complex with integrity of other protein complexes and assembly of newly produced proteins into complexes as previously proposed [70], is that the deletion of Not4 has an effect on the integrity of the proteasome [71].

Could then the Ccr4–Not complex be the, or a component of the, master regulator that orchestrates the different levels of gene expression? Would the site at which this buffering is regulated be the translating ribosome? The co-ordination of the buffering might occur through the docking of the different subunits on the Not1 scaffold. But at the same time the various subunits might affect first on association of the mRNA with Not1. The latter would occur in the nucleus as the Ccr4–Not complex can bind transcription elongation complexes [36,38,39] whereas the former would occur in the cytoplasm. The idea that the different Ccr4–Not subunits may impact on Not1 mRNA association stems from the finding that several subunits are able to bind mRNA. Indeed, UV cross-linking of poly(U) stretches to Not1, Not2 and to Not5 showed that these subunits can bind RNA in complex but individually also [67]. Moreover Not4 has an RNA recognition motif [72]. Hence, mRNAs might be imprinted in the nucleus and then marked by Not1 in polysomes where Not1 can sense and integrate environmental cues and modify the imprinted state. A differentially assembled complex on the mRNA and Not1 scaffold could serve as a protein signature for other proteins to identify what to do with the mRNA. Globally, the Ccr4–Not complex would define the number of mRNAs to be regulated immediately upon reception of environmental signals. At the same time define the responsive pool of mRNAs inside the cells. The pool of imprinted mRNAs that the cell can deal with is not infinite as cellular resources are limited (there are much more mRNAs in cells than ribosomes for example) and definition of the functional mRNA pool is therefore necessary. In the signalling cascades to define the responsive pool of mRNAs in given conditions, RNA-binding proteins and miRNAs that have the capacity to tether the Ccr4–Not complex to specific mRNAs are obviously also relevant [73]. The different roles of the Ccr4–Not complex in gene expression buffering discussed above are summarized on Figure 1. 

Schematic view of the Ccr4–Not complex's role in gene expression buffering

Figure 1
Schematic view of the Ccr4–Not complex's role in gene expression buffering

The different processes where the Ccr4–Not complex plays a role as discussed in the text are highlighted on the figure. The references to published work where the Ccr4–Not complex's role in the given process was discovered or reviewed are included. For simplification purposes, complex mRNPs are not depicted. Abbreviations: , transcription initiation site; 40S, small subunit of the ribosome; 60S, large subunit of the ribosome; NPC, nuclear pore complex; Pol2, RNA Polymerase II; RBP, RNA-binding protein.

Figure 1
Schematic view of the Ccr4–Not complex's role in gene expression buffering

The different processes where the Ccr4–Not complex plays a role as discussed in the text are highlighted on the figure. The references to published work where the Ccr4–Not complex's role in the given process was discovered or reviewed are included. For simplification purposes, complex mRNPs are not depicted. Abbreviations: , transcription initiation site; 40S, small subunit of the ribosome; 60S, large subunit of the ribosome; NPC, nuclear pore complex; Pol2, RNA Polymerase II; RBP, RNA-binding protein.

There is ample evidence that the Ccr4–Not complex exists in several forms. For instance the level of several Ccr4–Not subunits is variable between different types of tissues when the amount of the other subunits remains stable [74]. However, there is also evidence that depletion of certain Ccr4–Not subunits leads to depletion of all subunits [75,76] and this has been argued to suggest that the complex works as a unique entity. These latter experiments however, do not exclude dynamic assembly and disassembly of the complex for instance during translation where the Not1 scaffold might be protected from degradation through its interaction with the mRNA and translation machinery.

The existence of a unique machine that buffers the different levels of gene expression provides the cell with means to give a fast internal response to environmental signals and optimally use limited resources. Energy metabolism is very essentially connected to responses to the environment. Under certain conditions, typically under stress, cells have to shut down the expression of certain genes almost immediately; otherwise they run out of energy to maintain housekeeping functions. Hence, if a complex or machinery is responsible for orchestrating the different levels of gene expression, then this complex or machinery should also be directly linked to mitochondrial functions and/or biogenesis. In this context, it is interesting to note that several lines of evidence connect the Ccr4–Not complex to energy metabolism. A transcriptome analysis of the homozygous ccr4 null mutant in Candida albicans showed that a large proportion of the differentially-expressed genes are related to the function of mitochondria [77]. Specific effects on gene expression of mitochondrial functions have also been observed in S. cerevisiae ccr4–not mutants [37,50] In mice, CNOT3 is important for stress-induced cardiac functions and control of lipid storage [78,79], both linked to energy metabolism.

Dynamic responses to environmental changes require that the active pool of mRNAs can be modified. Some mRNAs must be stored, others should be degraded and their transcription should be turned off rapidly to maintain cellular homoeostasis. It seems that the Ccr4–Not complex has the capacity to provide this dynamic regulation and define the active pool of mRNAs; it can control imprinting of mRNAs in the nucleus and modify this nuclear imprinting in the cytoplasm upon receiving a signal in this compartment. It is able to initiate the destruction of the mRNA it is engaged with by its deadenylase subunits and our recent results suggest that, via Not5, it even can modify the pool of translated mRNAs [19]. Finally, it can determine how much new polymerase is produced. All these evidences determine that the Ccr4–Not complex fits the criteria required for the ability to respond fast to environmental changes by means of co-ordination of the different levels of gene expression. Exploring the signalling cascades of the Ccr4–Not regulation and the dynamics of Ccr4–Not assembly with mRNAs will be one of the most interesting future challenges and will greatly add to our understanding of how the different levels of gene expression are orchestrated in eukaryotes.

Funding

This work was supported by grant 31003a_135794 from the Swiss National Science foundation.

Abbreviations

     
  • Caf

    Ccr4 associated factor

  •  
  • CTD

    C terminal domain of Rpb1

  •  
  • RNA Pol II

    RNA polymerase II

  •  
  • Rpb4

    RNA polymerase B subunit 4

  •  
  • Xrn1

    exoribonuclease 1

Translation UK 2015: Held at the University of Aberdeen, U.K., 7–9 July 2015.

References

References
1
Dori-Bachash
M.
Shema
E.
Tirosh
I.
Coupled evolution of transcription and mRNAdegradation
PLoS Biol.
2011
, vol. 
9
 pg. 
e1001106
 
[PubMed]
2
Dori-Bachash
M.
Shalem
O.
Manor
Y.S.
Pilpel
Y.
Tirosh
I.
Widespread promoter-mediated coordination of transcription and mRNA degradation
Genome Biol.
2012
, vol. 
13
 pg. 
R114
 
[PubMed]
3
Sun
M.
Schwalb
B.
Schulz
D.
Pirkl
N.
Etzold
S.
Larivière
L.
Maier
K.C.
Seizl
M.
Tresch
A.
Cramer
P.
Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation
Genome Res.
2012
, vol. 
22
 (pg. 
1350
-
1359
)
[PubMed]
4
Bregman
A.
Avraham-Kelbert
M.
Barkai
O.
Duek
L.
Guterman
A.
Choder
M.
Promoter elements regulate cytoplasmic mRNA decay
Cell
2011
, vol. 
147
 (pg. 
1473
-
1483
)
[PubMed]
5
Trcek
T.
Larson
D.R.
Moldón
A.
Query
C.C.
Singer
R.H.
Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast
Cell
2011
, vol. 
147
 (pg. 
1484
-
1497
)
[PubMed]
6
Lotan
R.
Bar-On
V.G.
Harel-Sharvit
L.
Duek
L.
Melamed
D.
Choder
M.
The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs
Genes Dev.
2005
, vol. 
19
 (pg. 
3004
-
3016
)
[PubMed]
7
Goler-Baron
V.
Selitrennik
M.
Barkai
O.
Haimovich
G.
Lotan
R.
Choder
M.
Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes
Genes Dev.
2008
, vol. 
22
 (pg. 
2022
-
2027
)
[PubMed]
8
Harel-Sharvit
L.
Eldad
N.
Haimovich
G.
Barkai
O.
Duek
L.
Choder
M.
RNA polymerase II subunits link transcription and mRNA decay to translation
Cell
2010
, vol. 
143
 (pg. 
552
-
563
)
[PubMed]
9
Shalem
O.
Groisman
B.
Choder
M.
Dahan
O.
Pilpel
Y.
Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II
PLoS Genet.
2011
, vol. 
7
 pg. 
e1002273
 
[PubMed]
10
Cramer
P.
Bushnell
D.A.
Kornberg
R.D.
Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
Science
2002
, vol. 
2292
 (pg. 
1863
-
1876
)
11
Bushnell
D.A.
Cramer
P.
Kornberg
R.D.
Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution
Proc. Natl. Acad. Sci. U.S.A.
2002
, vol. 
99
 (pg. 
1218
-
1222
)
[PubMed]
12
Armache
K.J.
Mitterweger
S.
Meinhart
A.
Cramer
P.
Structures of complete RNA polymerase II and its subcomplex, Rpb4/7
J. Biol. Chem.
2005
, vol. 
280
 (pg. 
7131
-
7134
)
[PubMed]
13
Cramer
P.
Mechanistic studies of the mRNA transcription cycle
Biochem. Soc. Symp.
2006
, vol. 
73
 (pg. 
41
-
47
)
[PubMed]
14
Venters
B.J.
Pugh
B.F.
A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome
Genome Res.
2009
, vol. 
19
 (pg. 
360
-
371
)
[PubMed]
15
García-López
M.C.
Navarro
F.
RNA polymerase II conserved protein domains as platforms for protein-protein interactions
Transcription
2011
, vol. 
2
 (pg. 
193
-
197
)
[PubMed]
16
Soutourina
J.
Wydau
S.
Ambroise
Y.
Boschiero
C.
Werner
M.
Direct interaction of RNA polymerase II and mediator required for transcription in vivo
Science
2011
, vol. 
331
 (pg. 
1451
-
1454
)
[PubMed]
17
García-López
M.C.
Pelechano
V.
Mirón-García
M.C.
Garrido-Godino
A.I.
García
A.
Calvo
O.
Werner
M.
Pérez-Ortín
J.E.
Navarro
F.
The conserved foot domain of RNA pol II associates with proteins involved in transcriptional initiation and/or early elongation
Genetics
2011
, vol. 
189
 (pg. 
1235
-
1248
)
[PubMed]
18
Schulz
D.
Pirkl
N.
Lehmann
E.
Cramer
P.
Rpb4 subunit functions mainly in mRNA synthesis by RNA polymerase II
J. Biol. Chem.
2014
, vol. 
289
 (pg. 
17446
-
17452
)
[PubMed]
19
Villanyi
Z.
Ribaud
V.
Kassem
S.
Panasenko
O.O.
Pahi
Z.
Gupta
I.
Steinmetz
L.
Boros
I.
Collart
M.A.
The Not5 subunit of the ccr4-not complex connects transcription and translation
PLoS Genet.
2014
, vol. 
10
 pg. 
e1004569
 
[PubMed]
20
Sun
M.
Schwalb
B.
Pirkl
N.
Maier
K.C.
Schenk
A.
Failmezger
H.
Tresch
A.
Cramer
P.
Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels
Mol. Cell
2013
, vol. 
52
 (pg. 
52
-
62
)
[PubMed]
21
Haimovich
G.
Medina
D.A.
Causse
S.Z.
Garber
M.
Millán-Zambrano
G.
Barkai
O.
Chávez
S.
Pérez-Ortín
J.E.
Darzacq
X.
Choder
M.
Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis
Cell
2013
, vol. 
153
 (pg. 
1000
-
1011
)
[PubMed]
22
Medina
D.A.
Jordán-Pla
A.
Millán-Zambrano
G.
Chávez
S.
Choder
M.
Pérez-Ortín
J.E.
Cytoplasmic 5'-3' exonuclease Xrn1p is also a genome-wide transcription factor in yeast
Front. Genet.
2014
, vol. 
5
 pg. 
1
 
[PubMed]
23
McManus
C.J.
May
G.E.
Spealman
P.
Shteyman
A.
Ribosome profiling revealspost-transcriptional buffering of divergent gene expression in yeast
Genome Res.
2014
, vol. 
24
 (pg. 
422
-
430
)
[PubMed]
24
Badarinarayana
V.
Chiang
Y.C.
Denis
C.L.
Functional interaction of CCR4-NOT proteins with TATAA-binding protein (TBP) and its associated factors in yeast
Genetics
2000
, vol. 
155
 (pg. 
1045
-
1054
)
[PubMed]
25
Benson
J.D.
Benson
M.
Howley
P.M.
Struhl
K.
Association of distinct yeast Not2 functional domains with components of Gcn5 histone acetylase and Ccr4 transcriptional regulatory complexes
EMBO J.
1998
, vol. 
17
 (pg. 
6714
-
6722
)
[PubMed]
26
Deluen
C.
James
N.
Maillet
L.
Molinete
M.
Theiler
G.
Lemaire
M.
Paquet
N.
Collart
M.A.
The Ccr4-not complex and yTAF1 (yTaf(II)130p/yTaf(II)145p) show physical and functional interactions
Mol. Cell. Biol.
2002
, vol. 
22
 (pg. 
6735
-
6749
)
[PubMed]
27
Lemaire
M.
Collart
M.A.
The TATA-binding protein-associated factor yTafII19p functionally interacts with components of the global transcriptional regulator Ccr4-Not complex and physically interacts with the Not5 subunit
J. Biol. Chem.
2000
, vol. 
275
 (pg. 
26925
-
26934
)
[PubMed]
28
Liu
H.Y.
Chiang
Y.C.
Pan
J.
Chen
J.
Salvadore
C.
Audino
D.C.
Badarinarayana
V.
Palaniswamy
V.
Anderson
B.
Denis
C.L.
Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme
J. Biol. Chem.
2001
, vol. 
276
 (pg. 
7541
-
7548
)
[PubMed]
29
Reese
J.C.
Green
M.R.
Genetic analysis of TAF68/61 reveals links to cell cycle regulators
Yeast
2001
, vol. 
18
 (pg. 
1197
-
1205
)
[PubMed]
30
Sanders
S.L.
Jennings
J.
Canutescu
A.
Link
A.J.
Weil
P.A.
Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry
Mol. Cell. Biol.
2002
, vol. 
22
 (pg. 
4723
-
4738
)
[PubMed]
31
Lenssen
E.
Oberholzer
U.
Labarre
J.
De Virgilio
C.
Collart
M.A.
Saccharomyces cerevisiae Ccr4-not complex contributes to the control of Msn2p-dependent transcription by the Ras/cAMP pathway
Mol. Microbiol.
2002
, vol. 
43
 (pg. 
1023
-
1037
)
[PubMed]
32
Lenssen
E.
Azzouz
N.
Michel
A.
Landrieux
E.
Collart
M.A.
The Ccr4-not complex regulates Skn7 through Srb10 kinase
Eukaryot. Cell
2007
, vol. 
6
 (pg. 
2251
-
2259
)
[PubMed]
33
Lenssen
E.
James
N.
Pedruzzi
I.
Dubouloz
F.
Cameroni
E.
Bisig
R.
Maillet
L.
Werner
M.
Roosen
J.
Petrovic
K.
, et al. 
The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation via a newly identified Glc7/Bud14 type I protein phosphatase module and TFIID promoter distribution
Mol. Cell. Biol.
2005
, vol. 
25
 (pg. 
488
-
498
)
[PubMed]
34
Qiu
H.
Hu
C.
Yoon
S.
Natarajan
K.
Swanson
M.J.
Hinnebusch
A.G.
An array of coactivators is required for optimal recruitment of TATA binding protein and RNA polymerase II by promoter-bound Gcn4p
Mol. Cell. Biol.
2004
, vol. 
24
 (pg. 
4104
-
4117
)
[PubMed]
35
Swanson
M.J.
Qiu
H.
Sumibcay
L.
Krueger
A.
Kim
S.J.
Natarajan
K.
Yoon
S.
Hinnebusch
A.G.
A multiplicity of coactivators is required by Gcn4p at individual promoters in vivo
Mol. Cell. Biol.
2003
, vol. 
23
 (pg. 
2800
-
2820
)
[PubMed]
36
Kruk
J.A.
Dutta
A.
Fu
J.
Gilmour
D.S.
Reese
J.C.
The multifunctional Ccr4-Not complex directly promotes transcription elongation
Genes Dev.
2011
, vol. 
25
 (pg. 
581
-
593
)
[PubMed]
37
Azzouz
N.
Panasenko
O.O.
Deluen
C.
Hsieh
J.
Theiler
G.
Collart
M.A.
Specific roles for the Ccr4-Not complex subunits in expression of the genome
RNA
2009
, vol. 
15
 (pg. 
377
-
383
)
[PubMed]
38
Babbarwal
V.
Fu
J.
Reese
J.C.
The Rpb4/7 module of RNA polymerase II is required for carbon catabolite repressor protein 4-negative on TATA (Ccr4-not) complex to promote elongation
J. Biol. Chem.
2014
, vol. 
289
 (pg. 
33125
-
33130
)
[PubMed]
39
Dutta
A.
Babbarwal
V.
Fu
J.
Brunke-Reese
D.
Libert
D.M.
Willis
J.
Reese
J.C.
Ccr4-Not and TFIIS function cooperatively to rescue arrested RNA polymerase II
Mol. Cell. Biol.
2015
, vol. 
11
 (pg. 
1915
-
1925
)
40
Tucker
M.
Staples
R.R.
Valencia-Sanchez
M.A.
Muhlrad
D.
Parker
R.
Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae
EMBO J.
2002
, vol. 
21
 (pg. 
1427
-
1436
)
[PubMed]
41
Halter
D.
Collart
M.A.
Panasenko
O.O.
The Not4 E3 ligase and CCR4 deadenylase play distinct roles in protein quality control
PLoS One
2014
, vol. 
9
 pg. 
e86218
 
[PubMed]
42
Dimitrova
L.N.
Kuroha
K.
Tatematsu
T.
Inada
T.
Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome
J. Biol. Chem.
2009
, vol. 
284
 (pg. 
10343
-
10352
)
[PubMed]
43
Matsuda
R.
Ikeuchi
K.
Nomura
S.
Inada
T.
Protein quality control systems associated with no-go and nonstop mRNA surveillance in yeast
Genes Cells
2014
, vol. 
19
 (pg. 
1
-
12
)
[PubMed]
44
Preissler
S.
Reuther
J.
Koch
M.
Scior
A.
Bruderek
M.
Frickey
T.
Deuerling
E.
Not4-dependent translational repression is important for cellular protein homeostasis in yeast
EMBO J.
2015
, vol. 
34
 (pg. 
1905
-
1924
)
[PubMed]
45
Liu
H.Y.
Badarinarayana
V.
Audino
D.C.
Rappsilber
J.
Mann
M.
Denis
C.L.
The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively
EMBO J.
1998
, vol. 
17
 (pg. 
1096
-
1106
)
[PubMed]
46
Chen
J.
Rappsilber
J.
Chiang
Y.C.
Russell
P.
Mann
M.
Denis
C.L.
Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex
J. Mol. Biol.
2001
, vol. 
314
 (pg. 
683
-
694
)
[PubMed]
47
Collart
M.A.
Global control of gene expression in yeast by the Ccr4-Not complex
Gene
2003
, vol. 
313
 (pg. 
1
-
16
)
[PubMed]
48
Maillet
L.
Collart
M.A.
Interaction between Not1p, a component of the Ccr4-Not complex, a global regulator of transcription, and Dhh1p, a putative RNA helicase
J. Biol. Chem.
2002
, vol. 
277
 (pg. 
2835
-
2842
)
[PubMed]
49
Liu
H.Y.
Toyn
J.H.
Chiang
Y.C.
Draper
M.P.
Johnston
L.H.
Denis
C.L.
DBF2, a cell cycle-regulated protein kinase, is physically and functionally associated with the CCR4 transcriptional regulatory complex
EMBO J.
1997
, vol. 
16
 (pg. 
5289
-
5298
)
[PubMed]
50
Cui
Y.
Ramnarain
D.B.
Chiang
Y.C.
Ding
L.H.
McMahon
J.S.
Denis
C.L.
Genome wide expression analysis of the CCR4-NOT complex indicates that it consists of three modules with the NOT module controlling SAGA-responsive genes
Mol. Genet. Genomics
2008
, vol. 
279
 (pg. 
323
-
337
)
[PubMed]
51
Basquin
J.
Roudko
V.V.
Rode
M.
Basquin
C.
Séraphin
B.
Conti
E.
Architecture of the nuclease module of the yeast Ccr4-not complex: the Not1-Caf1-Ccr4 interaction
Mol. Cell
2012
, vol. 
48
 (pg. 
207
-
218
)
[PubMed]
52
Boland
A.
Chen
Y.
Raisch
T.
Jonas
S.
Kuzuoğlu-Öztürk
D.
Wohlbold
L.
Weichenrieder
O.
Izaurralde
E.
Structure and assembly of the NOT module of the human CCR4-NOT complex
Nat. Struct. Mol. Biol.
2013
, vol. 
20
 (pg. 
1289
-
1297
)
[PubMed]
53
Russell
P.
Benson
J.D.
Denis
C.L.
Characterization of mutations in NOT2 indicates that it plays an important role in maintaining the integrity of the CCR4-NOT complex
J. Mol. Biol.
2002
, vol. 
322
 (pg. 
27
-
39
)
[PubMed]
54
Collart
M.A.
Struhl
K.
NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization
Genes Dev.
1994
, vol. 
8
 (pg. 
525
-
537
)
[PubMed]
55
Collart
M.A.
Panasenko
O.O.
Nikolaev
S.I.
The Not3/5 subunit of the Ccr4-Not complex: a central regulator of gene expression that integrates signals between the cytoplasm and the nucleus in eukaryotic cells
Cell Signal.
2013
, vol. 
25
 (pg. 
743
-
751
)
[PubMed]
56
Oberholzer
U.
Collart
M.A.
Characterization of NOT5 that encodes a new component of the Not protein complex
Gene
1998
, vol. 
207
 (pg. 
61
-
69
)
[PubMed]
57
Mulder
K.W.
Inagaki
A.
Cameroni
E.
Mousson
F.
Winkler
G.S.
De Virgilio
C.
Collart
M.A.
Timmers
H.T.
Modulation of Ubc4p/Ubc5p-mediated stress responses by the RING-finger-dependent ubiquitin-protein ligase Not4p in Saccharomyces cerevisiae
Genetics
2007
, vol. 
176
 (pg. 
181
-
92
)
[PubMed]
58
Laribee
R.N.
Shibata
Y.
Mersman
D.P.
Collins
S.R.
Kemmeren
P.
Roguev
A.
Weissman
J.S.
Briggs
S.D.
Krogan
N.J.
Strahl
B.D.
CCR4/NOT complex associates with the proteasome and regulates histone methylation
Proc. Natl. Acad. Sci. U.S.A.
2007
, vol. 
104
 (pg. 
5836
-
5841
)
[PubMed]
59
Mersman
D.P
Harmeyer
K.M.
Briggs
S.D.
To be or NOT to be demethylated
Cell Cycle
2009
, vol. 
15
 (pg. 
2135
-
2137
)
60
Cooper
K.F.
Scarnati
M.S.
Krasley
E.
Mallory
M.J
Jin
C.
Law
M.J.
Strich
R.
Oxidative-stress-induced nuclear to cytoplasmic relocalization is required for Not4-dependent cyclin C destruction
J. Cell Sci.
2012
, vol. 
125
 (pg. 
1015
-
1026
)
[PubMed]
61
Gulshan
K.
Thommandru
B.
Moye-Rowley
W.S.
Proteolytic degradation of the Yap1 transcription factor is regulated by subcellular localization and the E3 ubiquitin ligase Not4
J. Biol. Chem.
2012
, vol. 
287
 (pg. 
26796
-
26805
)
[PubMed]
62
Panasenko
O.O.
Landrieux
E.
Feuermann
M.
Finka
A.
Paquet
N.
Collart
M.A.
The yeast Ccr4-Not complex controls ubiquitination of the nascent-associated polypeptide (NAC-EGD) complex
J. Biol. Chem.
2006
, vol. 
281
 (pg. 
31389
-
31398
)
[PubMed]
63
Panasenko
O.O.
Collart
M.A.
Presence of Not5 and ubiquitinated Rps7A in polysome fractions depends upon the Not4 E3 ligase
Mol. Microbiol.
2012
, vol. 
83
 (pg. 
640
-
653
)
[PubMed]
64
Panasenko
O.O.
The role of the E3 ligase Not4 in cotranslational quality control
Front. Genet.
2014
, vol. 
5
 pg. 
141
 
[PubMed]
65
Bai
Y.
Salvadore
C.
Chiang
Y.C.
Collart
M.A.
Liu
H.Y.
Denis
C.L.
The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4, and NOT5
Mol. Cell. Biol.
1999
, vol. 
19
 (pg. 
6642
-
6651
)
[PubMed]
66
Bhaskar
V.
Basquin
J.
Conti
E.
Architecture of the ubiquitylation module of the yeast Ccr4-Not complex
Structure
2015
, vol. 
23
 (pg. 
921
-
928
)
[PubMed]
67
Bhaskar
V.
Roudko
V.
Basquin
J.
Sharma
K.
Urlaub
H.
Séraphin
B.
Conti
E.
Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex
Nat. Struct. Mol. Biol.
2013
, vol. 
20
 (pg. 
1281
-
1288
)
[PubMed]
68
Collart
M.A.
Struhl
K.
CDC39, an essential nuclear protein that negatively regulates transcription and differentially affects the constitutive and inducible HIS3 promoters
EMBO J.
1993
, vol. 
1
 (pg. 
177
-
186
)
69
Hanzawa
H.
de Ruwe
M.J.
Albert
T.K.
van Der Vliet
P.C.
Timmers
H.T.
Boelens
R.
The structure of the C4C4 ring finger of human NOT4 reveals features distinct from those of C3HC4 RING fingers
J. Biol. Chem.
2001
, vol. 
276
 (pg. 
10185
-
10190
)
[PubMed]
70
Collart
M.A.
Panasenko
O.O.
The Ccr4-Not complex
Gene
2012
, vol. 
492
 (pg. 
42
-
53
)
[PubMed]
71
Panasenko
O.O.
Collart
M.A.
Not4 E3 ligase contributes to proteasome assembly and functional integrity in part through Ecm29
Mol. Cell. Biol.
2011
, vol. 
31
 (pg. 
1610
-
1623
)
[PubMed]
72
Albert
T.K.
Lemaire
M.
van Berkum
N.L.
Gentz
R.
Collart
M.A.
Timmers
H.T.
Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits
Nucleic Acids Res.
2000
, vol. 
28
 (pg. 
809
-
817
)
[PubMed]
73
Inada
T.
Makino
S.
Novel roles of the multi-functional CCR4-NOT complex in post-transcriptional regulation
Front. Genet.
2014
, vol. 
5
 pg. 
135
 
[PubMed]
74
Chen
C.
Ito
K.
Takahashi
A.
Wang
G.
Suzuki
T.
Nakazawa
T.
Yamamoto
T.
Yokoyama
K.
Distinct expression patterns of the subunits of the CCR4-NOT deadenylase complex during neural development
Biochem. Biophys. Res. Commun.
2011
, vol. 
411
 (pg. 
360
-
364
)
[PubMed]
75
Ito
K.
Takahashi
A.
Morita
M.
Suzuki
T.
Yamamoto
T.
The role of the CNOT1 subunit of the CCR4-NOT complex in mRNA deadenylation and cell viability
Protein Cell
2011
, vol. 
2
 (pg. 
755
-
763
)
[PubMed]
76
Boland
A.
Chen
Y.
Raisch
T.
Jonas
S.
Kuzuoğlu-Öztürk
D.
Wohlbold
L.
Weichenrieder
O.
Izaurralde
E.
Structure and assembly of the NOT module of the human CCR4-NOT complex
Nat. Struct. Mol. Biol.
2013
, vol. 
20
 (pg. 
1289
-
1297
)
[PubMed]
77
Dagley
M.J.
Gentle
I.E.
Beilharz
T.H.
Pettolino
F.A.
Djordjevic
J.T.
Lo
T.L.
Uwamahoro
N.
Rupasinghe
T.
Tull
D.L.
McConville
M.
, et al. 
Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2
Mol. Microbiol.
2011
, vol. 
79
 (pg. 
968
-
989
)
[PubMed]
78
Neely
G.G.
Kuba
K.
Cammarato
A.
Isobe
K.
Amann
S.
Zhang
L.
Murata
M.
Elmén
L.
Gupta
V.
Arora
S.
, et al. 
A global in vivo Drosophila RNAi screen identifies NOT3 as a conserved regulator of heart function
Cell
2010
, vol. 
141
 (pg. 
142
-
153
)
[PubMed]
79
Morita
M.
Oike
Y.
Nagashima
T.
Kadomatsu
T.
Tabata
M.
Suzuki
T.
Nakamura
T.
Yoshida
N.
Okada
M.
Yamamoto
T.
Obesity resistance and increased hepatic expression of catabolism-related mRNAs in Cnot3+/–mice
EMBO J.
2011
, vol. 
30
 (pg. 
4678
-
4691
)
[PubMed]