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Originally published In Press as doi:10.1074/jbc.M203354200 on May 15, 2002
J. Biol. Chem., Vol. 277, Issue 29, 26276-26280, July 19, 2002
Saccharomyces cerevisiae RNA Polymerase II Is
Affected by Kluyveromyces lactis Zymocin*
Daniel
Jablonowski and
Raffael
Schaffrath§
From the Institut für Genetik, Biologicum,
Martin-Luther-Universität Halle-Wittenberg, Weinbergweg
10, D-06120 Halle (Saale), Germany
Received for publication, April 8, 2002, and in revised form, May 3, 2002
 |
ABSTRACT |
The G1 arrest imposed by
Kluyveromyces lactis zymocin on Saccharomyces
cerevisiae cells requires a functional RNA polymerase II (pol II)
Elongator complex. In studying a link between zymocin and pol II,
progressively truncating the carboxyl-terminal domain (CTD) of pol II
was found to result in zymocin hypersensitivity as did mutations in
four different CTD kinase genes. Consistent with the notion that
Elongator preferentially associates with hyperphosphorylated (II0)
rather than hypophosphorylated (IIA) pol II, the II0/IIA ratio was
imbalanced toward II0 on zymocin treatment and suggests zymocin affects
pol II function, presumably in an Elongator-dependent
manner. As judged from chromatin immunoprecipitations, zymocin-arrested
cells were affected with regards to pol II binding to the
ADH1 promotor and pol II transcription of the
ADH1 gene. Thus, zymocin may interfere with pol II
recycling, a scenario assumed to lead to down-regulation of pol II
transcription and eventually causing the observed G1 arrest.
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INTRODUCTION |
Yeast killer toxins are genetically and biochemically diverse. The
double-stranded RNA-encoded viral toxins KT28 and K1 from Saccharomyces cerevisiae (1) bind to cell wall mannan and
glucan moieties (2, 3), while zymocin, a double-stranded
DNA-encoded three-subunit (  ) protein complex from
Kluyveromyces lactis, requires cell wall chitin for docking
(4, 5). KT28 and K1 use retrograde import (6), block DNA synthesis (7),
or destroy cytoplasmic membrane function through TOK1
K+-channel hyperactivation (8), whereas zymocin arrests
S. cerevisiae by a G1 cell cycle block (9-11).
Expression of the -subunit of zymocin, the -toxin, is sufficient
to mimic this arrest (12, 13). As for the target of -toxin
(TOT),1 mutations in seven
TOT genes lead to zymocin resistance. TOT1-3 and
TOT5-7 are identical with ELP1-6 coding for RNA
polymerase II (pol II) Elongator and TOT4 (KTI12)
specifies an Elongator-associated protein (14-24). In addition, loss
of SIT4, KTI11, and KTI13 results in a
tot phenotype, suggesting these genes may play a role in TOT
function too (25, 26). Elongator is conserved from yeast to man (27),
associates with hyperphosphorylated pol II (II0) (16), and is thought
to play a role in transcription by virtue of its Elp3p subunit, a
histone acetyltransferase (HAT) (17). Consistently, combining deletions
of ELP3 and CTK1 coding for the -subunit of
CTDK-I (28), a transcriptionally relevant pol II carboxyl-terminal
domain (CTD) kinase, is synthetically lethal (29). Reducing the HAT
activity of Elongator phenocopies zymocin resistance (19, 22), implying
that the HAT is essential for K. lactis zymocicity. TOT can
be dissociated from Elongator function by
ELP3/TOT3 mutagenesis, suggesting that Elongator
communicates with -toxin in a HAT-dependent manner (23).
As Elongator is non-essential, it cannot simply be blocked by
-toxin. Instead, its function may be modified so that pol II
activity becomes poisoned. Evidences demonstrating down-regulation of
pol II-dependent genes (22) and expression of partial
zymocin resistance on overproducing Fcp1p, the CTD phosphatase, support
this notion (23).
To study a link between zymocin action and pol II function, we found
progressive CTD truncations and mutations in CTD kinase genes to result
in zymocin hypersensitivity. Remarkably, zymocin treatment led to
accumulation of pol II form II0. As judged from chromatin immune
precipitations (CHIP), zymocin-arrested cells were affected with
regards to pol II binding to and transcription of the ADH1
locus. Our data imply that zymocin affects, in a manner presumably
dependent on Elongator, pol II function, a scenario assumed to lead to
down-regulation of pol II transcription and eventually cause the
observed G1 arrest.
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EXPERIMENTAL PROCEDURES |
All yeast strains used in this study are described in Table
I. Standard YPD (1% yeast extract, 2%
peptone, 2% dextrose) and SD (0.67% yeast nitrogen base, 2%
dextrose) media were prepared as described (30). Zymocin
sensitivity or resistance was assessed using the killer eclipse assay
(31) and zymocin YPD plate assays. The latter involved partial
purification of zymocin from AWJ137 cell-free culture supernatants and
supplementation to YPD plates (5, 23). Zymocin arrest of S. cerevisiae strain LS20 involved partial purification of zymocin
from K. lactis killer AWJ137 grown in YPD flask cultures for
48 h at 30 °C. After centrifugation (6,000 rpm) 50 ml of
cell-free supernatants were mixed with 50 ml of 2× YPD medium and
inoculated with LS20 cells. These were arrested by zymocin on further
incubating for 3-6 h at 30 °C. As controls, untreated LS20 cultures
were incubated for the same period of time. Following harvest (6,000 rpm at 4 °C), cells were disrupted by the glass bead method using a
multivortex (five 60-s bursts at 4 °C) in 500 µl of breaking
buffer B60 (32). After clearing the cell lysates protein content was
measured using the Bio-Rad kit. Identical amounts of total protein
obtained from three independent experiments of untreated and
zymocin-arrested cells were subjected to SDS-PAGE analysis using 6%
gels, electroblotted onto polyvinylidene difluoride membranes
(Immobilon), and probed with mouse monclonal anti-pol IIA and anti-pol
II0 antibodies 8WG16 and H14 (Covance). Protein loadings were compared
using a polyclonal rabbit antibody directed against the - and
-subunits of yeast Pfk1p (33). pol II quantitation used the Image
Master 2D (Amersham Biosciences) program.
CHIPs were carried out as described (34). In brief, untreated and
zymocin-arrested yeast cells grown to
A600 ~1.0 in YPD were cross-linked for
15 min in 1% (v/v) formaldehyde. Following addition of 2.5 ml of 2.5 M glycine and three 1× TBS (20 mM
Tris-HCl, pH 7.6, 137 mM NaCl) washes, cells were lysed
with glass beads in FA lysis buffer (34). Sheared chromatin solution
was added to the anti-CTD and anti-CTD-S5-P antibodies 8WG16 and H14
(Covance) and incubated for 90 min. Following the addition of secondary antibodies coupled to protein A-Sepharose CL-4B beads (Amersham Biosciences) and incubation for a further 60 min, chromatin was immunoprecipitated, washed, and incubated at 65 °C for 10 min. Following SDS treatment, chromatin was subjected to protease treatment and reversal of the cross-links (35). For all subsequent PCR reactions
a single preparation of immunoprecipitated chromatin served as
template. PCR conditions and electrophoresis were as described (34).
Primers used were as follows: ADH 235, TTC CTT CCT TCA TTC
ACG CAC ACT; ADH 13, GTT GAT TGT ATG CTT GGT ATA GCT TG;
ADH146, ACG CTT GGC ACG GTG ACT G; ADH372, ACC
GTC GTG GGT GTA ACC AGA; ADH935, GTT TGG TCA AGT CTC CAA
TCA AGG; ADH1271, ATA AGA GCG ACC TCA TGC TAT ACC;
IGRVII-1, CCC ACC ACC GAT AAC GAC AAG; and IGRVII-2, CCA ACA AAT GAG
GCG GAA CC.
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RESULTS |
Effects of Mutations in pol II CTD Kinase Genes on Zymocin
Sensitivity--
Our previous findings that pol II Elongator mutations
confer zymocin resistance (22) and that overexpression of Fcp1p, the pol II CTD-phosphatase (36), results in reduction of zymocin sensitivity (23) indicated a functional link between zymocin, pol II,
and Elongator. To ask whether pol II activity is correlated with
expression of zymocin sensitivity we studied the effects of genetic
conditions known or assumed to impair pol II activity on the response
of a yeast cell to zymocin. Of the four yeast cyclin-dependent kinases (CDKs) involved in pol II CTD
phosphorylation, we assayed deletions of
SRB10/SRB11 and
CTK1/CTK2/CTK3 and partial loss-of-function mutations in KIN28 and
BUR1/BUR2 (28, 34, 37-41). As became evident
from increased sizes of eclipses formed in a K. lactis/S.
cerevisiae colony interaction killer eclipse assay,
bur1-2 and bur2-1 mutants were hypersensitive
toward zymocin (Fig. 1A).
Similarly, deletion of CTK1, the -subunit structural gene
of the CTDK-I kinase, resulted in zymocin hypersensitivity, whereas
disruption of the - (CTK2) and - (CTK3)
subunit genes failed to have any effect (Fig. 1B). Moreover,
disruption of either the SRB10 CTD kinase gene or its
SRB11 cyclin gene led to zymocin hypersensitivity as judged
from YPD zymocin plate (Fig. 1C) and killer eclipse assays
(not shown); thus, compared with their isogenic wild-type parent,
srb10 and srb11 cells became arrested by
less amounts of zymocin. Consistently, a KIN28 mutant
(kin28T17D, Ref. 34) with reduced kinase activity was found
to be zymocin-hypersensitive, too, when tested in eclipse (Fig.
1D) or zymocin plate assays (not shown). In conclusion,
genetic scenarios that impair pol II function by (partial) loss of
CTD-CDK activities alter the responsivenss of a yeast cell to zymocin
and cause hypersensitive phenotypes. Thus, cells with reduced CDK
activities require less amounts of zymocin than wild-type cells to
become arrested in G1. This finding strongly suggests a
functional link between zymocin mode of action and the CTD of pol
II.

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Fig. 1.
Effect of mutations in the CTD-CDK genes on
zymocin sensitivity expression of S. cerevisiae.
A, killer eclipse assay with bur1-2 and
bur2-1 mutants. The indicated strains were tested against a
K. lactis strain (upper row, killer strain
AWJ137; lower row, non-killer strain NK40) and incubated for
1 day at 30 °C. Eclipse formation around the killer strain indicates
zymocin sensitivity. tot3 cells served as
zymocin-resistant control. B, YPD zymocin plate assays with
ctk1 , ctk2 , and ctk3 cells.
The indicated strains were serially diluted and spotted onto YPD-rich
medium lacking zymocin (control) or being supplemented with the
indicated amounts of zymocin (percent, v/v). C, YPD zymocin
plate assays with srb10 and srb11 cells.
Strains were prepared as in the legend to B. D, killer
eclipse assay with the kin28 mutant. Strains were processed
as described in the legend to A. Note that all CTD-CDK
mutants express hypersensitivity toward the K. lactis zymocin.
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Effects of pol II-CTD Truncation Mutations on Zymocin
Sensitivity--
Inspired by reports that underproduction of pol II
(42) phencopies the effects of CTD truncation mutations,
i.e. slow growth, inositol auxotrophy, and thermosensitivity
(43, 44), and by our observation that pol II underassembly leads to
zymocin hypersensitivity (23), we studied the effects of progressively
truncating the CTD of pol II on the response of a yeast cell to
zymocin. As can be deduced from the appropriate YPD zymocin plate
assays presented in Fig. 2B,
most viable CTD truncations (Ref. 45; Fig. 2, pV8, pV4, pV3, pV7, and pV19)
behaved comparable with wild-type full-length CTD and unaltered with
respect to zymocin sensitivity phenotypes on plates supplemented with
45-50% (v/v) zymocin. However, the penultimate and ultimate viable
CTD truncations (Ref. 45; Fig. 2, pV20 and pV17),
and all progressive ones reported to express conditional phenotypes
(Ref. 45; Fig. 2, pC2, pC23, pC6,
pC1, and pC3) were found to confer
hypersensitivity to zymocin (Fig. 2). Thus, hypersensitive phenotypes
could be correlated with conditional phenotypes of CTD truncations.
This appears to be consistent with the effects of pol II underassembly
on expression of hypersensitivity toward zymocin (23). Taken together
with the above findings on the effect of CTD-CDK mutants on zymocin
sensitivity, other scenarios that lead to an overall reduction of pol
II function convert sensitive yeast cells into hypersensitive ones.
This reinforces the notion that zymocin action is linked to a
functional pol II CTD.

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Fig. 2.
Effect of progressive CTD truncation
mutations on zymocin sensitivity expression of S. cerevisiae. A, the degree of CTD truncation
tested for zymocin sensitivity expression is shown for each mutant on
the horizontal axis, and the plasmid-encoded allele is
indicated (e.g. pV8). Viable CTD truncations are
distinguished from conditional and lethal ones. B, YPD
zymocin plate assays. 10-Fold serial dilutions of strains carrying a
wild-type (wt) CTD and progressive CTD truncation mutations
were tested for zymocin sensitivity expression as described in the
legend to Fig. 1B. tot3 cells served as
zymocin-resistant control. Note that progressively truncating the CTD
causes cells to express a zymocin hypersensitivity phenotype.
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pol II CTD Phosphorylation States in Response to Zymocin
Treatment--
Since pol II Elongator is essential for zymocicity (22)
and stably associates with pol II form II0 (16), we next asked whether
zymocin may require Elongator to be associated with II0 and whether
zymocin influences the phosphorylation equlibrium of pol II. To do so,
identical protein amounts obtained from untreated and zymocin-arrested
cells were subjected to SDS-PAGE analysis, electroblotted, and
immunoprobed with anti-IIA (8WG16) or anti-II0 (H14) antibodies to
distinguish hypo- from hyperphosphorylated pol II forms IIA and II0. As
illustrated in Fig. 3A, this
analysis revealed that while untreated cells had unaltered II0/IIA
ratios over a period of 6 h, zymocin treatment had an effect on
the phosphorylation states of pol II; 3 h post-treatment, pol II
form II0 accumulated 2-fold compared with the same time point of the
untreated sample, and pol II form IIA remained almost unchanged; 6 h post-treatment, however, pol II form IIA drastically declined,
consistent with a 5-fold increase of pol II form II0. Thus, on treating
cells with zymocin, the ratio between pol II forms IIA and II0 became dramatically shifted toward the latter, indicating that
zymocin-arrested cells accumulate pol II in its hyperphosphorylated
form II0. Similarly, pol II form II0 was found to accumulate in
zymocin-arrested cells that were subjected to cell fractionation, while
form IIA declined after zymocin treatment (Fig. 3B). These
results suggest that zymocin action interferes with pol II function by
preventing preinitiation complex formation-competent pol II form IIA to
be recycled from elongating form II0 during the pol II transcription
cycle.

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Fig. 3.
Effect of zymocin application on pol II
phosphorylation states. A, identical protein amounts
obtained from zymocin-untreated and zymocin-arrested cells after 3 and
6 h were subjected to 6% SDS-PAGE and immunoprobed with
monoclonal antibodies specific for the hypophosphorylated CTD of pol II
(IIA) and the hyperphosphorylated CTD of pol II (II0). Protein loading
was followed using a polyclonal antiserum specific for the - and
-subunits of phosphofructokinase 1 (Pfk1p) (33).
B, identical protein amounts obtained from cell
fractionation of untreated cells and cells arrested with zymocin for
3 h were subjected to 6% SDS-PAGE and immunoprobed with
antibodies specific for IIA and II0 (see A). Protein loading
was followed as described in the legend to A.
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pol II Transcription of and Promoter Binding to the ADH1 Locus in
Response to Zymocin--
As judged from reverse
transcriptase-PCR and Northern hybridization studies, zymocin
appears to preferentially affect pol II rather than pol I or pol III
function (22). Therefore, we decided to study pol II action in
untreated and zymocin-arrested cells while being bound to and
transcribing through the ADH1 locus. To do so, CHIPs were
carried out with anti-IIA (8WG16) or anti-II0 (H14) antibodies and
subjected to PCR using primers to amplify DNA fragments specific for
the ADH1 promoter or its coding sequences (Fig.
4A). Consistent with a
previous CHIP study (34), our analysis demonstrated that in untreated
cells the predominant fractions of pol II form IIA are found at the
ADH1 promoter and the early coding sequence (Fig.
4B, left upper panel), while hyperphosphorylated pol II form II0 was preferentially found to associate with the promoter. As soon as it clears the promoter there is a significant decrease of H14-mediated recognition, indicating that the CTD of pol II
is subject to dephosphorylation (Fig. 4B, left middle panel). Thus, initially in early elongation pol II is heavily phosphorylated on the Ser5 of CTD, whereas later in
elongation Ser5 becomes dephosphorylated (34). In striking
contrast to this pattern were CHIPs performed with zymocin-arrested
cells; while pol IIA bound to the promoter was drastically reduced
compared with untreated cells, it was found to be predominantly
associated within the early coding sequence of the ADH1 gene
after zymocin application (Fig. 4B, right upper
panel). As for pol II form II0, zymocin treatment significantly
interfered with its capability to bind to the ADH1 promoter,
resulting in a steep decrease compared with the parallel experiment
without zymocin (Fig. 4B, right middle panel).
While the latter finding suggests that zymocin-arrested cells are
transcriptionally impaired with regards to recruiting pol II form IIA
to the ADH1 promoter, the former observations may be
interpreted as pol II recognized by the 8WG16 antibody being stalled
during early ADH1 transcription elongation. Taken together,
these CHIP studies suggest that zymocin action is linked to pol II
function and imply that zymocin negatively interferes with the pol II
transcription cycle by affecting the recycling of initiation-competent
IIA from elongation-competent II0.

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Fig. 4.
Effect of zymocin treatment on pol II binding
to and transcription through the ADH1 locus.
A, schematic representation of the primer pairs used to
PCR-amplify regions upstream of and within the ADH1 locus
following CHIP experiments on untreated and zymocin-arrested cells. The
open bar represents the open reading frame
(ADH1); the gray bars indicate PCR products with
coordinates relative to the initiation codon of the open reading
frame. B, CHIP/PCR. Cross-linked and sheared
chromatin obtained from zymocin-untreated and zymocin-arrested cells
was immunoprecipitated with the indicated antibodies. After reversal of
cross-linking and purification of the DNA, PCR was used to test for the
presence of promotor or coding sequences (CDS). Each
CHIP/PCR panel contained a second primer pair that amplifies an
intergenic region (IGR) of chromosome VII, thus providing an
internal background control. Input (bottom) shows the signal
from the chromatin before immunoprecipitation.
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DISCUSSION |
The recent identification of the pol II Elongator complex as TOT,
the putative target of the K. lactis zymocin (22), has implied a link between zymocin action and pol II transcriptional elongation (23). Since TOT/Elongator is dispensable for life, its
function cannot simply be blocked by zymocin (and its -toxin subunit). Instead, it has been proposed that Elongator becomes modified
so that pol II activity is poisoned (22, 23). To check this model we
asked whether cells, compromised for pol II function, are altered with
respect to their response to zymocin too. Genetic scenarios leading to
reduced pol II function by mutating individual pol II CTD-CDK genes or
by progressively truncating the CTD itself were found to confer zymocin
hypersensitivity. Thus, the ability of a cell to express wild-type
zymocin sensitivity is at least in part determined by the length of the
CTD and the presence of each of the four known yeast CTD-CDK genes.
Presumed stability of the CTD of the pol II subunit in these mutants
was not affected (and for CTD truncation variants this has been shown; Ref. 44), but rather assembly of pol II holoenzyme was interfered with
so that its function was compromised with respect to interaction with
mediator (during initiation) or with Elongator (on CTD phosphorylation and promoter clearance); both scenarios, CTD truncation and CTD-CDK mutation, would ultimately lead to a decline of pol II activity. Consistently, CTD truncations and CTD-CDK mutations phenocopy the
effects of underproducing the largest CTD-subunit of pol II, Rpb1p,
which include slow growth, temperature sensitivity, inositol auxotrophy, and zymocin hypersensitivity (23, 42, 45). Together with
the facts that zymocin action requires a functional pol II Elongator
complex and that overexpressing Fcp1p, the CTD-phosphatase of pol II,
renders cells partially zymocin-resistant (23), these findings suggest
that zymocin action requires Elongator to be associated with pol II0
while elongating. Zymocin hypersenitivity due to the above conditions
(pol II underassembly, CTD deletions, and CTD-CDK mutations) may imply
that in the mutant cells the equilibrium between pol II-free and pol
II-bound Elongator is imbalanced, eventually leading to a net increase
of Elongator capable of signaling the presence of zymocin. In
support of this, the requirement of TOT for -toxin and zymocin
action was shown to be separable from Elongator wild-type function by
TOT3/ELP3 mutagenesis, suggesting that Elongator
communicates with -toxin (directly or indirectly) in a manner
dependent on its HAT subunit (23).
How to integrate these findings in a model that explains both
requirement of Elongator for and involvement of pol II in zymocin action? Our observations that zymocin-arrested cells accumulate pol II
form II0 and that binding of pol II to the ADH1 promoter is
dramatically reduced following zymocin treatment are indicative for pol
II function being affected. Consistently, we have demonstrated down-regulation of pol II activity (22) in the presence of zymocin, while pol I activity largely remains unaffected (22). Thus, zymocin
appears to preferentially affect pol II rather than pol I (or pol III)
function. An attractive, though speculative, model as to how zymocin
might work at the molecular level involves -toxin to transform
Elongator so that pol II becomes limiting. If this conversion conferred
a dominant negative effect onto pol II function for example by blocking
pol II in its II0 form, zymocin-treated cells would be expected to be
seriously affected with regards to pol II recycling during
transcription. In favor of this are our findings showing that the
IIA/II0 ratio is imbalanced toward form II0 following zymocin
application. Also, the CHIP studies demonstrate that form IIA
predominantly accumulates during early transcription elongation within
the ADH1 gene, while pol II0 is significantly impaired with
regards to ADH1 promoter binding and clearance. Thus, pol II
recycling necessary for preinitiation complex formation is likely
affected by zymocin. Such a scenario can be ultimately envisaged to
result in a decline of overall pol II activity and might eventually,
due to a transcriptional shutdown of the START-specific gene program,
culminate in the observed G1 cell cycle arrest. Consistent
with this notion are temperature-sensitive mutations in the largest CTD
subunits of yeast and hamster pol II, which cause a conditional
G1 arrest at START (46, 47). Thus, cell cycle progression
and START execution appear to be particularly sensitive to an impaired
pol II function.
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ACKNOWLEDGEMENTS |
We thank S. Buratowski, A. Greenleaf, D. Skaar, G. Prelich, and R. Young for providing yeast CTD and CTD-CDK
mutants. We also thank K. Breunig for critically reading the manuscript.
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FOOTNOTES |
*
This work was supported by a grant from the Deutsche
Forschungsgemeinschaft (Scha 750/2) (to R. S.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
Supported by a grant sponsored by the "Graduierten
Förderung des Landes Sachsen-Anhalt."
§
To whom correspondence should be addressed. Tel.:
49-345-5526333; Fax: 49-345-5527151; E-mail:
schaffrath@genetik.uni-halle.de.
Published, JBC Papers in Press, May 15, 2002, DOI 10.1074/jbc.M203354200
 |
ABBREVIATIONS |
The abbreviations used are:
TOT, -toxin
target;
pol II, RNA polymerase II;
HAT, histone
acetyltransferase;
CHIP, chromatin immune precipitation;
CTD, carboxyl-terminal domain;
IIA, hypophosphorylated pol II;
II0, hyperphosphorylated pol II;
CDK, cyclin-dependent
kinase.
 |
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