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From the § Department of Biochemistry, Saint Louis
University School of Medicine, St. Louis, Missouri 63104 and the
Received for publication, June 8, 2002, and in revised form, June 10, 2002
The DNA of eukaryotes is wrapped around
nucleosomes and packaged into chromatin. Covalent modifications of the
histone proteins that comprise the nucleosome alter chromatin structure
and have major effects on gene expression. Methylation of lysine 4 of
histone H3 by COMPASS is required for silencing of genes located near chromosome telomeres and within the rDNA (Krogan, N. J, Dover, J.,
Khorrami, S., Greenblatt, J. F., Schneider, J., Johnston, M., and
Shilatifard, A. (2002) J. Biol. Chem. 277, 10753-10755; Briggs, S. D., Bryk, M., Strahl, B. D., Cheung,
W. L., Davie, J. K., Dent, S. Y., Winston, F., and
Allis, C. D. (2001) Genes. Dev. 15, 3286-3295). To
learn about the mechanism of histone methylation, we surveyed the
genome of the yeast Saccharomyces cerevisiae for genes
necessary for this process. By analyzing ~4800 mutant
strains, each deleted for a different non-essential gene, we discovered that the ubiquitin-conjugating enzyme Rad6 is required for methylation of lysine 4 of histone H3. Ubiquitination of histone H2B on lysine 123 is the signal for the methylation of histone H3, which leads to
silencing of genes located near telomeres.
Heritable, quasistable modifications of histone proteins, such as
acetylation, phosphorylation, and methylation, play essential roles in
the regulation of gene expression in eukaryotic organisms and have been
proposed to be required for development and cellular commitment in
metazoans (1-3). Histone acetylations on histones H3 and H4 are the
best characterized covalent modifications of histones and have been
demonstrated to have wide ranging effects on the regulation of gene
expression (1). Phosphorylation has been demonstrated to be an
important modification of histone in transcriptional activation,
condensation of chromosomes during mitosis and meiosis, and regulation
of cell division.
Methylation of lysine 4 in the amino-terminal tail of histone H3,
mediated by a multiprotein complex we call
COMPASS1 (complex
of proteins associated with Set1) (4-7,
9), is required for silencing of expression of genes located near
chromosome telomeres and within the rDNA (5, 6). We and others have
demonstrated that COMPASS includes Set1, a member of the
chromatin-associated proteins (the Trithorax (Trx) group) that possess
a sequence motif called the SET domain, and seven other polypeptides
(4-7, 9). The SET domain takes its name from the Drosophila
proteins Su(var)3-9, Enhancer of zeste (E(z)),
and Trx. Also, COMPASS contains another yeast
protein related to the human Trx protein ASH2. SET domain-containing proteins have been implicated in histone methylation and regulation of
transcription in several organisms (5, 8-12). Although the SET
domain-containing proteins play fundamental roles in development and
oncogenesis, their molecular function is poorly understood (13-16).
To better understand the mechanism of histone H3 lysine 4 methylation,
we surveyed the genome of the yeast Saccharomyces cerevisiae for genes necessary in this process. Analysis of ~4800
mutant strains resulted in the discovery of the ubiquitin-conjugating enzyme Rad6 as a protein required for methylation of lysine 4 of
histone H3. We have demonstrated that ubiquitination of histone H2B on
lysine 123 is the signal for the methylation of histone H3 by COMPASS,
which leads to silencing of genes located near telomeres.
Preparation of Yeast Cell Extracts from 96-well
Plates--
Using a 96-well pinning device, the entire collection of
4800 yeast non-essential gene deletion mutants was inoculated from Preparation of Total Yeast Cell Extracts and Analysis for Histone
H3 Lys-4 Methylation--
Yeast cells were grown to mid-log
phase in YPD medium, pelleted, washed with distilled water, pelleted,
and resuspended in lysis buffer (20 mM Tris, pH 7.5, 50 mM KCl, 1 mM EDTA, 0.1% Nonidet P-40, 1 mM dithiothreitol, and fresh protease and phosphatase inhibitors (1 µg/ml aprotinin, leupeptin, and pepstatin A, 1 mM phenylmethylsulfonyl fluoride, 1 µM
microcystin-LR, 2 mM
p-chloromercuriphenylsulfonic acid). Cells were then
disrupted by vortexing with glass beads (0.5 mm, Biospec Products) for
15 min at 4 °C. The bottoms of the microcentrifuge tubes were
punctured, and cell extracts were recovered into a larger tube by brief
centrifugation in a microcentrifuge. The lysate was clarified by
centrifugation at 20,000 × g for 30 min, subjected to
SDS-PAGE, transferred to nitrocellulose membrane, and probed with
anti-methylhistone antiserum at 1:1000 dilution followed by
detection of the bound antibody with horseradish
peroxidase-conjugated anti-rabbit IgG secondary antibodies
(1:10,000 dilution).
Development of a Biochemical Screen in 96-well Plates to Identify
Genes Essential for Lys-4 Methylation of Histone H3--
To learn more
about the mechanism of histone methylation by COMPASS, we sought to
identify all the (non-essential) proteins in S. cerevisiae
necessary for methylation of Lys-4 of histone H3. As described under
"Materials and Methods," we developed a method to survey the genome
of S. cerevisiae for genes required for this histone
modification by testing extracts of each of the ~4800 viable mutants
for the presence of Lys-4-methylated histone H3. Mutants missing a
component of COMPASS are defective in this histone H3 modification. As
shown in Fig. 1A, cells
deleted for set1 are defective for the methylation of Lys-4
of histone H3. When this assay was performed in a 96-well plate, the
mutant cell missing Cps50/Yar003 was found to be defective for the
methylation of Lys-4 of histone H3. However, all of the other 95 mutants in this microtiter plate possess this modification (Fig.
1B).
Rad6 Is Essential for Lys-4 Methylation of Histone
H3--
Screening of all 52 microtiter plates containing the 4827 mutants we tested revealed that the rad6 deletion mutant is
defective in histone H3 Lys-4 methylation (Fig.
2A). This was confirmed by
testing histone H3 Lys-4 methylation in two independently generated rad6 mutants and the homozygous diploid generated from them
(Fig. 2, B and C). Also, the H3 Lys-4
methylation-deficient phenotype of the rad6 Lysine 123 of Rad6 Is Essential for Lys-4 Methylation of Histone
H3--
Rad6 is a ubiquitin-conjugating enzyme (E2) (17) involved in
DNA repair (17, 18), DNA damage-induced mutagenesis (19, 20), meiosis
(21), transposition of retrotransposons (22), and gene silencing (23).
Rad6 catalyzes ubiquitination of Lys-123 of histone H2B (24). It seemed
possible that this modification of histone H2B is responsible for the
requirement of Rad6 for methylation of histone H3. Indeed, histone H3
is not Lys-4-methylated in a strain that is unable to attach ubiquitin
to Lys-123 of histone H2B (due to a change of Lys-123 to Arg) (Fig.
3). We conclude that ubiquitination of
H2B at Lys-123 is required for methylation of Lys-4 of histone H3. This
is consistent with the observation that RAD6 is required for
telomeric gene silencing (23) since methylation of histone H3 Lys-4 is
required for telomeric and rDNA silencing (5, 6).
Involvement of Other Rad6-interacting Proteins in Lys-4 Methylation
of Histone H3--
Several proteins are involved with Rad6 in
diverse cellular processes (17-22). However, our genome-wide survey of
S. cerevisiae revealed that none of the mutants missing
these (non-essential) Rad6-interacting proteins, including those that
act with Rad6 in DNA damage repair (Rad18 and Rex4) and the N-end
rule-dependent protein degradation pathway (Ubr1 and Ubr2),
are involved in methylation of histone H3 Lys-4 (Fig. 3C).
This indicates that Rad6 functions in the regulation of gene expression
by controlling methylation of histone H3 independently of the above proteins.
To define the biochemical characteristics of Rad6 protein, we used
Rad6-specific polyclonal antibody to determine whether Rad6
exists in a large macromolecular complex. Our analysis suggests that at
least a portion of Rad6 protein is found in a large complex in yeast
extracts (Fig. 3D). Perhaps this complex includes an E3
ligase required for the recognition of histone H2B as specific substrate.
Our understanding of the role of the Trx class of proteins in
regulation of gene expression and development is
rudimentary. The Set1 protein of yeast is
similar to the Drosophila and human trithorax proteins (Trx
and MLL, respectively). The Trx protein may function as a DNA-binding
protein and appears to be a regulator of gene expression. Mutations
affecting MLL, the human homologue of Trx, result in the development of
hematological malignancies. Our molecular and biochemical
characterization of the Set1-containing protein complex we call COMPASS
is a first step toward understanding the function of SET
domain-containing proteins in regulation of gene expression. We and
others have now provided evidence that COMPASS is a histone
methyltransferase that catalyzes methylation of Lys-4 of histone H3
(4-7, 9).
Our analysis of ~4800 mutant strains of the yeast S. cerevisiae for a defect in histone H3 Lys-4 methylation resulted
in the discovery of the ubiquitin-conjugating enzyme Rad6 as a protein required for this process (Fig. 4). We have shown that lysine 123 of
histone H2B, which is ubiquitinated by Rad6 (24), is essential for the
methylation of histone H3 by COMPASS, which leads to silencing of genes
located near telomeres. Our results presented here (Fig. 4) suggest
that histone H2B in nucleosomes in "active" regions of chromatin is
recognized by the Rad6 complex and ubiquitinated on Lys-123. The
ubiquitination of histone H2B provides a signal for either direct or
indirect recruitment and/or activation of COMPASS. COMPASS can then
catalyze the methylation of lysine 4 of histone H3, which leads to
silencing of that region of chromosomal DNA (5, 6). An important,
unanswered question is whether ubiquitination and/or methylation of
histones is limited to certain (silent) regions of chromosomes or
whether these modifications occur throughout chromosomes.
Ubiquitination has recently been demonstrated to be involved in the
regulation of gene expression in eukaryotic cells (25). Although the
work presented here cannot at this time rule out a role for proteasomes
in this process, our results suggest a mechanism by which
ubiquitination of histone H2B can control transcription by regulation
of methylation on histone H3 via COMPASS.
We thank Dr. Mary Ann Osley for the gift of
histone H2B mutants.
*
This work was supported in part by American Cancer Society
Grant RP69921801, National Institutes of Health Grant 1R01CA089455, and
a Mallinckrodt Foundation Award (to A. S.) and by funds from the James
S. McDonnell Foundation (to M. J.).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.
¶
A scholar of the Leukemia and Lymphoma Society. To whom
correspondence should be addressed: Dept. of Biochemistry, St. Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO
63104. Tel.: 314-577-8137; Fax: 314-268-5737; E-mail:
shilatia@slu.edu.
Published, JBC Papers in Press, June 17, 2002, DOI 10.1074/jbc.C200348200
The abbreviations used are:
COMPASS, complex of
proteins associated with Set1;
Trx, Trithorax;
E2, ubiquitin-conjugating enzyme;
E3, ubiquitin-protein isopeptide
ligase.
ACCELERATED PUBLICATION
Methylation of Histone H3 by COMPASS Requires Ubiquitination
of Histone H2B by Rad6*
,, and Department of Genetics, Washington University School of
Medicine, St. Louis, Missouri 63110
ABSTRACT
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS AND DISCUSSION
REFERENCES
INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS AND DISCUSSION
REFERENCES
MATERIALS AND METHODS
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS AND DISCUSSION
REFERENCES
80 °C stocks onto agar plates containing YPD (1% yeast extract, 2% proteo-peptone, 2% dextrose) + 200 µg/ml Geneticin
(Invitrogen), allowed to grow for 48 h, and used to inoculate
96-tube PCR plates filled with 100 µl of YPD. After 48 h of
growth at 30 °C the plates were centrifuged at 2000 × g for 10 min. Medium was removed by wrist-snap inversion and
draining into absorbent towels. Plates were then covered and frozen at
80 °C for up to 1 week. Cells were thawed at room temperature,
resuspended in 30 µl of lysis buffer (20 mM Tris, pH 7.5, 50 mM KCl, 1 mM EDTA, 1 mM
dithiothreitol, 0.1% Nonidet P-40, 1 mg/ml Zymolyase 100T), and
incubated at 37 °C for 15 min. 10 µl of 4× Laemmli loading buffer
were added, and the samples were vortexed briefly before heating at
100 °C for 5 min.
RESULTS AND DISCUSSION
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS AND DISCUSSION
REFERENCES
View larger version (35K):
[in a new window]
Fig. 1.
Surveying the S.
cerevisiae genome for genes required for methylation
of lysine 4 of histone H3. A, whole cell extracts from
wild-type S. cerevisiae or a set1 deletion mutant
were tested for the presence of Lys-4-methylated histone H3. Cell
extracts were subjected to 16% SDS-PAGE, blotted to nitrocellulose
membrane, and probed with affinity-purified polyclonal antiserum
(obtained from Abcam) specific for Lys-4 of histone H3 as described
previously (4 and 5). B, whole cell extracts from a
microtiter plate containing 96 different yeast strains, each missing a
different (non-essential) gene, one of which (row e,
lane 3) is the cps50/yar003w mutant
missing a subunit of COMPASS that is essential for histone H3 Lys-4
methylation, were analyzed for this histone modification as described
above. Arrows at position a1 and h3
indicates empty wells as plate markers. WT, wild type;
Meth., methylated.
cells was
complemented by a plasmid containing RAD6 (Fig.
2D).
View larger version (33K):
[in a new window]
Fig. 2.
Rad6 is essential for the methylation of
lysine 4 of histone H3. A, extracts of S. cerevisiae mutants missing one of the ~4800 non-essential genes
were tested for the presence of Lys-4-methylated histone H3. One of the
mutants lacking this histone modification is rad6 (row
f, lane 12). Arrows at position
a1 and h3 indicates empty wells as plate markers.
B and C, extracts of wild-type or two
independently generated mutant strains (MATa and MAT 
, and the
homozygous diploid generated from them) were tested for the presence of
Lys-4-methylated histone H3. D, the methylation-deficient
phenotype of the rad6 cells was complemented by an
episomal vector containing Rad6 cDNA both in rad6 strain and also rad6 homozygous diploid strain.
WT, wild type; Meth.,
methylated.
View larger version (28K):
[in a new window]
Fig. 3.
Ubiquitination of lysine 123 of histone H2B
is essential for Lys-4 methylation of histone H3. A,
schematic representation of histone H2B and its lysine 123 that is
ubiquitinated by Rad6 (24). B, cell extracts from haploid
strains missing htb1-1 and htb2-1 and
containing a CEN-URA3 plasmid with HTA1 and either wild-type
HTB1 or htb1 with lysine 123 converted to
arginine (K123R, generously provided by Mary Anne Osley, Ref. 24) were
analyzed for the presence of Lys-4-methylated histone H3. C,
the presence of methylation of Lys-4 of histone H3 in yeast strains
missing genes encoding Rad6, Ubr1, Ubr2, Rad18, and Rex4 was determined
by subjecting 2000 ng of whole cell extracts from cells deleted for
these genes to 16% SDS-PAGE followed by immunoblotting as described
above. D, the presence of Rad6-containing macromolecular
complexes was determined by the application of wild-type yeast extract
on a Superose-6 PC size exclusion column. 100-µl fractions were
collected, and 25 µl were subjected to SDS-PAGE, then transferred to
nylon membranes, and probed with a Rad6-specific polyclonal antibody.
WT, wild type; Meth., methylated.
View larger version (51K):
[in a new window]
Fig. 4.
Model of the role of Rad6 and COMPASS in
regulating chromatin structure and gene silencing. Histone H2B
within the active region of chromosomal DNA is recognized by the Rad6
protein complex and ubiquitinated on its lysine 123. This
ubiquitination of histone H2B serves as a direct or indirect
recognition signal and/or activation signal for COMPASS, which
catalyzes methylation of lysine 4 of histone H3 and results in
silencing of that region of chromosomal DNA. Ub,
ubiquitination; CH3, methylation.
ACKNOWLEDGEMENT
FOOTNOTES
ABBREVIATIONS
REFERENCES
TOP
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS AND DISCUSSION
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 F. Geng and W. P. Tansey Polyubiquitylation of Histone H2B Mol. Biol. Cell, September 1, 2008; 19(9): 3616 - 3624. [Abstract] [Full Text] [PDF]
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T. Nakagawa, T. Kajitani, S. Togo, N. Masuko, H. Ohdan, Y. Hishikawa, T. Koji, T. Matsuyama, T. Ikura, M. Muramatsu, et al. Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation Genes & Dev., January 1, 2008; 22(1): 37 - 49. [Abstract] [Full Text] [PDF]
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 K. M. Nyswaner, M. A. Checkley, M. Yi, R. M. Stephens, and D. J. Garfinkel Chromatin-Associated Genes Protect the Yeast Genome From Ty1 Insertional Mutagenesis Genetics, January 1, 2008; 178(1): 197 - 214. [Abstract] [Full Text] [PDF]
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I. M. Fingerman, H.-C. Li, and S. D. Briggs A charge-based interaction between histone H4 and Dot1 is required for H3K79 methylation and telomere silencing: identification of a new trans-histone pathway Genes & Dev., August 15, 2007; 21(16): 2018 - 2029. [Abstract] [Full Text] [PDF]
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 T. Tasaki, R. Sohr, Z. Xia, R. Hellweg, H. Hortnagl, A. Varshavsky, and Y. T. Kwon Biochemical and Genetic Studies of UBR3, a Ubiquitin Ligase with a Function in Olfactory and Other Sensory Systems J. Biol. Chem., June 22, 2007; 282(25): 18510 - 18520. [Abstract] [Full Text] [PDF]
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 W. M. Baarends, E. Wassenaar, J. W. Hoogerbrugge, S. Schoenmakers, Z.-W. Sun, and J. A. Grootegoed Increased phosphorylation and dimethylation of XY body histones in the Hr6b-knockout mouse is associated with derepression of the X chromosome J. Cell Sci., June 1, 2007; 120(11): 1841 - 1851. [Abstract] [Full Text] [PDF]
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M. Zofall and S. I. S. Grewal HULC, a Histone H2B Ubiquitinating Complex, Modulates Heterochromatin Independent of Histone Methylation in Fission Yeast J. Biol. Chem., May 11, 2007; 282(19): 14065 - 14072. [Abstract] [Full Text] [PDF]
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S. Kundu, P. J. Horn, and C. L. Peterson SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster Genes & Dev., April 15, 2007; 21(8): 997 - 1004. [Abstract] [Full Text] [PDF]
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R. N. Laribee, Y. Shibata, D. P. Mersman, S. R. Collins, P. Kemmeren, A. Roguev, J. S. Weissman, S. D. Briggs, N. J. Krogan, and B. D. Strahl CCR4/NOT complex associates with the proteasome and regulates histone methylation PNAS, April 3, 2007; 104(14): 5836 - 5841. [Abstract] [Full Text] [PDF]
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K. W. Mulder, A. B. Brenkman, A. Inagaki, N. J. F. van den Broek, and H. Th. Marc Timmers Regulation of histone H3K4 tri-methylation and PAF complex recruitment by the Ccr4-Not complex Nucleic Acids Res., April 1, 2007; 35(7): 2428 - 2439. [Abstract] [Full Text] [PDF]
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R. N. Laribee, S. M. Fuchs, and B. D. Strahl H2B ubiquitylation in transcriptional control: a FACT-finding mission Genes & Dev., April 1, 2007; 21(7): 737 - 743. [Full Text] [PDF]
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J. C. Tanny, H. Erdjument-Bromage, P. Tempst, and C. D. Allis Ubiquitylation of histone H2B controls RNA polymerase II transcription elongation independently of histone H3 methylation Genes & Dev., April 1, 2007; 21(7): 835 - 847. [Abstract] [Full Text] [PDF]
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A. Wood, A. Shukla, J. Schneider, J. S. Lee, J. D. Stanton, T. Dzuiba, S. K. Swanson, L. Florens, M. P. Washburn, J. Wyrick, et al. Ctk Complex-Mediated Regulation of Histone Methylation by COMPASS Mol. Cell. Biol., January 15, 2007; 27(2): 709 - 720. [Abstract] [Full Text] [PDF]
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P.-M. Dehe, B. Dichtl, D. Schaft, A. Roguev, M. Pamblanco, R. Lebrun, A. Rodriguez-Gil, M. Mkandawire, K. Landsberg, A. Shevchenko, et al. Protein Interactions within the Set1 Complex and Their Roles in the Regulation of Histone 3 Lysine 4 Methylation J. Biol. Chem., November 17, 2006; 281(46): 35404 - 35412. [Abstract] [Full Text] [PDF]
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D. G. E. Martin, K. Baetz, X. Shi, K. L. Walter, V. E. MacDonald, M. J. Wlodarski, O. Gozani, P. Hieter, and L. Howe The Yng1p Plant Homeodomain Finger Is a Methyl-Histone Binding Module That Recognizes Lysine 4-Methylated Histone H3 Mol. Cell. Biol., November 1, 2006; 26(21): 7871 - 7879. [Abstract] [Full Text] [PDF]
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R. J. Sims III and D. Reinberg Histone H3 Lys 4 methylation: caught in a bind? Genes & Dev., October 15, 2006; 20(20): 2779 - 2786. [Full Text] [PDF]
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A. Kohler, P. Pascual-Garcia, A. Llopis, M. Zapater, F. Posas, E. Hurt, and S. Rodriguez-Navarro The mRNA Export Factor Sus1 Is Involved in Spt/Ada/Gcn5 Acetyltransferase-mediated H2B Deubiquitinylation through Its Interaction with Ubp8 and Sgf11 Mol. Biol. Cell, October 1, 2006; 17(10): 4228 - 4236. [Abstract] [Full Text] [PDF]
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K. D. Wendt and A. Shilatifard Packing for the germy: the role of histone H4 Ser1 phosphorylation in chromatin compaction and germ cell development Genes & Dev., September 15, 2006; 20(18): 2487 - 2491. [Full Text] [PDF]
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M. G. Lee, C. Wynder, D. A. Bochar, M.-A. Hakimi, N. Cooch, and R. Shiekhattar Functional Interplay between Histone Demethylase and Deacetylase Enzymes. Mol. Cell. Biol., September 1, 2006; 26(17): 6395 - 6402. [Abstract] [Full Text] [PDF]
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 M. A. Osley Regulation of histone H2A and H2B ubiquitylation Brief Funct Genomic Proteomic, September 1, 2006; 5(3): 179 - 189. [Abstract] [Full Text] [PDF]
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J. Wei, L. Zhai, J. Xu, and H. Wang Role of Bmi1 in H2A Ubiquitylation and Hox Gene Silencing J. Biol. Chem., August 11, 2006; 281(32): 22537 - 22544. [Abstract] [Full Text] [PDF]
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K. Tenney, M. Gerber, A. Ilvarsonn, J. Schneider, M. Gause, D. Dorsett, J. C. Eissenberg, and A. Shilatifard Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling PNAS, August 8, 2006; 103(32): 11970 - 11974. [Abstract] [Full Text] [PDF]
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J. C. Game, M. S. Williamson, T. Spicakova, and J. M. Brown The RAD6/BRE1 Histone Modification Pathway in Saccharomyces Confers Radiation Resistance Through a RAD51-Dependent Process That Is Independent of RAD18 Genetics, August 1, 2006; 173(4): 1951 - 1968. [Abstract] [Full Text] [PDF]
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A. Shukla, N. Stanojevic, Z. Duan, T. Shadle, and S. R. Bhaumik Functional Analysis of H2B-Lys-123 Ubiquitination in Regulation of H3-Lys-4 Methylation and Recruitment of RNA Polymerase II at the Coding Sequences of Several Active Genes in Vivo J. Biol. Chem., July 14, 2006; 281(28): 19045 - 19054. [Abstract] [Full Text] [PDF]
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W. Zhang, X. Xia, M. R. Reisenauer, C. S. Hemenway, and B. C. Kone Dot1a-AF9 Complex Mediates Histone H3 Lys-79 Hypermethylation and Repression of ENaC{alpha} in an Aldosterone-sensitive Manner J. Biol. Chem., June 30, 2006; 281(26): 18059 - 18068. [Abstract] [Full Text] [PDF]
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M. G. Rosenfeld, V. V. Lunyak, and C. K. Glass Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response Genes & Dev., June 1, 2006; 20(11): 1405 - 1428. [Abstract] [Full Text] [PDF]
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J. E. Mueller, M. Canze, and M. Bryk The Requirements for COMPASS and Paf1 in Transcriptional Silencing and Methylation of Histone H3 in Saccharomyces cerevisiae Genetics, June 1, 2006; 173(2): 557 - 567. [Abstract] [Full Text] [PDF]
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J. K. Sims, S. I. Houston, T. Magazinnik, and J. C. Rice A Trans-tail Histone Code Defined by Monomethylated H4 Lys-20 and H3 Lys-9 Demarcates Distinct Regions of Silent Chromatin J. Biol. Chem., May 5, 2006; 281(18): 12760 - 12766. [Abstract] [Full Text] [PDF]
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A. Shukla, N. Stanojevic, Z. Duan, P. Sen, and S. R. Bhaumik Ubp8p, a Histone Deubiquitinase Whose Association with SAGA Is Mediated by Sgf11p, Differentially Regulates Lysine 4 Methylation of Histone H3 In Vivo. Mol. Cell. Biol., May 1, 2006; 26(9): 3339 - 3352. [Abstract] [Full Text] [PDF]
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H. Qiu, C. Hu, C.-M. Wong, and A. G. Hinnebusch The Spt4p Subunit of Yeast DSIF Stimulates Association of the Paf1 Complex with Elongating RNA Polymerase II Mol. Cell. Biol., April 15, 2006; 26(8): 3135 - 3148. [Abstract] [Full Text] [PDF]
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A. Wood and A. Shilatifard Transcriptional blackjack with p21. Genes & Dev., March 15, 2006; 20(6): 643 - 647. [Full Text] [PDF]
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S. Huang, M. Litt, and G. Felsenfeld Methylation of histone H4 by arginine methyltransferase PRMT1 is essential in vivo for many subsequent histone modifications Genes & Dev., August 15, 2005; 19(16): 1885 - 1893. [Abstract] [Full Text] [PDF]
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R. G. Gardner, Z. W. Nelson, and D. E. Gottschling Ubp10/Dot4p Regulates the Persistence of Ubiquitinated Histone H2B: Distinct Roles in Telomeric Silencing and General Chromatin Mol. Cell. Biol., July 15, 2005; 25(14): 6123 - 6139. [Abstract] [Full Text] [PDF]
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F. Miao and R. Natarajan Mapping Global Histone Methylation Patterns in the Coding Regions of Human Genes Mol. Cell. Biol., June 1, 2005; 25(11): 4650 - 4661. [Abstract] [Full Text] [PDF]
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 H K Kinyamu, J Chen, and T K Archer Linking the ubiquitin-proteasome pathway to chromatin remodeling/modification by nuclear receptors J. Mol. Endocrinol., April 1, 2005; 34(2): 281 - 297. [Abstract] [Full Text] [PDF]
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W. M. Baarends, E. Wassenaar, R. van der Laan, J. Hoogerbrugge, E. Sleddens-Linkels, J. H. J. Hoeijmakers, P. de Boer, and J. A. Grootegoed Silencing of Unpaired Chromatin and Histone H2A Ubiquitination in Mammalian Meiosis Mol. Cell. Biol., February 1, 2005; 25(3): 1041 - 1053. [Abstract] [Full Text] [PDF]
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K. Ingvarsdottir, N. J. Krogan, N. C. T. Emre, A. Wyce, N. J. Thompson, A. Emili, T. R. Hughes, J. F. Greenblatt, and S. L. Berger H2B Ubiquitin Protease Ubp8 and Sgf11 Constitute a Discrete Functional Module within the Saccharomyces cerevisiae SAGA Complex Mol. Cell. Biol., February 1, 2005; 25(3): 1162 - 1172. [Abstract] [Full Text] [PDF]
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X. Zhang, A. Kolaczkowska, F. Devaux, S. L. Panwar, T. C. Hallstrom, C. Jacq, and W. S. Moye-Rowley Transcriptional Regulation by Lge1p Requires a Function Independent of Its Role in Histone H2B Ubiquitination J. Biol. Chem., January 28, 2005; 280(4): 2759 - 2770. [Abstract] [Full Text] [PDF]
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T. Xiao, C.-F. Kao, N. J. Krogan, Z.-W. Sun, J. F. Greenblatt, M. A. Osley, and B. D. Strahl Histone H2B Ubiquitylation Is Associated with Elongating RNA Polymerase II Mol. Cell. Biol., January 15, 2005; 25(2): 637 - 651. [Abstract] [Full Text] [PDF]
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J. Fang, T. Chen, B. Chadwick, E. Li, and Y. Zhang Ring1b-mediated H2A Ubiquitination Associates with Inactive X Chromosomes and Is Involved in Initiation of X Inactivation J. Biol. Chem., December 17, 2004; 279(51): 52812 - 52815. [Abstract] [Full Text] [PDF]
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R. J. Sims III, R. Belotserkovskaya, and D. Reinberg Elongation by RNA polymerase II: the short and long of it Genes & Dev., October 15, 2004; 18(20): 2437 - 2468. [Abstract] [Full Text] [PDF]
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K. Sawada, Z. Yang, J. R. Horton, R. E. Collins, X. Zhang, and X. Cheng Structure of the Conserved Core of the Yeast Dot1p, a Nucleosomal Histone H3 Lysine 79 Methyltransferase J. Biol. Chem., October 8, 2004; 279(41): 43296 - 43306. [Abstract] [Full Text] [PDF]
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R. van der Laan, E.-J. Uringa, E. Wassenaar, J. W. Hoogerbrugge, E. Sleddens, H. Odijk, H. P. Roest, P. de Boer, J. H. J. Hoeijmakers, J. A. Grootegoed, et al. Ubiquitin ligase Rad18Sc localizes to the XY body and to other chromosomal regions that are unpaired and transcriptionally silenced during male meiotic prophase J. Cell Sci., October 1, 2004; 117(21): 5023 - 5033. [Abstract] [Full Text] [PDF]
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N. J. Krogan, K. Baetz, M.-C. Keogh, N. Datta, C. Sawa, T. C. Y. Kwok, N. J. Thompson, M. G. Davey, J. Pootoolal, T. R. Hughes, et al. Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4 PNAS, September 14, 2004; 101(37): 13513 - 13518. [Abstract] [Full Text] [PDF]
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G. Gill SUMO and ubiquitin in the nucleus: different functions, similar mechanisms? Genes & Dev., September 1, 2004; 18(17): 2046 - 2059. [Abstract] [Full Text] [PDF]
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H. P. Roest, W. M. Baarends, J. de Wit, J. W. van Klaveren, E. Wassenaar, J. W. Hoogerbrugge, W. A. van Cappellen, J. H. J. Hoeijmakers, and J. A. Grootegoed The Ubiquitin-Conjugating DNA Repair Enzyme HR6A Is a Maternal Factor Essential for Early Embryonic Development in Mice Mol. Cell. Biol., June 15, 2004; 24(12): 5485 - 5495. [Abstract] [Full Text] [PDF]
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E. Citterio, R. Papait, F. Nicassio, M. Vecchi, P. Gomiero, R. Mantovani, P. P. Di Fiore, and I. M. Bonapace Np95 Is a Histone-Binding Protein Endowed with Ubiquitin Ligase Activity Mol. Cell. Biol., March 15, 2004; 24(6): 2526 - 2535. [Abstract] [Full Text] [PDF]
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L. Dong and C. W. Xu Carbohydrates Induce Mono-ubiquitination of H2B in Yeast J. Biol. Chem., January 16, 2004; 279(3): 1577 - 1580. [Abstract] [Full Text] [PDF]
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J. A. Daniel, M. S. Torok, Z.-W. Sun, D. Schieltz, C. D. Allis, J. R. Yates III, and P. A. Grant Deubiquitination of Histone H2B by a Yeast Acetyltransferase Complex Regulates Transcription J. Biol. Chem., January 16, 2004; 279(3): 1867 - 1871. [Abstract] [Full Text] [PDF]
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C.-F. Kao, C. Hillyer, T. Tsukuda, K. Henry, S. Berger, and M. A. Osley Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B Genes & Dev., January 15, 2004; 18(2): 184 - 195. [Abstract] [Full Text] [PDF]
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 N.C.T. EMRE and S.L. BERGER Histone H2B Ubiquitylation and Deubiquitylation in Genomic Regulation Cold Spring Harb Symp Quant Biol, January 1, 2004; 69(0): 289 - 300. [Abstract] [PDF]
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Y. Zhang Transcriptional regulation by histone ubiquitination and deubiquitination Genes & Dev., November 15, 2003; 17(22): 2733 - 2740. [Full Text] [PDF]
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K. W. Henry, A. Wyce, W.-S. Lo, L. J. Duggan, N.C. T. Emre, C.-F. Kao, L. Pillus, A. Shilatifard, M. A. Osley, and S. L. Berger Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8 Genes & Dev., November 1, 2003; 17(21): 2648 - 2663. [Abstract] [Full Text] [PDF]
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J. D. Schnell and L. Hicke Non-traditional Functions of Ubiquitin and Ubiquitin-binding Proteins J. Biol. Chem., September 19, 2003; 278(38): 35857 - 35860. [Full Text] [PDF]
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A. Wood, J. Schneider, J. Dover, M. Johnston, and A. Shilatifard The Paf1 Complex Is Essential for Histone Monoubiquitination by the Rad6-Bre1 Complex, Which Signals for Histone Methylation by COMPASS and Dot1p J. Biol. Chem., September 12, 2003; 278(37): 34739 - 34742. [Abstract] [Full Text] [PDF]
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H. H. Ng, S. Dole, and K. Struhl The Rtf1 Component of the Paf1 Transcriptional Elongation Complex Is Required for Ubiquitination of Histone H2B J. Biol. Chem., September 5, 2003; 278(36): 33625 - 33628. [Abstract] [Full Text] [PDF]
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M. Gerber and A. Shilatifard Transcriptional Elongation by RNA Polymerase II and Histone Methylation J. Biol. Chem., July 11, 2003; 278(29): 26303 - 26306. [Abstract] [Full Text] [PDF]
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N. J. Krogan, M. Kim, A. Tong, A. Golshani, G. Cagney, V. Canadien, D. P. Richards, B. K. Beattie, A. Emili, C. Boone, et al. Methylation of Histone H3 by Set2 in Saccharomyces cerevisiae Is Linked to Transcriptional Elongation by RNA Polymerase II Mol. Cell. Biol., June 15, 2003; 23(12): 4207 - 4218. [Abstract] [Full Text] [PDF]
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 N. M. Springer, C. A. Napoli, D. A. Selinger, R. Pandey, K. C. Cone, V. L. Chandler, H. F. Kaeppler, and S. M. Kaeppler Comparative Analysis of SET Domain Proteins in Maize and Arabidopsis Reveals Multiple Duplications Preceding the Divergence of Monocots and Dicots Plant Physiology, June 1, 2003; 132(2): 907 - 925. [Abstract] [Full Text] [PDF]
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F. Tie, J. Prasad-Sinha, A. Birve, A. Rasmuson-Lestander, and P. J. Harte A 1-Megadalton ESC/E(Z) Complex from Drosophila That Contains Polycomblike and RPD3 Mol. Cell. Biol., May 1, 2003; 23(9): 3352 - 3362. [Abstract] [Full Text] [PDF]
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T. Xiao, H. Hall, K. O. Kizer, Y. Shibata, M. C. Hall, C. H. Borchers, and B. D. Strahl Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast Genes & Dev., March 1, 2003; 17(5): 654 - 663. [Abstract] [Full Text] [PDF]
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A. Roguev, D. Schaft, A. Shevchenko, R. Aasland, A. Shevchenko, and A. F. Stewart High Conservation of the Set1/Rad6 Axis of Histone 3 Lysine 4 Methylation in Budding and Fission Yeasts J. Biol. Chem., February 28, 2003; 278(10): 8487 - 8493. [Abstract] [Full Text] [PDF]
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W. M. Baarends, E. Wassenaar, J. W. Hoogerbrugge, G. van Cappellen, H. P. Roest, J. Vreeburg, M. Ooms, J. H. J. Hoeijmakers, and J. A. Grootegoed Loss of HR6B Ubiquitin-Conjugating Activity Results in Damaged Synaptonemal Complex Structure and Increased Crossing-Over Frequency during the Male Meiotic Prophase Mol. Cell. Biol., February 15, 2003; 23(4): 1151 - 1162. [Abstract] [Full Text] [PDF]
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Y.-H. Goo, Y. C. Sohn, D.-H. Kim, S.-W. Kim, M.-J. Kang, D.-J. Jung, E. Kwak, N. A. Barlev, S. L. Berger, V. T. Chow, et al. Activating Signal Cointegrator 2 Belongs to a Novel Steady-State Complex That Contains a Subset of Trithorax Group Proteins Mol. Cell. Biol., January 1, 2003; 23(1): 140 - 149. [Abstract] [Full Text]
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H. H. Ng, R.-M. Xu, Y. Zhang, and K. Struhl Ubiquitination of Histone H2B by Rad6 Is Required for Efficient Dot1-mediated Methylation of Histone H3 Lysine 79 J. Biol. Chem., September 13, 2002; 277(38): 34655 - 34657. [Abstract] [Full Text] [PDF]
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