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First published online 8 December 2005
doi: 10.1242/dev.02199
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Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.
* Author for correspondence (e-mail: kristen{at}iastate.edu)
Accepted 7 November 2005
| SUMMARY |
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Key words: JIL-1 kinase, Chromatin, Histone modifications, HP1, Drosophila
| INTRODUCTION |
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Ebert et al. (Ebert et al.,
2004
) recently identified the Su(var)3-1 mutations as
alleles of the JIL-1 locus that antagonize the expansion of
heterochromatin formation in Drosophila. JIL-1 is a tandem kinase
that localizes specifically to euchromatic interband regions of polytene
chromosomes (Jin et al.,
1999
). Analysis of JIL-1 null and hypomorphic alleles
showed that JIL-1 is essential for viability, and that reduced levels
of JIL-1 protein lead to a global disruption of chromosome structure
(Jin et al., 2000
;
Wang et al., 2001
;
Zhang et al., 2003
;
Deng et al., 2005
). These
defects are correlated with severely decreased levels of histone H3S10
phosphorylation (pH3S10), providing evidence that JIL-1 is the predominant
kinase regulating the phosphorylation state of this residue at interphase
(Wang et al., 2001
). However,
as the Su(var)3-1 alleles generate proteins with COOH-terminal
deletions that are dominant gain-of-function mutations, the experiments of
Ebert et al. (Ebert et al.,
2004
) did not directly address the normal function of JIL-1. In
this study, we show that the reduction in JIL-1 protein levels and histone
H3S10 phosphorylation caused by hypomorphic or null loss-of-function alleles
of the JIL-1 locus results in the spreading of the major
heterochromatin markers dimethyl H3K9 (dmH3K9) and HP1 to ectopic locations on
the chromosome arms, with the most pronounced increase on the X chromosomes.
Furthermore, genetic interaction assays demonstrated that JIL-1 functions
antagonistically to Su(var)3-9, which is the major catalyst for dimethylation
of the histone H3K9 residue (Schotta et
al., 2002
). These findings suggest a model where JIL-1 kinase
activity functions to mark euchromatic domains, and counteract
heterochromatization and gene silencing at ectopic locations by
Su(var)3-9-mediated histone H3K9 dimethylation and HP1 recruitment.
| MATERIALS AND METHODS |
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Immunohistochemistry
Third instar salivary gland `smush' preparations of polytene nuclei were
prepared essentially as described by Wang et al.
(Wang et al., 2001
). Polytene
chromosome squash preparations were performed as described by Kelley et al.
(Kelley et al., 1999
), using
the 5-minute fixation and antibody-labeling protocol described by Jin et al.
(Jin et al., 1999
). Primary
antibodies used include: affinity-purified Hope rabbit antiserum raised
against JIL-1 residues 886-1013 (Jin et
al., 1999
); anti-tubulin mAb (Sigma); histone H3 goat antiserum
(Santa Cruz); phospho-histone H3S10 rabbit antiserum (Upstate Biotechnology);
dmH3K9 rabbit antiserum (Upstate Biotechnology); anti-HP1 mAb C1A9
(Developmental Studies Hybridoma Bank, University of Iowa); anti-MSL-1 rabbit
antiserum [generous gift of Drs M. Kuroda (Harvard Medical School, Boston, MA)
and R. Kelley (Baylor College of Medicine, Houston)]; and anti-GFP chicken IgY
(Aves Laboratory). DNA was visualized by staining with Hoechst 33258
(Molecular Probes) in PBS. The appropriate species- and isotype-specific Texas
Red-, TRITC- and FITC-conjugated secondary antibodies (Cappel/ICN, Southern
Biotech) were used (1:200 dilution) to visualize primary antibody labeling.
The final preparations were mounted in 90% glycerol containing 0.5%
n-propyl gallate. The preparations were examined using
epifluorescence optics on a Zeiss Axioskop microscope and images were captured
and digitized using a high resolution Spot CCD camera. Confocal microscopy was
performed with a Leica confocal TCS NT microscope system equipped with
separate Argon-UV, Argon and Krypton lasers, and the appropriate filter sets
for Hoechst, FITC, Texas Red and TRITC imaging. A separate series of confocal
images for each fluorophor of double-labeled preparations were obtained
simultaneously with z-intervals of, typically, 0.5 µm, using a PL
APO 100x/1.40-0.70 oil objective. A maximum projection image for each of
the image stacks was obtained using the ImageJ software
(http://rsb.info.nih.gov/ij/).
In some cases, individual slices or projection images from only two to three
slices were obtained. Images were imported into Adobe PhotoShop, where they
were pseudocoloured, image processed and merged. In some images, non-linear
adjustments were made for optimal visualization of the Hoechst labeling of
chromosomes.
|
| RESULTS |
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In order to determine the degree of change in the levels of chromatin modification markers in JIL-1 mutant backgrounds, we analyzed immunoblots of protein lysates from wild-type, JIL-1z2/JIL-1h9 and JIL-1z2/JIL-1z2 third instar larvae. The immunoblots were probed with anti-pH3S10, anti-dmH3K9, anti-histone H3 and anti-tubulin antibodies. As illustrated in Fig. 1E, both JIL-1z2/ JIL-1h9 (15.2±4.0%, n=4) and JIL-1z2/JIL-1z2 (9.4%±5.0%, n=6) mutants showed greatly reduced levels of phosphorylated histone H3S10, when compared with that in wild-type larvae, indicating that JIL-1z2/JIL-1h9 has the properties of a strong hypomorph. By contrast, the levels of both dmH3K9 and HP1 were at or near wild-type levels (Fig. 1E). In the JIL-1z2/JIL-1z2 null background, the level of dmH3K9 was at 109.0±31.0% (n=9) of the wild-type level, and HP1 was at 99.3±17.8% (n=9). Thus, in JIL-1 mutant backgrounds the level of phosphorylated histone H3S10 was dramatically reduced, whereas the levels of the heterochromatin markers dmH3K9 and HP1 were unaffected.
|
JIL-1Su(var)3-1 alleles act differently from JIL-1 loss-of-function alleles
Ebert et al. (Ebert et al.,
2004
) recently demonstrated that JIL-1 Su(var)3-1 alleles
are dominant gain-of-function mutations that are likely to antagonize the
expansion of heterochromatin. However, in contrast to JIL-1
loss-of-function alleles, JIL-1Su(var)3-1 homozygous
mutants exhibit no change in the distribution of the heterochromatin marker
dmH3K9 or in histone H3S10 phosphorylation
(Ebert et al., 2004
). We
confirmed these results in heteroallelic mutants with only one copy of
JIL-1Su(var)3-1[3] together with the null
JIL-1z2 allele (Fig.
3). The JIL-1Su(var)3-1[3] allele is a point
mutation that introduces a premature in-frame stop codon, leading to a JIL-1
protein with a 166-amino acid truncation of the COOH-terminal domain. In order
to determine the distribution of the truncated JIL-1Su(var)3-1[3]
protein in relation to other chromatin constituents, we double-labeled
polytene squashes from
JIL-1z2/JIL-1Su(var)3-1[3] larvae with either
anti-dmH3K9 or anti-MSL-1 antibody, and with anti-JIL-1 antibody
(Fig. 3A-C).
Fig. 3A shows that one copy of
the JIL-1Su(var)3-1[3] allele is sufficient to prevent
ectopic spreading of the dmH3K9 marker, which is localized at the chromocenter
as in wild-type preparations. Interestingly, one copy of the
JIL-1Su(var)3-1[3] allele is also sufficient to largely
rescue the abnormal chromosome morphology of JIL-1 null mutants,
including the male X chromosome. This is despite the finding that the
JIL-1Su(var)3-1[3] protein is mislocalized on the chromosomes when
compared with wild-type JIL-1. Fig.
3A,B shows that although the JIL-1Su(var)3-1[3] protein
is associated with the chromosomes, the antibody labeling is diffuse, does not
define clear banded regions, and overlaps with Hoechst-labeled banded regions,
a distribution that was never observed for the wild-type JIL-1 protein
(Jin et al., 1999
;
Wang et al., 2001
).
Furthermore, the JIL-1Su(var)3-1[3] protein is not upregulated on
the male X chromosome (Fig. 3B)
and is present along the chromosome arms at ectopic locations. This is shown
at higher magnification in Fig.
3C, in a double labeling with JIL-1 and MSL-1 antibodies. In
wild-type preparations, MSL-1 and JIL-1 are colocalized on the male X
chromosome (except for the telomere) (Jin
et al., 2000
); however, as indicated by the arrows in
Fig. 3C, the
JIL-1Su(var)3-1[3] protein is associated with many regions of the X
chromosome not labeled by MSL-1 antibody. Immunoblot analysis of protein
lysate from wild-type, JIL-1z2/+ and
JIL-1z2/JIL-1Su(var)3-1[3] larvae show that the
level of histone H3S10 phosphorylation in
JIL-1z2/JIL-1Su(var)3-1[3] mutants is
comparable to that of JIL-1z2/+ larvae, suggesting that
JIL-1Su(var)3-1[3] mutants have normal JIL-1 kinase
activity (see also Ebert et al.,
2004
). Taken together, these data suggest that the COOH-terminal
domain of JIL-1 is required for proper chromosome localization, and indicate
that the dominant gain-of-function effect of the
JIL-1Su(var)3-1[3] allele
(Ebert et al., 2004
) may be
attributable to JIL-1 kinase activity at ectopic locations.
|
To determine whether Su(var)3-9 and JIL-1 genetically interact in the same
pathway in vivo, we explored interactions between mutant alleles of
Su(var)3-9 and JIL-1 by generating double-mutant
individuals. Because Su(var)3-9 and JIL-1 are both located
on the third chromosome, we first recombined the
Su(var)3-91 allele onto the JIL-1z60
chromosome. Subsequently, JIL-1z60 Su(var)3-91/TM6
Sb Tb males were crossed with JIL-1z2/TM6 Sb Tb
virgin females generating JIL-1z2/JIL-1z60
Su(var)3-91 progeny, identified as non-Sb. In control
experiments in which Su(var)3-9 activity was not altered, we crossed
JIL-1z60/TM6 Sb Tb males with JIL-1z2/TM6
Sb Tb virgin females generating
JIL-1z2/JIL-1z60 progeny.
JIL-1z2 is a null allele and JIL-1z60
is a strong hypomorph producing less than 0.3% of the levels of JIL-1
wild-type protein, resulting in semi-lethality of this heteroallelic
combination (Wang et al.,
2001
; Zhang et al.,
2003
). Consequently, in the control crosses, we observed only one
fly of the JIL-1z2/JIL-1z60 genotype out of a
total of 871 eclosed flies. However, in the double mutant combination
(JIL-1z2/JIL-1z60 Su(var)3-91) with
one copy of the Su(var)3-91 allele, the number of
surviving flies with the JIL-1z2/JIL-1z60
genotype increased dramatically to 243 out of a total of 789 eclosed flies. In
this cross, one-third of the eclosed flies would be expected to be of the
JIL-1z2/JIL-1z60 Su(var)3-91
genotype, assuming full rescue, indicating that the reduction of Su(var)3-9
activity in these animals resulted in a 92% viability rate compared with a
rate of 0.3% for JIL-1z2/JIL-1z60 flies without
the reduction in Su(var)3-9 activity. Consistent with the observed rescue of
viability, there was no detectable spreading of histone H3K9 dimethylation to
ectopic locations in polytene squashes from
JIL-1z2/JIL-1z60 Su(var)3-91 larvae,
and the morphology of the polytene chromosomes was markedly improved
(Fig. 4F).
|
| DISCUSSION |
|---|
|
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According to the histone code hypothesis
(Strahl and Allis, 2000
) and
the recently proposed binary switch model
(Fischle et al., 2003
),
phosphorylation of a site adjacent to a methyl mark that engages an effector
molecule may regulate its binding. JIL-1 phosphorylates the histone H3S10
residue in euchromatic regions of polytene chromosomes
(Jin et al., 1999
;
Wang et al., 2001
), raising
the possibility that this phosphorylation at interphase prevents the
recruitment of Su(var)3-9 and/or the dimethylation of the neighboring K9
residue. This, in turn, would affect the binding of HP1, thus antagonizing the
formation of silenced heterochromatin at interbands. That different regions of
chromatin may have different combinations of posttranslational modifications
controlling effector/histone interactions, as predicted by the histone code
hypothesis (Strahl and Allis,
2000
), is underscored by the finding that, in JIL-1 null
backgrounds, the level of the dmH3K9 marker and HP1 are preferentially
increased on the male and female X chromosomes. It is well documented that the
male X chromosome is unique because of the activity of the MSL dosage
compensation complex and the MOF histone acetyltransferase, which leads to
hyperacetylation of histone H4 (Bone et
al., 1994
; Hilfiker et al.,
1997
). However, comparable markers for the female X chromosome
have yet to be discovered, and our results are the first indication that
markers may exist that distinguish male and female X chromosomes from
autosomes, and that this difference may increase the affinity for Su(var)3-9.
That the spreading of heterochromatic markers in the absence of JIL-1 occurs
on both the male and female X chromosome further indicates that these changes
are independent of dosage compensation processes.
Unfortunately, in this study, we could not directly address the possibility
that the observed spreading of heterochromatin markers occurred preferentially
to specific euchromatic sites. In JIL-1 null and hypomorphic
backgrounds, chromosome morphology is greatly perturbed, and there is an
intermixing not only of euchromatin and the compacted chromatin characteristic
of banded regions, but also of non-homologous chromatid regions, which become
fused and confluent (Deng et al.,
2005
). Thus, we cannot rule out as an alternative hypothesis that
JIL-1 activity may regulate boundary elements
(West et al., 2002
) that
control the spreading of heterochromatic factors, or that the two mechanisms
may act in concert. However, the spreading of the dmH3K9 marker and HP1 to
ectopic locations on the chromosomes is likely to lead to heterochromatization
and repression of gene expression at these sites. Our results further suggest
the possibility that the lethality of JIL-1 null mutants may be due
to the repression of essential genes at these ectopic sites as a consequence
of the spreading of Su(var)3-9 activity. This hypothesis is supported by
genetic interaction assays that demonstrated that the lethality of a severely
hypomorphic JIL-1 heteroallelic combination could be almost
completely rescued by a reduction in Su(var)3-9 dosage that prevented
the ectopic dimethylation of histone H3K9.
It has recently been demonstrated that the Su(var)3-1 alleles of
JIL-1 consist of dominant gain-of-function alleles that antagonize
the expansion of heterochromatin formation
(Ebert et al., 2004
). However,
we provide evidence that the underlying molecular mechanism of this antagonism
is different from that occurring in the loss-of-function null and hypomorphic
JIL-1 alleles described in this study.
JIL-1Su(var)3-1 alleles are characterized by deletions of
the COOH-terminal domain that do not affect JIL-1 kinase activity or the
spreading of heterochromatin markers (Ebert
et al., 2004
) (this study). Furthermore, our results indicate that
the COOH-terminal domain of JIL-1 is required for proper chromosomal
localization and that JIL-1Su(var)3-1 proteins are mislocalized to
ectopic chromosome sites. Thus, we propose that the dominant gain-of-function
effect of the JIL-1Su(var)3-1 alleles may be attributable
to JIL-1 kinase activity at ectopic locations, possibly through the
phosphorylation of novel target proteins (see also
Ebert et al., 2004
), or by
mis-regulated localization of the phosphorylated histone H3S10 marker.
Although the JIL-1Su(var)3-1 proteins are mislocalized, they still
associate with chromosomes and phosphorylate the histone H3S10 residue,
suggesting that other regions of the protein have a binding affinity for at
least some of the substrates and interaction partners of JIL-1. This is
supported by the finding that each of the two kinase domains of JIL-1 can
interact with the MSL-complex in vitro
(Jin et al., 2000
).
In summary, we provide evidence that the JIL-1 kinase is a major regulator of histone modifications that affect gene activation, gene silencing and chromatin structure. Thus, it will be informative in future experiments to further explore the interaction of JIL-1 with genes controlling heterochromatin formation, in order to gain a better understanding of the molecular mechanisms of epigenetic gene regulation.
| ACKNOWLEDGMENTS |
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