Download Cohesin: A Multi-purpose Chromatin Glue

58 j Journal of Molecular Cell Biology (2009), 1, 58 –60
doi:10.1093/jmcb/mjp014
Published online August 14, 2009
Research Highlight
Cohesin: A Multi-purpose Chromatin Glue
Laura A. Dı´az-Martı´nez and Hongtao Yu*
Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
* Correspondence to: Hongtao Yu, E-mail: [email protected]
Long thought to be the glue responsible for holding sister chromatids together, cohesin has been found to be stickier than previously
thought. Recent discoveries point to cohesin having a role in transcription regulation by mediating long-distance intra-chromosomal
interactions.
In higher eukaryotes, cohesin is known to
bind to chromatin during interphase. As
cells advance into mitosis, most cohesin
is removed from chromosomes and only a
tiny amount remains bound to the centromeres (Figure 1). This remaining cohesin,
which contributes to sister-chromatid
cohesion, is removed at the moment of
anaphase onset. Almost immediately
after that, in telophase, cohesin binds
again to the chromatin. For a complex
whose main function is thought to be in
mitosis, this cycle of cohesin binding
peaking in interphase and being removed
in mitosis seems counterintuitive. If the
main function of the cohesin complex is
to hold sister chromatids together, then
why would a cell want so much cohesin
bound to the chromatin in G1, when the
chromosomes have not been duplicated?
And why is most cohesin removed from
chromosomes in mitosis, when the definitive test of sister chromatid cohesion
occurs? The answer to these questions,
thanks to new discoveries, seems to be
that cohesin also plays important roles in
interphase through a contribution to chromatin structure and spatial organization.
The first hints of a role for cohesin in
interphase were the gene silencing
defects observed in yeasts and flies containing mutations in cohesin subunits
and cohesin loading factors (reviewed by
Dorsett, 2009). These defects in gene
expression involved the malfunction of
enhancers, insulators or other transcription regulatory elements found kilobases
away from the affected genes. These regulatory elements are thought to influence
gene expression via formation of chromatin loops which bring them in close proximity to their targets. Central to this idea
is the 11-zinc finger protein CTCF, which
binds to both the nuclear matrix and the
chromatin and has therefore been proposed to act as a tether that brings
together
specific
chromatin
sites.
Although CTCF binding to DNA is sequence
specific, there are an estimated 14 000 –
20 000 CTCF binding sites in the human
genome, which happen to lie in gene-rich
regions, hinting at an important role of
CTCF in the regulation of gene expression.
More importantly, CTCF has been shown to
be involved in the formation of chromatin
loops at several loci including the
imprinted region Igf2/H19 and has therefore been considered the corner stone of
chromatin organization in interphase
(reviewed in Zlatanova and Caiafa, 2009).
Interestingly, a link between CTCF and
the cohesin complex has been discovered
indicating that cohesin contributes to the
formation of chromatin loops.
The initial evidence for a role of cohesin
in CTCF-related control of gene expression
came from ChIP studies that mapped
cohesin-binding sites in the human
genome (Parelho et al., 2008; Wendt
et al., 2008). These studies showed that
the binding sites of cohesin overlapped
with CTCF-binding sites, with 71% of the
identified sites binding both cohesin and
CTCF while 19% and 10% bind cohesin or
CTCF alone, respectively (Parelho et al.,
2008). The association of CTCF and
cohesin at CTCF-binding sites was confirmed independently by an in vitro assay
that examined proteins bound to a
169 bp DNA probe containing a
CTCF-binding site. This assay identified
the cohesin component Scc3/SA1 as a
protein enriched in the fraction bound to
the CTCF site, but not to a mutated site
(Rubio et al., 2008). Using siRNAs to
knock-down Rad21 or CTCF (Parelho
et al., 2008; Wendt et al., 2008) or a
mutant CTCF-binding site (Rubio et al.,
2008), these studies showed that cohesin
enrichment at CTCF sites was drastically
diminished in the absence of CTCF, while
cohesin inactivation did not significantly
affect CTCF binding (Parelho et al., 2008;
Wendt et al., 2008). More importantly,
experiments using reporter plasmids containing
enhancer/insulator elements
demonstrated that binding of both CTCF
and cohesin is necessary for the proper
function of these elements (Parelho
et al., 2008; Wendt et al., 2008).
But, how does cohesin influence gene
expression? The beautiful work of Hadjur
et al. (2009) has now provided us with
important clues. By studying the CTCF
and cohesin association at the IFNG
locus, they showed that cohesin and
CTCF association at certain CTCF sites is
increased in TH1 effector memory cells,
which express higher amounts of IFNG
compared with their precursors (nonpolarized CD4 T cells). That is, gene
expression correlated with CTCF/cohesin
binding at the endogenous locus. Using
chromosome conformation capture (3C)
techniques, they demonstrated that the
increase in CTCF/cohesin binding at these
regulatory sites, which are tens of
# The Author (2009). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, IBCB, SIBS, CAS. All rights reserved.
Journal of Molecular Cell Biology
j 59
Figure 1 Cohesin as a multi-purpose glue. Cohesin is long known to form inter-chromatid bridges on replicated sister chromatids that are
required for sister-chromatid cohesion. Recent studies have shown that cohesin collaborates with CTCF to form intra-chromosomal bridges
in interphase, which play important roles in transcription regulation. This active role of cohesin as a chromatin glue involved in nuclear architecture is consistent with the large amounts of chromatin-bound cohesin observed in interphase. However, chromatin structures such as intraand inter-chromosomal interactions are incompatible with chromosome individualization and condensation and therefore have to be removed
during mitosis. A small amount of cohesin (and CTCF) is known to remain at centromeres in mitosis.
kilobases away from each other, correlates
with an increase in crosslinking of such
sites. Furthermore, these long-distance
intra-chromosomal interactions depend
on both CTCF and cohesin. They are cell
type specific and correlate with the induction of IFNG expression. In sum, these
studies indicate that CTCF and cohesin collaborate to establish long-range intrachromosomal interactions that are necessary for regulation of gene expression and
can have developmental and environmental plasticity.
Although these findings constitute a
giant leap in our understanding of the
role of cohesins inside the cells, a myriad
of questions remain to be answered. For
example, how are these linkages established? Does cohesin bind directly to
CTCF? Are known cohesin-loading components involved in cohesin binding to
these sites? How are the two chromatin
regions brought together? Why are loops
needed to regulate transcription?
Importantly, the implications of these
findings extend to more than just finding
a novel role for cohesin in interphase,
they also greatly contribute to our understanding of the other functions of
cohesin. These findings compel us to
consider cohesin as a multi-purpose
chromatin glue that can be used to hold
together two segments of chromatin,
regardless of whether these segments
belong to the same chromatid or two
sister chromatids (Figure 1). It is tempting
to speculate that cohesin may also be
involved in the long-range interactions
between genomic loci on different chromosomes observed during coordinated transcriptional events (Hu et al., 2008). Under
this view, the cohesin complex might not
only be involved in sister chromatid
cohesion or in the formation of intrachromosomal loops involved in transcription, but perhaps the specific chromatin
structures formed by cohesin linkages
might also be important for other processes, such as DNA replication and
repair or the formation of chromatinprotein nuclear bodies. The abundance of
cohesin binding sites in interphase and
its dramatic decline in mitosis suggest
that most of these linkages are removed
upon mitotic entry, perhaps to allow chromatin compaction and proper mitotic progression (Yanagida, 2009). Although most
cohesin is removed during early mitosis,
a small amount of cohesin remains at the
centromeres. Strikingly, CTCF has also
been shown to localize at the centromeres
of mitotic chromosomes (Rubio et al.,
2008). It will be interesting to test
whether CTCF is involved in the recruitment or maintenance of cohesin at the
centromeres and whether these proteins
play an architectural role at the centromeres in addition to their role in cohesion.
References
Dorsett, D. (2009). Cohesin, gene expression and
development:
lessons
from
Drosophila.
Chromosome Res. 17, 185 –200.
Hadjur, S., Williams, L.M., Ryan, N.K., Cobb, B.S.,
Sexton, T., Fraser, P., Fisher, A.G., and
Merkenschlager, M. (2009). Cohesins form chromosomal cis-interactions at the developmentally
regulated IFNG locus. Nature 460, 410 – 413.
Hu, Q., Kwon, Y.S., Nunez, E., Cardamone, M.D., Hutt,
K.R., Ohgi, K.A., Garcia-Bassets, I., Rose, D.W.,
Glass, C.K., Rosenfeld, M.G., et al. (2008).
Enhancing nuclear receptor-induced transcription
60 j Journal of Molecular Cell Biology
requires nuclear motor and LSD1-dependent gene
networking in interchromatin granules. Proc. Natl
Acad. Sci. USA 105, 19199–19204.
Parelho, V., Hadjur, S., Spivakov, M., Leleu, M., Sauer,
S., Gregson, H.C., Jarmuz, A., Canzonetta, C.,
Webster, Z., Nesterova, T., et al. (2008). Cohesins
functionally associate with CTCF on mammalian
chromosome arms. Cell 132, 422–433.
Dı´az-Martı´nez and Yu
Rubio, E.D., Reiss, D.J., Welcsh, P.L., Disteche, C.M.,
Filippova, G.N., Baliga, N.S., Aebersold, R.,
Ranish, J.A., and Krumm, A. (2008). CTCF physically links cohesin to chromatin. Proc. Natl
Acad. Sci. USA 105, 8309– 8314.
Wendt, K.S., Yoshida, K., Itoh, T., Bando, M., Koch,
B., Schirghuber, E., Tsutsumi, S., Nagae, G.,
Ishihara, K., Mishiro, T., et al. (2008). Cohesin
mediates
transcriptional
insulation
by
CCCTC-binding factor. Nature 451, 796 –801.
Yanagida, M. (2009). Clearing the way for mitosis:
is cohesin a target? Nat. Rev. Mol. Cell Biol. 10,
489 –496.
Zlatanova, J., and Caiafa, P. (2009). CTCF and its
protein partners: divide and rule? J. Cell Sci.
122, 1275 – 1284.