Cohesin
has
a
well-established
role
in
sister
chromatid
cohesion
and
postreplicative
DNA
repair.
In
addition,
previous
work
in
our
laboratory
suggested
a
positive
correlation
between
cohesin
binding
and
gene
expression
(Parelho
et
al.
2008).
We
decided
to
establish
the
ChIP-seq
technique
to
address
the
relationship
between
cohesin
binding
and
gene
expression
at
the
genome-wide
level.
However,
in
the
meantime,
several
other
groups
reported
genome-wide
binding
maps
of
cohesin
in
embryonic
stem
(ES)
cells,
demonstrating
cell-type-specific
cohesin
binding
and
its
correlation
with
gene
expression
(Schmidt
et
al.
2010;
Kagey
et
al.
2010;
Nitzsche
et
al.
2011).
Kagey
and
colleagues
argue
that
cohesin
is
required
for
the
expression
of
pluripotency-associated
genes,
based
on
cohesin
downregulation
for
an
extended
time
period.
We
believe
this
method
generates
indirect
effects
such
as
cell
stress,
death
and
enrichment
for
slowly
cycling
differentiating
cells,
biasing
the
results
towards
differentiated
cells.
We
have
generated
ES
cells
homozygous
for
conditional
Rad21
alleles
and
have
found
that,
unlike
the
Kagey
approach,
rapid
24-hour
cohesin
depletion
does
not
induce
cell
stress
responses.
We
detect
a
stronger
correlation
between
cohesin-bound
genes
and
gene
expression
changes,
suggesting
our
approach
is
more
accurate
in
understanding
the
role
of
cohesin
in
gene
expression.
We
have
expanded
our
analysis
of
cohesin
binding
by
generating
ES
cells
expressing
epitope-tagged
BORIS,
a
paralogue
of
CTCF.
We
have
mapped
BORIS
binding
sites
in
ES
cells
and
data
suggest
that
BORIS,
unlike
CTCF,
does
not
recruit
cohesin.
To
study
the
specific
involvement
of
cohesin
in
gene
expression,
two
developmentally
regulated
models,
T
cell
receptor
α
(Tcrα)
rearrangement
and
X
chromosome
inactivation
(XCI),
have
been
used.
Cohesin
loss
in
non-cycling
developing
thymocytes
leads
to
impaired
Tcrα
rearrangement.
Finally,
we
present
evidence
that
cohesin
contributes
to
creating
chromatin
boundaries
that
segregate
facultative
heterochromatin
from
active
chromatin
on
the
inactive
X
chromosome
in
differentiating
female
ES
cells
