ACS Nano,
Journal Year:
2016,
Volume and Issue:
10(7), P. 7073 - 7084
Published: June 30, 2016
The
organization
of
eukaryotic
DNA
into
nucleosomes
and
chromatin
undergoes
dynamic
structural
changes
to
regulate
genome
processing,
including
transcription
repair.
Critical
rearrangements
occur
over
a
wide
range
distances,
the
mesoscopic
length
scale
tens
nanometers.
However,
there
is
lack
methodologies
that
probe
this
within
chromatin.
We
have
designed,
constructed,
implemented
DNA-based
nanocaliper
probes
scale.
developed
an
approach
integrating
our
at
two
attachment
points
with
50%
efficiency.
Here,
we
focused
on
attaching
ends
nucleosome
arms,
so
hinge
angle
readout
end-to-end
distance.
demonstrate
integrated
6,
26,
51
bp
linker
are
partially
unwrapped
by
amount
consistent
previously
observed
transitions.
In
contrast,
longer
75
remain
fully
wrapped.
found
sensitive
measure
disassembly
can
read
out
factor
(TF)
binding
its
target
site
nucleosome.
Interestingly,
not
only
detects
TF
but
also
significantly
increases
probability
occupancy
unwrapping
These
studies
feasibility
using
nanotechnology
both
detect
manipulate
structure,
which
provides
foundation
future
mesoscale
dynamics.
Cold Spring Harbor Perspectives in Biology,
Journal Year:
2014,
Volume and Issue:
6(7), P. a018762 - a018762
Published: July 1, 2014
Ronen
Marmorstein1
and
Ming-Ming
Zhou2
1Program
in
Gene
Expression
Regulation,
Wistar
Institute,
Department
of
Chemistry,
University
Pennsylvania,
Philadelphia,
19104
2Department
Structural
Chemical
Biology,
Icahn
School
Medicine
at
Mount
Sinai,
New
York,
York
10065
Correspondence:
marmor{at}wistar.org
Epigenomics,
Journal Year:
2015,
Volume and Issue:
7(6), P. 1051 - 1073
Published: April 30, 2015
How
DNA
methylation
is
interpreted
and
influences
genome
regulation
remains
largely
unknown.
Proteins
of
the
methyl-CpG-binding
domain
(MBD)
family
are
primary
candidates
for
readout
as
they
recruit
chromatin
remodelers,
histone
deacetylases
methylases
to
methylated
associated
with
gene
repression.
MBD
protein
binding
requires
both
functional
domains
methyl-CpGs;
however,
some
proteins
also
bind
unmethylated
active
regulatory
regions
via
alternative
or
interaction
nucleosome
remodeling
deacetylase
(NuRD/Mi-2)
complex
members.
Mutations
within
occur
in
many
diseases,
including
neurological
disorders
cancers,
leading
loss
specificity
sites
deregulation.
Here,
we
summarize
current
state
knowledge
about
their
role
readers
epigenome.
Cold Spring Harbor Perspectives in Biology,
Journal Year:
2014,
Volume and Issue:
6(12), P. a019315 - a019315
Published: Dec. 1, 2014
Craig
S.
Pikaard1
and
Ortrun
Mittelsten
Scheid2
1Department
of
Biology,
Department
Molecular
Cellular
Biochemistry,
Howard
Hughes
Medical
Institute,
Indiana
University,
Bloomington,
47405
2Gregor
Mendel-Institute
Plant
Austrian
Academy
Sciences,
1030
Vienna,
Austria
Correspondence:
ortrun.mittelsten_scheid{at}gmi.oeaw.ac.at
Cold Spring Harbor Perspectives in Biology,
Journal Year:
2015,
Volume and Issue:
7(1), P. a019364 - a019364
Published: Jan. 1, 2015
Steven
Henikoff1
and
M.
Mitchell
Smith2
1Howard
Hughes
Medical
Institute,
Fred
Hutchinson
Cancer
Research
Center,
Seattle,
Washington
98109-1024
2Department
of
Microbiology,
University
Virginia,
Charlottesville,
Virginia
22908
Correspondence:
steveh{at}fhcrc.org
Antioxidants and Redox Signaling,
Journal Year:
2017,
Volume and Issue:
29(11), P. 1023 - 1040
Published: Oct. 5, 2017
A
growing
body
of
clinical
and
experimental
evidence
has
challenged
the
traditional
understanding
that
only
adaptive
immune
system
can
mount
immunological
memory.
Recent
findings
describe
characteristics
innate
system,
underscored
by
its
ability
to
remember
antecedent
foreign
encounters
respond
in
a
nonspecific
sensitized
manner
reinfection.
This
been
termed
trained
immunity.
Although
beneficial
context
recurrent
infections,
this
might
actually
contribute
chronic
immune-mediated
diseases,
such
as
atherosclerosis.
Advances:
In
line
with
proposed
role
sustaining
cellular
memories,
epigenetic
reprogramming
emerged
critical
determinant
technological
computational
advances
improve
unbiased
acquisition
epigenomic
profiles
have
significantly
enhanced
our
appreciation
for
complexities
chromatin
architecture
contexts
diverse
challenges.Key
resolving
distinct
signatures
memory
is
comprehensive
precise
physiological
targets
regulatory
proteins
recognize,
deposit,
remove
chemical
modifications
from
well
other
gene-regulating
factors.
Drawing
rapidly
expanding
compendium
studies,
review
details
current
perspective
pathways
support
adapted
phenotypes
monocytes
macrophages.We
explore
future
strategies
are
aimed
at
exploiting
mechanism
immunity
prevention
treatment
infections
disorders.
