Frontiers in Plant Science,
Год журнала:
2022,
Номер
13
Опубликована: Июль 26, 2022
TGA
transcription
factors
are
essential
regulators
of
various
cellular
processes,
their
activity
connected
to
different
hormonal
pathways,
interacting
proteins
and
regulatory
elements.
Belonging
the
basic
region
leucine
zipper
(bZIP)
family,
TGAs
operate
by
binding
target
DNA
sequence
as
dimers
through
a
conserved
bZIP
domain.
Despite
sharing
core
DNA-binding
sequence,
paralogues
exert
somewhat
preferences.
Sequence
variability
N-
C-terminal
protein
parts
indicates
importance
in
defining
functional
specificity
interactions
with
diverse
proteins,
affecting
properties.
In
this
review,
we
provide
short
concise
summary
on
plant
from
structural
point
view,
including
relation
characteristics
roles
regulation.
Nature Physics,
Год журнала:
2022,
Номер
18(3), С. 271 - 276
Опубликована: Фев. 3, 2022
Abstract
Biomolecular
condensates
are
dense
assemblies
of
proteins
that
form
distinct
biochemical
compartments
without
being
surrounded
by
a
membrane.
Some,
such
as
P
granules
and
stress
granules,
behave
droplets
contain
many
millions
molecules.
Others,
transcriptional
on
the
surface
DNA,
small
thousands
The
physics
behind
formation
DNA
surfaces
is
still
under
discussion.
Here
we
investigate
nature
transcription
factor
using
pioneer
Krüppel-like
4
(Klf4).
We
show
Klf4
can
phase
separate
its
own
at
high
concentrations,
but
low
only
forms
DNA.
Using
optical
tweezers,
demonstrate
these
type
condensation.
This
condensation
involves
switch-like
transition
from
thin
adsorbed
layer
to
thick
condensed
layer,
which
shows
hallmarks
prewetting
transition.
localization
correlates
with
sequence,
suggesting
condensate
sequence-dependent
Prewetting
together
sequence
specificity
explain
size
position
control
condensates.
speculate
factors
underlies
positioning
provides
robustness
regulation.
Short
tandem
repeats
(STRs)
are
enriched
in
eukaryotic
cis-regulatory
elements
and
alter
gene
expression,
yet
how
they
regulate
transcription
remains
unknown.
We
found
that
STRs
modulate
factor
(TF)-DNA
affinities
apparent
on-rates
by
about
70-fold
directly
binding
TF
DNA-binding
domains,
with
energetic
impacts
exceeding
many
consensus
motif
mutations.
maximize
the
number
of
weakly
preferred
microstates
near
target
sites,
thereby
increasing
density,
well
predicted
statistical
mechanics.
Confirming
also
affect
cells,
neural
networks
trained
only
on
vivo
occupancies
effects
identical
to
those
observed
vitro.
Approximately
90%
TFs
preferentially
bound
need
not
resemble
known
motifs,
providing
a
mechanism
genomic
sites.
International Journal of Molecular Sciences,
Год журнала:
2021,
Номер
22(17), С. 9150 - 9150
Опубликована: Авг. 24, 2021
The
transcriptome
of
every
cell
is
orchestrated
by
the
complex
network
interaction
between
transcription
factors
(TFs)
and
their
binding
sites
on
DNA.
Disruption
this
can
result
in
many
forms
organism
malfunction
but
also
be
substrate
positive
natural
selection.
However,
understanding
specific
determinants
each
these
individual
TF-DNA
interactions
a
challenging
task
as
it
requires
integrating
multiple
possible
mechanisms
which
given
TF
ends
up
interacting
with
genomic
region.
These
include
DNA
motif
preferences,
determined
nucleotide
sequence
DNA’s
shape;
post-translational
modifications
TF,
such
phosphorylation;
dimerization
partners
co-factors,
mediate
direct
or
indirect
cooperative
binding.
Binding
affected
epigenetic
putative
target
regions,
including
methylation
nucleosome
occupancy.
In
review,
we
describe
how
all
have
role
crosstalk
one
family
TFs,
basic
helix-loop-helix
(bHLH),
very
conserved
domain
similar
preferred
motif,
E-box.
Here,
compile
discuss
rich
catalog
strategies
used
bHLH
to
acquire
TF-specific
genome-wide
landscapes
sites.
Cold Spring Harbor Perspectives in Biology,
Год журнала:
2021,
Номер
13(11), С. a040949 - a040949
Опубликована: Май 17, 2021
Feiyue
Lu
and
Timothée
Lionnet
Institute
for
Systems
Genetics
Cell
Biology
Department,
NYU
School
of
Medicine,
New
York,
York
10016,
USA
Correspondence:
Timothee.lionnet{at}nyulangone.org
