BTB
(bric-a-brack,
Tramtrack,
and
broad
complex)
is
a
diverse
group
of
protein-protein
interaction
domains
found
within
metazoan
proteins.
Transcription
factors
contain
dimerizing
subtype
with
characteristic
N-terminal
extension.
The
Tramtrack
(TTK)
distinct
type
domain,
which
can
multimerize.
Single-particle
cryo-EM
microscopy
revealed
that
the
TTK-type
assemble
into
hexameric
structure
consisting
three
canonical
dimers
connected
through
previously
uncharacterized
interface.
We
demonstrated
are
only
in
Arthropods
have
undergone
lineage-specific
expansion
modern
insects.
Drosophila
genome
encodes
24
transcription
domains,
whereas
four
non-TTK-type
domains.
Yeast
two-hybrid
analysis
an
unusually
potential
for
heteromeric
associations
presumably
dimer-dimer
Thus,
structurally
functionally
protein
specific
to
Arthropodan
factors.
Trends in Genetics,
Journal Year:
2024,
Volume and Issue:
40(2), P. 160 - 174
Published: Jan. 12, 2024
Recent
imaging
studies
have
captured
the
dynamics
of
regulatory
events
transcription
inside
living
cells.
These
include
factor
(TF)
DNA
binding,
chromatin
remodeling
and
modification,
enhancer-promoter
(E-P)
proximity,
cluster
formation,
preinitiation
complex
(PIC)
assembly.
Together,
these
molecular
culminate
in
stochastic
bursts
RNA
synthesis,
but
their
kinetic
relationship
remains
largely
unclear.
In
this
review,
we
compare
timescales
upstream
steps
(input)
with
kinetics
transcriptional
bursting
(output)
to
generate
mechanistic
models
single
We
highlight
open
questions
potential
technical
advances
guide
future
endeavors
toward
a
quantitative
understanding
regulation.
Nature Communications,
Journal Year:
2022,
Volume and Issue:
13(1)
Published: March 4, 2022
Abstract
To
maintain
cellular
identities
during
development,
gene
expression
profiles
must
be
faithfully
propagated
through
cell
generations.
The
reestablishment
of
patterns
upon
mitotic
exit
is
mediated,
in
part,
by
transcription
factors
(TF)
bookmarking.
However,
the
mechanisms
and
functions
TF
bookmarking
early
embryogenesis
remain
poorly
understood.
In
this
study,
taking
advantage
naturally
synchronized
mitoses
Drosophila
embryos,
we
provide
evidence
that
GAGA
pioneer
factor
(GAF)
acts
as
a
stable
bookmarker
zygotic
genome
activation.
We
show
that,
mitosis,
GAF
remains
associated
to
large
fraction
its
interphase
targets,
including
at
cis
-regulatory
sequences
key
developmental
genes
with
both
active
repressive
chromatin
signatures.
targets
are
globally
accessible
mitosis
bookmarked
via
histone
acetylation
(H4K8ac).
By
monitoring
kinetics
transcriptional
activation
living
report
binding
establishes
competence
for
rapid
exit.
Developmental Cell,
Journal Year:
2023,
Volume and Issue:
58(19), P. 1898 - 1916.e9
Published: Aug. 8, 2023
Chromatin
accessibility
is
integral
to
the
process
by
which
transcription
factors
(TFs)
read
out
cis-regulatory
DNA
sequences,
but
it
difficult
differentiate
between
TFs
that
drive
and
those
do
not.
Deep
learning
models
learn
complex
sequence
rules
provide
an
unprecedented
opportunity
dissect
this
problem.
Using
zygotic
genome
activation
in
Drosophila
as
a
model,
we
analyzed
high-resolution
TF
binding
chromatin
data
with
interpretable
deep
performed
genetic
validation
experiments.
We
identify
hierarchical
relationship
pioneer
Zelda
involved
axis
patterning.
consistently
pioneers
proportional
motif
affinity,
whereas
patterning
augment
contexts
where
they
mediate
enhancer
activation.
conclude
occurs
two
tiers:
one
through
pioneering,
makes
enhancers
accessible
not
necessarily
active,
second
when
correct
combination
of
leads
Annual Review of Cell and Developmental Biology,
Journal Year:
2023,
Volume and Issue:
39(1), P. 277 - 305
Published: Aug. 4, 2023
Cells
must
tightly
regulate
their
gene
expression
programs
and
yet
rapidly
respond
to
acute
biochemical
biophysical
cues
within
environment.
This
information
is
transmitted
the
nucleus
through
various
signaling
cascades,
culminating
in
activation
or
repression
of
target
genes.
Transcription
factors
(TFs)
are
key
mediators
these
signals,
binding
specific
regulatory
elements
chromatin.
While
live-cell
imaging
has
conclusively
proven
that
TF-chromatin
interactions
highly
dynamic,
how
such
transient
can
have
long-term
impacts
on
developmental
trajectories
disease
progression
still
largely
unclear.
In
this
review,
we
summarize
our
current
understanding
dynamic
nature
TF
functions,
starting
with
a
historical
overview
early
experiments.
We
highlight
govern
dynamics
dynamics,
turn,
affect
downstream
transcriptional
bursting.
Finally,
conclude
open
challenges
emerging
technologies
will
further
regulation.
