A Compendium of G-flipon Biological Functions that have Experimental Validation
Опубликована: Авг. 23, 2024
As
with
all
new
fields
of
discovery,
work
on
the
biological
role
G-quadruplexes
(GQ)
has
produced
a
number
results
that
at
first
glance
are
quite
baffling,
sometimes
because
they
do
not
fit
well
together,
but
mostly
different
from
commonly
held
expectations.
Like
other
classes
flipons,
those
form
have
repeat
sequence
motif
enables
fold.
The
canonical
DNA
(G3N1-7)3G3,
where
N
is
any
nucleotide
and
G
guanine,
feature
under
active
selection
in
avian
mammalian
genomes.
involvement
G-flipons
genome
maintenance
traces
back
to
invertebrate
C.
elegans
ancient
repair
pathways.
A
for
GQ
transcription
supported
by
observation
yeast
Rap1
protein
binds
both
B-DNA,
sequence-specific
manner,
GQ,
structure-specific
through
same
helix.
Other
factors
(TF)
also
engage
conformations.
RNAs
can
modulate
formation
manner
cellular
machinery
as
localized
TF,
linking
RNA
world
modern
world.
coevolution
proteins
studies
early
embryonic
development,
transient
potentially
coordinates
epigenetic
specification
cell
fate.
Язык: Английский
A Compendium of G-Flipon Biological Functions That Have Experimental Validation
International Journal of Molecular Sciences,
Год журнала:
2024,
Номер
25(19), С. 10299 - 10299
Опубликована: Сен. 25, 2024
As
with
all
new
fields
of
discovery,
work
on
the
biological
role
G-quadruplexes
(GQs)
has
produced
a
number
results
that
at
first
glance
are
quite
baffling,
sometimes
because
they
do
not
fit
well
together,
but
mostly
different
from
commonly
held
expectations.
Like
other
classes
flipons,
those
form
have
repeat
sequence
motif
enables
fold.
The
canonical
DNA
(G3N1–7)3G3,
where
N
is
any
nucleotide
and
G
guanine,
feature
under
active
selection
in
avian
mammalian
genomes.
involvement
G-flipons
genome
maintenance
traces
back
to
invertebrate
Caenorhabditis
elegans
ancient
repair
pathways.
GQs
transcription
supported
by
observation
yeast
Rap1
protein
binds
both
B-DNA,
sequence-specific
manner,
GQs,
structure-specific
through
same
helix.
Other
factors
(TFs)
also
engage
conformations
actuate
cellular
transactions.
Noncoding
RNAs
can
modulate
GQ
formation
manner
machinery
as
localized
TFs,
linking
RNA
world
modern
world.
coevolution
noncoding
proteins
studies
early
embryonic
development,
transient
coordinates
epigenetic
specification
cell
fate.
Язык: Английский
Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июнь 25, 2024
Abstract
Alternative
DNA
conformation
formed
by
sequences
called
flipons
potentially
alter
the
readout
of
genetic
information
directing
shape-specific
assembly
complexes
on
The
biological
roles
G-quadruplexes
motifs
rich
in
guanosine
repeats
have
been
investigated
experimentally
using
many
different
methodologies
including
G4-seq,
G4
ChIP-seq,
permanganate
nuclease
footprinting
(KEx),
KAS-seq,
CUT&Tag
with
varying
degrees
overlap
between
results.
Here
we
trained
large
language
model
DNABERT
existing
data
generated
KEx,
a
rapid
chemical
technique
performed
live,
intact
cells
potassium
permanganate.
snapshot
flipon
state
when
combined
results
from
other
vitro
methods
that
are
permeabilized
cells,
allows
high
confidence
mapping
G-flipons
to
proximal
enhancer
and
promoter
sequences.
Using
G4-DNABERT
predictions,with
ENdb,
Zoonomia
cCREs
single
cell
experiments,
found
support
for
where
G4-quadruplexes
regulate
gene
expression
through
chromatin
loop
formation.
Язык: Английский