Molecular Cell,
Год журнала:
2019,
Номер
76(4), С. 600 - 616.e6
Опубликована: Ноя. 1, 2019
Highlights•R-loops
formed
within
plasmids
promote
antisense
transcription
in
nuclear
extracts•TSS
of
lncRNA
and
eRNA
are
often
near
R-loop
structures
sensitive
to
RNase
H1•Preinitiation
complexes
associated
with
synthesis
dependent•Many
mammalian
derive
from
promoter
activitySummaryWidespread
long
noncoding
RNA
(lncRNA)
overlap
many
protein-coding
genes
mammals
emanate
gene
promoter,
enhancer,
termination
regions.
However,
their
origin
biological
purpose
remain
unclear.
We
show
that
these
can
be
generated
by
R-loops
form
when
nascent
transcript
invades
the
DNA
duplex
behind
elongating
polymerase
II
(Pol
II).
Biochemically,
act
as
intrinsic
Pol
promoters
induce
de
novo
synthesis.
Furthermore,
removal
across
human
genome
H1
overexpression
causes
selective
reduction
transcription.
Consequently,
we
predict
facilitate
proximal
lncRNA.
Not
only
widely
damage
repair,
but
now
they
have
capacity
may
aided
evolution
regulation.Graphical
abstract
Abstract
Background
The
binding
of
transcription
factors
(TF)
to
genomic
targets
is
critical
in
the
regulation
gene
expression.
Short,
double-stranded
DNA
sequence
motifs
are
routinely
implicated
TF
recruitment,
but
many
questions
remain
on
how
site
specificity
governed.
Results
Herein,
we
reveal
a
previously
unappreciated
role
for
secondary
structures
as
key
features
recruitment.
In
systematic,
genome-wide
study,
discover
that
endogenous
G-quadruplex
(G4s)
prevalent
sites
human
chromatin.
Certain
TFs
bind
G4s
with
affinities
comparable
targets.
We
demonstrate
that,
chromatin
context,
this
interaction
competed
out
small
molecule.
Notably,
prominent
large
number
TFs,
particularly
at
promoters
highly
expressed
genes.
Conclusions
Our
results
novel
non-canonical
mechanism
whereby
operate
common
hubs
different
promote
increased
transcription.
Genome Research,
Год журнала:
2018,
Номер
28(9), С. 1405 - 1414
Опубликована: Авг. 14, 2018
RNA/DNA
hybrids
form
when
RNA
hybridizes
with
its
template
DNA
generating
a
three-stranded
structure
known
as
the
R-loop.
Knowledge
of
how
they
and
resolve,
well
their
functional
roles,
is
limited.
Here,
by
pull-down
assays
followed
mass
spectrometry,
we
identified
803
proteins
that
bind
to
hybrids.
Because
these
were
using
in
vitro
assays,
confirmed
R-loops
vivo.
They
include
are
involved
variety
functions,
including
most
steps
processing.
The
enriched
for
K
homology
(KH)
helicase
domains.
Among
them,
more
than
300
preferred
binding
double-stranded
DNA.
These
serve
starting
points
mechanistic
studies
elucidate
what
regulate
regulated.
Nucleic Acids Research,
Год журнала:
2021,
Номер
50(3), С. e13 - e13
Опубликована: Окт. 21, 2021
Abstract
Single-stranded
genomic
DNA
can
fold
into
G-quadruplex
(G4)
structures
or
form
DNA:RNA
hybrids
(R
loops).
Recent
evidence
suggests
that
such
non-canonical
affect
gene
expression,
methylation,
replication
fork
progression
and
genome
stability.
When
how
G4
are
resolved
remains
unclear.
Here
we
report
the
use
of
Cleavage
Under
Targets
Tagmentation
(CUT&Tag)
for
mapping
native
in
mammalian
cell
lines
at
high
resolution
low
background.
Mild
conditions
used
procedure
retain
more
provide
a
higher
signal-to-noise
ratio
than
ChIP-based
methods.
We
determine
landscape
mouse
embryonic
stem
cells
(ESC),
observing
widespread
formation
active
promoters,
poised
enhancers.
discover
presence
motifs
distinguishes
primed
enhancers
ESCs.
Upon
differentiation
to
neural
progenitor
(NPC),
enhancer
G4s
lost.
Further,
performing
R-loop
CUT&Tag,
demonstrate
genome-wide
co-occurrence
single-stranded
DNA,
R
loops
promoters
confirm
exist
independent
ongoing
transcription,
suggesting
an
intricate
relationship
between
transcription
structures.
Nature Communications,
Год журнала:
2021,
Номер
12(1)
Опубликована: Дек. 16, 2021
Transcription
poses
a
threat
to
genomic
stability
through
the
formation
of
R-loops
that
can
obstruct
progression
replication
forks.
are
three-stranded
nucleic
acid
structures
formed
by
an
RNA-DNA
hybrid
with
displaced
non-template
DNA
strand.
We
developed
Proximity
Proteomics
map
R-loop
proximal
proteome
human
cells
using
quantitative
mass
spectrometry.
implicate
different
cellular
proteins
in
regulation
and
identify
role
tumor
suppressor
DDX41
opposing
double
strand
break
accumulation
promoters.
is
enriched
promoter
regions
vivo,
unwind
hybrids
vitro.
upon
loss
accompanied
stress,
increase
breaks
transcriptome
changes
associated
inflammatory
response.
Germline
loss-of-function
mutations
lead
predisposition
acute
myeloid
leukemia
adulthood.
propose
instability-associated
response
may
contribute
development
familial
AML
mutated
DDX41.
Molecular Cell,
Год журнала:
2022,
Номер
82(4), С. 833 - 851.e11
Опубликована: Фев. 1, 2022
HOTTIP
lncRNA
is
highly
expressed
in
acute
myeloid
leukemia
(AML)
driven
by
MLL
rearrangements
or
NPM1
mutations
to
mediate
HOXA
topologically
associated
domain
(TAD)
formation
and
drive
aberrant
transcription.
However,
the
mechanism
through
which
accesses
CCCTC-binding
factor
(CTCF)
chromatin
boundaries
regulates
CTCF-mediated
genome
topology
remains
unknown.
Here,
we
show
that
directly
interacts
with
a
fraction
of
CTCF-binding
sites
(CBSs)
AML
recruiting
CTCF/cohesin
complex
R-loop-associated
regulators
form
R-loops.
HOTTIP-mediated
R-loops
reinforce
CTCF
boundary
facilitate
TADs
gene
Either
deleting
CBS
targeting
RNase
H
eliminate
β-catenin
TAD
impaired
activity,
inhibited
promoter/enhancer
interactions,
reduced
target
expression,
mitigated
leukemogenesis
xenograft
mouse
models
expression.
Thus,
R-loop
reinforces
activity
integrity
oncogene
transcription
development.