The
interplay
between
G4s
and
R-loops
are
emerging
in
regulating
DNA
repair,
replication,
transcription.
A
comprehensive
picture
of
native
co-localized
living
cells
is
currently
lacking.
Here,
we
describe
the
development
HepG4-seq
an
optimized
HBD-seq
methods,
which
robustly
capture
R-loops,
respectively,
cells.
We
successfully
employed
these
methods
to
establish
maps
human
HEK293
mouse
embryonic
stem
(mESCs).
discovered
that
dynamically
altered
a
cell
type-dependent
manner
largely
localized
at
active
promoters
enhancers
transcriptional
genes.
further
demonstrated
helicase
Dhx9
as
direct
major
regulator
modulates
formation
resolution
R-loops.
Depletion
impaired
self-renewal
differentiation
capacities
mESCs
by
altering
transcription
-associated
Taken
together,
our
work
established
endogenous
prevalently
persisted
regulatory
regions
genes
involved
regulation
their
linked
genes,
opening
door
for
exploring
broader
roles
disease.
Current Opinion in Genetics & Development,
Journal Year:
2024,
Volume and Issue:
85, P. 102159 - 102159
Published: Feb. 20, 2024
Chromosome
structure
regulates
DNA-templated
processes
such
as
transcription
of
genes.
Dynamic
changes
to
chromosome
occur
during
development
and
in
disease
contexts.
The
cohesin
complex
is
a
molecular
motor
that
by
generating
DNA
loops
bring
two
distal
genomic
sites
into
close
spatial
proximity.
There
are
many
open
questions
regarding
the
formation
dissolution
loops,
well
role(s)
regulating
interphase
genome.
This
review
focuses
on
recent
discoveries
provide
insights
role
gene
disease.
NAR Genomics and Bioinformatics,
Journal Year:
2025,
Volume and Issue:
7(1)
Published: Jan. 7, 2025
Repetitive
DNA
sequences
can
form
noncanonical
structures
such
as
H-DNA.
The
new
telomere-to-telomere
genome
assembly
for
the
human
has
eliminated
gaps,
enabling
examination
of
highly
repetitive
regions
including
centromeric
and
pericentromeric
repeats
ribosomal
arrays.
We
find
that
H-DNA
appears
once
every
25
000
base
pairs
in
genome.
Its
distribution
is
inhomogeneous
with
motif
hotspots
being
detectable
acrocentric
chromosomes.
Ribosomal
arrays
are
genomic
element
a
40.94-fold
enrichment.
Across
chromosomes,
we
report
54.82%
motifs
found
these
chromosomes
rDNA
array
loci.
discover
binding
sites
PRDM9-B
allele,
variant
PRDM9
protein,
enriched
motifs.
further
investigate
findings
through
an
analysis
PRDM-9
ChIP-seq
data
across
various
alleles,
observing
enrichment
A-like
alleles
(including
A,
B,
N
alleles),
but
not
C-like
C
L4
alleles).
at
consistent
nonhuman
great
ape
genomes.
conclude
most
loci
other
Genes & Development,
Journal Year:
2024,
Volume and Issue:
unknown
Published: July 10, 2024
Genome
integrity
relies
on
the
accuracy
of
DNA
metabolism,
but
as
appreciated
for
more
than
four
decades,
transcription
enhances
mutation
and
recombination
frequencies.
More
recent
research
provided
evidence
a
previously
unforeseen
link
between
RNA
which
is
often
related
to
accumulation
DNA–RNA
hybrids
R-loops.
In
addition
physiological
roles,
R-loops
interfere
with
replication
repair,
providing
molecular
scenario
origin
genome
instability.
Here,
we
review
current
knowledge
multiple
factors
that
prevent
or
resolve
consequent
transcription–replication
conflicts
thus
act
modulators
dynamics.
PLoS Pathogens,
Journal Year:
2024,
Volume and Issue:
20(8), P. e1012454 - e1012454
Published: Aug. 23, 2024
R-loops
are
trimeric
nucleic
acid
structures
that
form
when
an
RNA
molecule
hybridizes
with
its
complementary
DNA
strand,
displacing
the
opposite
strand.
These
regulate
transcription
as
well
replication,
but
aberrant
can
form,
leading
to
breaks
and
genomic
instability
if
unresolved.
R-loop
levels
elevated
in
many
cancers
cells
maintain
high-risk
human
papillomaviruses.
We
investigated
how
distribution
function
of
changed
between
normal
keratinocytes
HPV
positive
derived
from
a
precancerous
lesion
cervix
(CIN
I).
The
associated
cellular
genes
were
found
be
up
10-fold
higher
than
while
increases
at
ALU1
elements
increased
by
500-fold.
presence
enhanced
resulted
altered
gene
transcription,
equal
numbers
decreased.
While
no
uniform
global
effects
on
due
detected,
several
pathways
coordinately
or
decreased
expression
only
cells.
This
included
downregulation
innate
immune
pathway,
such
DDX58,
IL-6,
STAT1,
IFN-β,
NLRP3.
All
differentially
expressed
dependent
also
H3K36me3
modified
histones.
Genes
upregulated
those
damage
repair
ATM,
ATRX,
members
Fanconi
Anemia
pathway.
exhibited
linkage
γH2AX
histone
marks
studies
identify
potential
link
regulatory
γH2AX/H3K36me3
may
contribute
regulating
important
functions
for
pathogenesis.
Although
the
role
of
G-quadruplex
(G4)
DNA
structures
has
been
suggested
in
chromosomal
looping
this
was
not
tested
directly.
Here,
to
test
causal
function,
an
array
G4s,
or
control
sequence
that
does
form
were
inserted
within
chromatin
cells.
In
vivo
G4
formation
array,
and
sequence,
confirmed
using
G4-selective
antibody.
Compared
insert,
we
observed
a
remarkable
increase
number
3D
interactions
from
array.
This
evident
immediate
topologically
associated
domain
(TAD)
throughout
genome.
Locally,
recruitment
enhancer
histone
marks
transcriptional
coactivator
p300/Acetylated-p300
increased
G4-array,
but
insertion.
Resulting
promoter-enhancer
gene
activation
clear
up
5
Mb
away
insertion
site.
Together,
these
show
G4s
function
long-range
interactions.
Mechanisms
topology
are
primarily
based
on
DNA-bound
architectural
proteins
induce/stabilize
Involvement
underlying
intrinsic
sequence/structure
shown
here
therefore
throws
new
light
how
might
be
induced
maintained.
