Nature Cell Biology,
Journal Year:
2024,
Volume and Issue:
26(5), P. 797 - 810
Published: April 10, 2024
Abstract
Covalent
DNA–protein
cross-links
(DPCs)
are
toxic
DNA
lesions
that
block
replication
and
require
repair
by
multiple
pathways.
Whether
transcription
blockage
contributes
to
the
toxicity
of
DPCs
how
cells
respond
when
RNA
polymerases
stall
at
is
unknown.
Here
we
find
DPC
formation
arrests
induces
ubiquitylation
degradation
polymerase
II.
Using
genetic
screens
a
method
for
genome-wide
mapping
adducts,
sequencing,
discover
Cockayne
syndrome
(CS)
proteins
CSB
CSA
provide
resistance
DPC-inducing
agents
promoting
in
actively
transcribed
genes.
Consequently,
CSB-
or
CSA-deficient
fail
efficiently
restart
after
induction
DPCs.
In
contrast,
nucleotide
excision
factors
act
downstream
ultraviolet
light-induced
dispensable.
Our
study
describes
transcription-coupled
pathway
suggests
defects
this
may
contribute
unique
neurological
features
CS.
Nature Cell Biology,
Journal Year:
2024,
Volume and Issue:
26(5), P. 770 - 783
Published: April 10, 2024
DNA-protein
crosslinks
(DPCs)
arise
from
enzymatic
intermediates,
metabolism
or
chemicals
like
chemotherapeutics.
DPCs
are
highly
cytotoxic
as
they
impede
DNA-based
processes
such
replication,
which
is
counteracted
through
proteolysis-mediated
DPC
removal
by
spartan
(SPRTN)
the
proteasome.
However,
whether
affect
transcription
and
how
transcription-blocking
repaired
remains
largely
unknown.
Here
we
show
that
severely
RNA
polymerase
II-mediated
preferentially
in
active
genes
transcription-coupled
(TC-DPC)
repair.
TC-DPC
repair
initiated
recruiting
nucleotide
excision
(TC-NER)
factors
CSB
CSA
to
DPC-stalled
II.
indispensable
for
repair;
however,
downstream
TC-NER
UVSSA
XPA
not,
a
result
indicative
of
non-canonical
mechanism.
functions
independently
SPRTN
but
mediated
ubiquitin
ligase
CRL4
Nucleic Acids Research,
Journal Year:
2024,
Volume and Issue:
52(14), P. 8271 - 8285
Published: June 19, 2024
Abstract
Formaldehyde
(FA)
is
a
recognized
environmental
and
metabolic
toxin
implicated
in
cancer
development
aging.
Inherited
mutations
the
FA-detoxifying
enzymes
ADH5
ALDH2
genes
lead
to
FA
overload
severe
multisystem
AMeD
syndrome.
accumulation
causes
genome
damage
including
DNA–protein-,
inter-
intra-strand
crosslinks
oxidative
lesions.
However,
influence
of
distinct
DNA
repair
systems
on
organismal
resistance
remains
elusive.
We
have
here
investigated
consequence
range
mutants
model
endogenous
generated
by
downregulating
orthologs
human
C.
elegans.
focused
components
nucleotide
excision
(NER)
during
developmental
growth,
reproduction
Our
results
reveal
three
modes
FA-induced
damage:
Transcription-coupled
(TCR)
operating
NER-independently
growth
or
through
NER
adulthood,
and,
concert
with
global-genome
(GG-)
NER,
germline
early
embryonic
development.
Additionally,
we
show
that
Cockayne
syndrome
B
(CSB)
factor
involved
resolution
DNA–protein
crosslinks,
antioxidant
quencher
N-acetyl-l-cysteine
(NAC)
reverses
sensitivity
detoxification
defects
development,
suggesting
therapeutic
intervention
revert
FA-pathogenic
consequences.
ACS Synthetic Biology,
Journal Year:
2025,
Volume and Issue:
unknown
Published: May 6, 2025
Homology-directed
repair
(HDR)
allows
the
precise
introduction
of
functional
constructs
into
human
genome
through
nonviral
gene-editing
reagents.
However,
its
application
in
large
DNA
sequence
gene
editing
remains
limited
due
to
challenges
such
as
low
efficiency
and
off-target
effect.
To
address
these
limitations,
a
new
method
named
AOLP
was
developed
synthesize
chemically
modified
long
single-stranded
(lssDNA)
template
donor
for
Cas9-based
editing,
which
has
been
proven
be
more
stable
than
that
prepared
using
commercial
phosphorylation
method.
We
propose
novel
strategy
involving
ligation-based
interstrand
cross-linking
between
lssDNA
sgRNA
cyanovinylcarbazole
nucleoside
(CNVK),
enhancing
upregulation
HDR
pathway
DSB
induced
by
Cas9.
The
light-activated
ligation
Cas9/sgRNA
improves
knock-in
(KI)
efficiency,
overcomes
KI
surpasses
effect
accompanied
donor.
Moreover,
can
subtly
control
sites
degree
enhance
accuracy
HDR.
Our
approach
K562,
HEK293T,
HepG2
cells
4-
12-fold
relative
conventional
donors
Furthermore,
HEK293T
is
enhanced
>4.7-fold
previous
lssDNA.
Leveraging
this
approach,
we
achieved
an
unprecedented
rate
approximately
36%
gene-sized
1.4
kilobase
insertion
cells.
Life,
Journal Year:
2023,
Volume and Issue:
13(6), P. 1360 - 1360
Published: June 9, 2023
A
pangenome
is
a
collection
of
the
common
and
unique
genomes
that
are
present
in
given
species.
It
combines
genetic
information
all
sampled,
resulting
large
diverse
range
material.
Pangenomic
analysis
offers
several
advantages
compared
to
traditional
genomic
research.
For
example,
not
bound
by
physical
constraints
single
genome,
so
it
can
capture
more
variability.
Thanks
introduction
concept
pangenome,
possible
use
exceedingly
detailed
sequence
data
study
evolutionary
history
two
different
species,
or
how
populations
within
species
differ
genetically.
In
wake
Human
Pangenome
Project,
this
review
aims
at
discussing
around
human
variation,
which
then
framed
pangenomic
inform
population
genetics,
phylogenetics,
public
health
policy
providing
insights
into
basis
diseases
determining
personalized
treatments,
targeting
specific
profile
an
individual.
Moreover,
technical
limitations,
ethical
concerns,
legal
considerations
discussed.
Nucleic Acids Research,
Journal Year:
2023,
Volume and Issue:
52(2), P. 525 - 547
Published: Dec. 12, 2023
Abstract
DNA–protein
crosslinks
(DPCs)
are
toxic
DNA
lesions
wherein
a
protein
is
covalently
attached
to
DNA.
If
not
rapidly
repaired,
DPCs
create
obstacles
that
disturb
replication,
transcription
and
damage
repair,
ultimately
leading
genome
instability.
The
persistence
of
associated
with
premature
ageing,
cancer
neurodegeneration.
In
mammalian
cells,
the
repair
mainly
relies
on
proteolytic
activities
SPRTN
26S
proteasome,
complemented
by
other
enzymes
including
TDP1/2
MRN
complex,
many
involved
essential,
restricting
genetic
approaches.
For
years,
study
DPC
in
cells
was
hindered
lack
standardised
assays,
most
notably
assays
reliably
quantified
proteins
or
fragments
bound
Recent
interest
field
has
spurred
development
several
biochemical
methods
for
analysis.
Here,
we
critically
analyse
latest
techniques
isolation
benefits
drawbacks
each.
We
aim
assist
researchers
selecting
suitable
method
their
experimental
requirements
questions,
facilitate
comparison
results
across
different
laboratories
using
