Molecular Cell,
Journal Year:
2021,
Volume and Issue:
81(10), P. 2216 - 2230.e10
Published: April 13, 2021
DNA
double-strand
break
(DSB)
repair
is
mediated
by
multiple
pathways.
It
thought
that
the
local
chromatin
context
affects
pathway
choice,
but
underlying
principles
are
poorly
understood.
Using
a
multiplexed
reporter
assay
in
combination
with
Cas9
cutting,
we
systematically
measure
relative
activities
of
three
DSB
pathways
as
function
>1,000
genomic
locations.
This
reveals
non-homologous
end-joining
(NHEJ)
broadly
biased
toward
euchromatin,
while
contribution
microhomology-mediated
(MMEJ)
higher
specific
heterochromatin
contexts.
In
H3K27me3-marked
heterochromatin,
inhibition
H3K27
methyltransferase
EZH2
reverts
balance
NHEJ.
Single-stranded
template
(SSTR),
often
used
for
precise
CRISPR
editing,
competes
MMEJ
and
moderately
linked
to
context.
These
results
provide
insight
into
impact
on
guidance
design
Cas9-mediated
genome
editing
experiments.
Nucleic Acids Research,
Journal Year:
2019,
Volume and Issue:
47(W1), P. W171 - W174
Published: May 6, 2019
Abstract
The
CRISPR–Cas
system
is
a
powerful
genome
editing
tool
that
functions
in
diverse
array
of
organisms
and
cell
types.
technology
was
initially
developed
to
induce
targeted
mutations
DNA,
but
has
now
been
adapted
target
nucleic
acids
for
range
purposes.
CHOPCHOP
web
identifying
single
guide
RNA
(sgRNA)
targets.
In
this
major
update
CHOPCHOP,
we
expand
our
toolbox
beyond
knockouts.
We
introduce
functionality
targeting
with
Cas13,
which
includes
support
alternative
transcript
isoforms
accessibility
predictions.
incorporate
new
DNA
modes,
including
CRISPR
activation/repression,
enrichment
loci
long-read
sequencing,
prediction
Cas9
repair
outcomes.
Finally,
results
page
visualization
reveal
downstream
ATG
sites,
will
aid
users
avoiding
the
expression
truncated
proteins.
supports
over
200
genomes
have
released
command-line
script
running
larger
jobs
handling
unsupported
genomes.
v3
can
be
found
at
https://chopchop.cbu.uib.no
Science,
Journal Year:
2019,
Volume and Issue:
364(6437), P. 286 - 289
Published: April 19, 2019
Spotting
off-targets
from
gene
editing
Unintended
genomic
modifications
limit
the
potential
therapeutic
use
of
gene-editing
tools.
Available
methods
to
find
generally
do
not
work
in
vivo
or
detect
single-nucleotide
changes.
Three
papers
this
issue
report
new
for
monitoring
tools
(see
Perspective
by
Kempton
and
Qi).
Wienert
et
al.
followed
recruitment
a
DNA
repair
protein
breaks
induced
CRISPR-Cas9,
enabling
unbiased
detection
off-target
cellular
animal
models.
Zuo
identified
without
interference
natural
genetic
heterogeneity
injecting
base
editors
into
one
blastomere
two-cell
mouse
embryo
leaving
other
genetically
identical
unedited.
Jin
performed
whole-genome
sequencing
on
individual,
genome-edited
rice
plants
identify
unintended
mutations.
Cytosine,
but
adenine,
numerous
variants
both
rice.
Science
,
p.
286
289
292
;
see
also
234
