Life Science Alliance,
Год журнала:
2021,
Номер
5(3), С. e202101217 - e202101217
Опубликована: Дек. 8, 2021
Nonsense-mediated
mRNA
decay
(NMD)
is
an
essential,
highly
conserved
quality
control
pathway
that
detects
and
degrades
mRNAs
containing
premature
termination
codons.
Although
the
essentiality
of
NMD
frequently
ascribed
to
its
prevention
truncated
protein
accumulation,
extent
which
actually
suppresses
proteins
encoded
by
NMD-sensitive
transcripts
less
well-understood
than
NMD-mediated
suppression
mRNA.
Here,
we
describe
a
reporter
system
permits
accurate
quantification
both
levels
via
stable
integration
paired
reporters
encoding
NMD-insensitive
into
AAVS1
safe
harbor
loci
in
human
cells.
We
use
this
demonstrate
up
eightfold
more
itself.
Our
data
indicate
limits
accumulation
substrates
mechanisms
beyond
degradation,
such
even
when
escape
destruction,
their
are
still
effectively
suppressed.
Abstract
mRNA
surveillance
pathways
are
essential
for
accurate
gene
expression
and
to
maintain
translation
homeostasis,
ensuring
the
production
of
fully
functional
proteins.
Future
insights
into
quality
control
will
enable
us
understand
how
cellular
levels
controlled,
defective
or
unwanted
mRNAs
can
be
eliminated,
dysregulation
these
contribute
human
disease.
Here
we
review
translation‐coupled
mechanisms,
including
non‐stop
no‐go
decay
pathways,
describing
their
shared
trans‐acting
factors,
differences.
We
also
describe
advances
in
our
understanding
nonsense‐mediated
(NMD)
pathway,
highlighting
recent
mechanistic
findings,
discovery
novel
as
well
role
NMD
physiology
its
impact
on
Abstract
The
human
genome
contains
instructions
to
transcribe
more
than
200,000
RNAs.
However,
many
RNA
transcripts
are
generated
from
the
same
gene,
resulting
in
alternative
isoforms
that
highly
similar
and
remain
difficult
quantify.
To
evaluate
ability
study
transcript
expression,
we
profiled
seven
cell
lines
with
five
different
RNA-sequencing
protocols,
including
short-read
cDNA,
Nanopore
long-read
direct
RNA,
amplification-free
cDNA
PCR-amplified
sequencing,
PacBio
IsoSeq,
multiple
spike-in
controls,
additional
transcriptome-wide
N
6
-methyladenosine
profiling
data.
We
describe
differences
read
length,
coverage,
throughput
reporting
sequencing
robustly
identifies
major
isoforms.
illustrate
value
of
SG-NEx
data
identify
isoforms,
novel
transcripts,
fusion
modifications.
Together,
provide
a
comprehensive
resource
enabling
development
benchmarking
computational
methods
for
complex
transcriptional
events
at
isoform-level
resolution.
Nonsense-mediated
mRNA
decay
(NMD)
is
a
eukaryotic,
translation-dependent
degradation
pathway
that
targets
mRNAs
with
premature
termination
codons
and
also
regulates
the
expression
of
some
encode
full-length
proteins.
Although
many
genes
express
NMD-sensitive
transcripts,
identifying
them
based
on
short-read
sequencing
data
remains
challenge.
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Май 6, 2023
Abstract
Alternative
splicing
of
neuronal
genes
is
controlled
partly
by
the
coordinated
action
polypyrimidine
tract
binding
proteins
(PTBPs).
While
PTBP1
ubiquitously
expressed,
PTBP2
predominantly
neuronal.
Here,
we
define
footprint
in
human
transcriptome
using
brain
tissue
and
induced
pluripotent
stem
cell-derived
neurons
(iPSC-neurons).
We
map
sites,
characterize
PTBP2-dependent
alternative
events,
identify
novel
targets
including
SYNGAP1
,
a
synaptic
gene
whose
loss-of-function
leads
to
complex
neurodevelopmental
disorder.
find
that
mRNA
promotes
nonsense-mediated
decay,
antisense
oligonucleotides
(ASOs)
disrupt
PTBP
redirect
increase
protein
expression.
In
haploinsufficient
iPSC-neurons
generated
from
two
patients,
show
PTBP2-targeting
ASOs
partially
restore
Our
data
comprehensively
cerebral
cortex,
guiding
development
therapeutic
tools
benefit
disorders.
mRNA
translation
and
decay
are
tightly
interconnected
processes
both
in
the
context
of
quality-control
pathways
for
degradation
functional
mRNAs.
Cotranslational
through
codon
usage,
ribosome
collisions,
recruitment
specific
proteins
to
ribosomes
is
an
important
determinant
turnover.
However,
extent
which
translation-dependent
(TDD)
translation-independent
(TID)
participate
mRNAs
has
not
been
studied
yet.
Here
we
describe
a
comprehensive
analysis
basal
signal-induced
TDD
TID
mouse
primary
CD4
+
T
cells.
Our
results
indicate
that
most
cellular
transcripts
decayed
some
manner.
further
identifies
length
untranslated
regions,
density
ribosomes,
GC3
content
as
determinants
magnitude.
Consistently,
all
undergo
changes
within
their
coding
sequence
upon
cell
activation
display
corresponding
change
level.
Moreover,
reveal
dynamic
modulation
relationship
between
activation,
with
reversal
impact
GC3-
AU3-rich
codons.
Altogether,
our
data
show
strong
interconnection
mammalian
Nucleic Acids Research,
Год журнала:
2025,
Номер
53(9)
Опубликована: Май 10, 2025
Abstract
Nonsense-mediated
RNA
decay
(NMD)
is
a
highly
conserved
turnover
pathway
that
influences
several
biological
processes.
Specific
features
in
messenger
RNAs
(mRNAs)
have
been
found
to
trigger
by
NMD,
leading
the
assumption
NMD
sensitivity
an
intrinsic
quality
of
given
transcript.
Here,
we
provide
evidence
that,
instead,
overriding
factor
dictating
cell
environment.
Using
genome-wide
techniques
detect
NMD-target
mRNAs,
find
hundreds
mRNAs
are
sensitized
as
human
embryonic
stem
cells
progress
form
neural
progenitor
cells.
Another
class
escape
from
during
this
developmental
progression.
We
show
differential
extends
vivo
scenarios,
and
RNA-binding
protein,
HNRNPL,
has
role
type-specific
NMD.
also
addressed
another
issue
field—whether
factors
core
or
branch-specific
their
action.
Surprisingly,
UPF3B,
critical
for
nervous
system,
shares
only
30%
transcripts
with
UPF2.
Together,
our
findings
implications
how
defined
measured,
acts
different
contexts,
branches
influence
diseases.
