Nature Biotechnology,
Год журнала:
2023,
Номер
42(1), С. 72 - 86
Опубликована: Апрель 6, 2023
Transfer
RNAs
(tRNAs)
play
a
central
role
in
protein
translation.
Studying
them
has
been
difficult
part
because
simple
method
to
simultaneously
quantify
their
abundance
and
chemical
modifications
is
lacking.
Here
we
introduce
Nano-tRNAseq,
nanopore-based
approach
sequence
native
tRNA
populations
that
provides
quantitative
estimates
of
both
abundances
modification
dynamics
single
experiment.
We
show
default
nanopore
sequencing
settings
discard
the
vast
majority
reads,
leading
poor
yields
biased
representations
based
on
transcript
length.
Re-processing
raw
current
intensity
signals
leads
12-fold
increase
number
recovered
reads
enables
recapitulation
accurate
abundances.
then
apply
Nano-tRNAseq
Saccharomyces
cerevisiae
populations,
revealing
crosstalks
interdependencies
between
different
types
within
same
molecule
changes
response
oxidative
stress.
Nucleic Acids Research,
Год журнала:
2017,
Номер
46(D1), С. D303 - D307
Опубликована: Окт. 18, 2017
MODOMICS
is
a
database
of
RNA
modifications
that
provides
comprehensive
information
concerning
the
chemical
structures
modified
ribonucleosides,
their
biosynthetic
pathways,
location
residues
in
sequences,
and
RNA-modifying
enzymes.
In
current
version,
we
included
following
new
features
data:
extended
mass
spectrometry
liquid
chromatography
data
for
nucleosides;
links
between
human
tRNA
sequences
MINTbase
-
framework
interactive
exploration
mitochondrial
nuclear
fragments;
new,
machine-friendly
system
unified
abbreviations
nucleoside
names;
sets
two
bacterial
species,
updated
collection
mammalian
modifications,
19
newly
identified
ribonucleosides
66
functionally
characterized
proteins
involved
modification.
Data
from
have
been
linked
to
RNAcentral
sequences.
available
at
http://modomics.genesilico.pl.
Nature Communications,
Год журнала:
2019,
Номер
10(1)
Опубликована: Сен. 9, 2019
Abstract
The
epitranscriptomics
field
has
undergone
an
enormous
expansion
in
the
last
few
years;
however,
a
major
limitation
is
lack
of
generic
methods
to
map
RNA
modifications
transcriptome-wide.
Here,
we
show
that
using
direct
sequencing,
N
6
-methyladenosine
(m
A)
can
be
detected
with
high
accuracy,
form
systematic
errors
and
decreased
base-calling
qualities.
Specifically,
find
our
algorithm,
trained
m
A-modified
unmodified
synthetic
sequences,
predict
A
~90%
accuracy.
We
then
extend
findings
yeast
data
sets,
finding
method
identify
vivo
accuracy
87%.
Moreover,
further
validate
by
showing
these
‘errors’
are
typically
not
observed
ime4
-knockout
strains,
which
modifications.
Our
results
open
avenues
investigate
biological
roles
their
native
context.
Experimental & Molecular Medicine,
Год журнала:
2020,
Номер
52(3), С. 400 - 408
Опубликована: Март 1, 2020
Many
studies
have
highlighted
the
importance
of
tight
regulation
mRNA
stability
in
control
gene
expression.
largely
depends
on
nucleotide
sequence,
which
affects
secondary
and
tertiary
structures
mRNAs,
accessibility
various
RNA-binding
proteins
to
mRNAs.
Recent
advances
high-throughput
RNA-sequencing
techniques
resulted
elucidation
important
roles
played
by
modifications
sequences
regulating
stability.
To
date,
hundreds
different
RNA
been
characterized.
Among
them,
several
modifications,
including
N
Abstract
RNA
modifications
have
recently
emerged
as
critical
posttranscriptional
regulators
of
gene
expression
programmes.
Significant
advances
been
made
in
understanding
the
functional
role
regulating
coding
and
non-coding
processing
function,
which
turn
thoroughly
shape
distinct
They
affect
diverse
biological
processes,
correct
deposition
many
these
is
required
for
normal
development.
Alterations
their
are
implicated
several
diseases,
including
cancer.
In
this
Review,
we
focus
on
occurrence
N
6
-methyladenosine
(m
A),
5-methylcytosine
5
C)
pseudouridine
(Ψ)
RNAs
describe
physiopathological
We
will
highlight
latest
insights
into
mechanisms
how
influence
tumour
development,
maintenance,
progression.
Finally,
summarize
development
small
molecule
inhibitors
that
target
specific
writers
or
erasers
to
rewind
epitranscriptome
a
cancer
cell
therapeutic
potential.
