Structural Features of 5′ Untranslated Region in Translational Control of Eukaryotes
International Journal of Molecular Sciences,
Год журнала:
2025,
Номер
26(5), С. 1979 - 1979
Опубликована: Фев. 25, 2025
Gene
expression
is
a
complex
process
regulated
at
multiple
levels
in
eukaryotic
cells.
Translation
frequently
represents
pivotal
step
the
control
of
gene
expression.
Among
stages
translation,
initiation
particularly
important,
as
it
governs
ribosome
recruitment
and
efficiency
protein
synthesis.
The
5'
untranslated
region
(5'
UTR)
mRNA
plays
key
role
this
process,
often
exhibiting
complicated
structured
landscape.
Numerous
mRNAs
possess
long
UTRs
that
contain
diverse
regulatory
elements,
including
RNA
secondary
structures,
specific
nucleotide
motifs,
chemical
modifications.
These
structural
features
can
independently
modulate
translation
through
their
intrinsic
properties
or
by
serving
platforms
for
trans-acting
factors
such
RNA-binding
proteins.
dynamic
nature
UTR
elements
allows
cells
to
fine-tune
response
environmental
cellular
signals.
Understanding
these
mechanisms
not
only
fundamental
molecular
biology
but
also
holds
significant
biomedical
potential.
Insights
into
UTR-mediated
regulation
could
drive
advancements
synthetic
mRNA-based
targeted
therapies.
This
review
outlines
current
knowledge
UTR,
interplay
between
them,
combined
functional
impact
on
translation.
Язык: Английский
Enhancing the annotation of small ORF-altering variants using MORFEE: introducing MORFEEdb, a comprehensive catalog of SNVs affecting upstream ORFs in human 5'UTRs.
PubMed,
Год журнала:
2025,
Номер
7(1), С. lqaf017 - lqaf017
Опубликована: Март 1, 2025
Non-canonical
small
open
reading
frames
(sORFs)
are
among
the
main
regulators
of
gene
expression.
The
most
studied
these
upstream
ORFs
(upORFs)
located
in
5'-untranslated
region
(UTR)
coding
genes.
Internal
(intORFs)
sequence
and
downstream
(dORFs)
3'UTR
have
received
less
attention.
Different
bioinformatics
tools
permit
prediction
single
nucleotide
variants
(SNVs)
altering
upORFs,
mainly
those
creating
AUGs
or
deleting
stop
codons,
but
no
tool
predicts
non-canonical
translation
initiation
sites
intORFs
dORFs.
We
propose
an
upgrade
our
MORFEE
to
identify
SNVs
that
may
alter
all
types
sORFs
transcripts
from
a
VCF
file.
Moreover,
we
generate
exhaustive
catalog,
named
MORFEEdb,
reporting
possible
existing
upORFs
new
ones
human
transcripts,
provide
R
script
for
visualizing
results.
MORFEEdb
has
been
implemented
public
platform
Mobidetails.
Finally,
annotation
ClinVar
with
reveals
>
45%
UTR-SNVs
can
In
conclusion,
potential
improve
molecular
diagnosis
rare
diseases
facilitate
identification
functional
genome-wide
association
studies
complex
traits.
Язык: Английский
LncRNAs Ride the Storm of Epigenetic Marks
Genes,
Год журнала:
2025,
Номер
16(3), С. 313 - 313
Опубликована: Март 6, 2025
Advancements
in
genome
sequencing
technologies
have
uncovered
the
multifaceted
roles
of
long
non-coding
RNAs
(lncRNAs)
human
cells.
Recent
discoveries
identified
lncRNAs
as
major
players
gene
regulatory
pathways,
highlighting
their
pivotal
role
cell
growth
and
development.
Their
dysregulation
is
implicated
onset
genetic
disorders
age-related
diseases,
including
cancer.
Specifically,
they
been
found
to
orchestrate
molecular
mechanisms
impacting
epigenetics,
DNA
methylation
hydroxymethylation,
histone
modifications,
chromatin
remodeling,
thereby
significantly
influencing
expression.
This
review
provides
an
overview
current
knowledge
on
lncRNA-mediated
epigenetic
regulation
expression,
emphasizing
biomedical
implications
development
different
types
cancers
diseases.
Язык: Английский
Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors
BMC Genomics,
Год журнала:
2025,
Номер
26(1)
Опубликована: Март 14, 2025
Abstract
Understanding
the
dark
genome
is
a
priority
task
following
complete
sequencing
of
human
genome.
Short
open
reading
frames
(sORFs)
are
group
largely
unexplored
elements
with
potential
for
being
translated
into
microproteins.
The
definitive
number
coding
and
regulatory
sORFs
not
known,
however
they
could
account
up
to
1–2%
This
corresponds
an
order
magnitude
in
range
canonical
genes.
For
few
clinical
relevance
has
already
been
demonstrated,
but
majority
biological
function
remains
unclear.
A
major
limitation
predicting
their
disease
using
large-scale
genomic
data
fact
that
no
population-level
constraint
metrics
genetic
variants
yet
available.
To
overcome
this,
we
used
recently
released
gnomAD
4.0
dataset
analyzed
consensus
set
neighbors.
We
demonstrate
mostly
embedded
moderately
constrained
context,
within
gencode
identified
subset
highly
comparable
Язык: Английский
RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling
Briefings in Bioinformatics,
Год журнала:
2025,
Номер
26(2)
Опубликована: Март 1, 2025
Ribosome
profiling
is
a
high-throughput
sequencing
technique
that
captures
the
positions
of
translating
ribosomes
on
RNAs.
Recent
advancements
in
ribosome
include
achieving
highly
phased
footprints
for
plant
translatomes
and
more
recently
bacterial
translatomes.
This
substantially
increases
specificity
detecting
open
reading
frames
(ORFs)
can
be
translated,
such
as
small
ORFs
located
upstream
downstream
annotated
ORFs.
However,
most
genomes
(e.g.
genomes)
lack
annotations
transcription
start
termination
sites.
hinders
systematic
discovery
novel
'untranslated'
regions
data.
Here,
we
develop
new
computational
pipeline
called
RIBOSS
to
discover
noncanonical
assess
their
translational
potential
against
The
Python
modules
are
versatile,
use
them
analyse
both
prokaryotic
eukaryotic
We
present
resulting
list
with
high
Homo
sapiens,
Arabidopsis
thaliana,
Salmonella
enterica.
further
illustrate
utility
when
studying
organisms
incomplete
transcriptome
annotations.
leverage
long-read
short-read
data
reference-guided
assembly
events
assembled
S.
In
sum,
first
integrated
ORF
detection
assessment
incorporates
long-
technologies
investigate
translation.
freely
available
at
https://github.com/lcscs12345/riboss.
Язык: Английский
Editorial: Translational control in cancer
NAR Cancer,
Год журнала:
2024,
Номер
6(3)
Опубликована: Июль 9, 2024
Enhancing the annotation of small ORF-altering variants using MORFEE: introducing MORFEEdb, a comprehensive catalog of SNVs affecting upstream ORFs in human 5’UTRs
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 10, 2024
Abstract
Non-canonical
small
Open
Reading
Frames
(sORFs)
are
among
main
regulators
of
gene
expression.
The
most
studied
ones
upstream
ORFs
(upORFs)
located
in
the
5’UTR
coding
genes.
Internal
(intORFs)
sequence
and
downstream
(dORFs)
3’UTR
have
received
less
attention.
Different
bioinformatics
tools
permit
to
predict
single
nucleotide
variants
(SNVs)
altering
upORFs,
mainly
those
creating
AUGs
or
deleting
stop
codons,
but
no
tool
non-canonical
translation
initiation
sites
intORFs
dORFs.
We
propose
an
upgrade
our
MORFEE
identify
SNVs
that
may
alter
all
types
sORFs
transcripts
from
a
VCF
file.
Moreover,
we
generate
exhaustive
catalog,
named
MORFEEdb,
reporting
possible
existing
upORFs
new
human
provide
R
script
for
visualizing
results.
MORFEEdb
has
been
implemented
public
platform
Mobidetails.
Finally,
annotation
ClinVar
with
reveals
more
than
45%
UTR-SNVs
can
In
conclusion,
potential
improve
molecular
diagnosis
rare
diseases
facilitate
identification
functional
genome-wide
association
studies
complex
traits.
Язык: Английский