International Journal of Molecular Sciences,
Journal Year:
2024,
Volume and Issue:
25(15), P. 8247 - 8247
Published: July 28, 2024
Salinity
is
a
common
abiotic
stress
that
limits
crop
productivity.
Although
there
wealth
of
evidence
suggesting
miRNA
and
lncRNA
play
important
roles
in
the
response
to
salinity
rice
seedlings
reproductive
stages,
mechanism
by
which
competing
endogenous
RNAs
(ceRNAs)
influence
salt
tolerance
yield
has
been
rarely
reported.
In
this
study,
we
conducted
full
whole-transcriptome
sequencing
panicles
during
period
clarify
role
ceRNAs
yield.
A
total
214
lncRNAs,
79
miRNAs,
584
mRNAs
were
identified
as
differentially
expressed
under
stress.
Functional
analysis
indicates
they
GO
terms
such
stress,
biosynthesis
processes,
stimuli,
stimulus,
well
KEGG
pathways
secondary
metabolite
biosynthesis,
carotenoid
metabolic
pathways,
phenylpropanoid
biosynthesis.
ceRNA
network
comprising
95
lncRNA-miRNA-mRNA
triplets
was
constructed.
Two
MSTRG.51634.2
MSTRG.48576.1,
predicted
bind
osa-miR172d-5p
regulate
expression
Non-Coding RNA,
Journal Year:
2024,
Volume and Issue:
10(1), P. 13 - 13
Published: Feb. 7, 2024
Plant
species
utilize
a
variety
of
regulatory
mechanisms
to
ensure
sustainable
productivity.
Within
this
intricate
framework,
numerous
non-coding
RNAs
(ncRNAs)
play
crucial
role
in
plant
biology,
surpassing
the
essential
functions
RNA
molecules
as
messengers,
ribosomal,
and
transfer
RNAs.
ncRNAs
represent
an
emerging
class
regulators,
operating
directly
form
small
interfering
(siRNAs),
microRNAs
(miRNAs),
long
noncoding
(lncRNAs),
circular
(circRNAs).
These
exert
control
at
various
levels,
including
transcription,
post-transcription,
translation,
epigenetic.
Furthermore,
they
interact
with
each
other,
contributing
biological
processes
associated
stress
resilience.
This
review
primarily
concentrates
on
recent
advancements
ncRNAs,
delineating
their
growth
development
across
organs
such
root,
leaf,
seed/endosperm,
seed
nutrient
development.
Additionally,
broadens
its
scope
by
examining
response
environmental
stresses
drought,
salt,
flood,
heat,
cold
plants.
compilation
offers
updated
information
insights
guide
characterization
potential
growth,
development,
resilience
future
research.
Trends in Plant Science,
Journal Year:
2024,
Volume and Issue:
29(7), P. 770 - 785
Published: Feb. 16, 2024
The
plant
long
noncoding
(lnc)RNA
field
is
on
the
brink
of
transitioning
from
large-scale
identification
lncRNAs
to
their
functional
characterization.
Due
cross-kingdom
conservation
interaction
types
and
molecular
functions,
there
much
be
learned
mammalian
lncRNA
research.
Here,
we
discuss
different
processes
involving
regulation
chromatin
splicing.
Furthermore,
interactome,
which
includes
proteins,
other
RNAs,
DNA.
We
explore
how
functionalities
could
reflected
in
similar
pathways
plants
hypothesize
that
several
breakthroughs
research
lead
discovery
novel
functions.
Expanding
our
knowledge
biological
role
multiple
applications
paves
way
for
future
agricultural
applications.
ABSTRACT
Epigenetic
mechanisms,
including
DNA
methylation,
histone
modifications,
and
Noncoding
RNAs,
play
a
critical
role
in
enabling
plants
to
adapt
environmental
changes
without
altering
their
sequence.
These
processes
dynamically
regulate
gene
expression
response
diverse
stressors,
making
them
essential
for
plant
resilience
under
changing
global
conditions.
This
review
synthesises
research
on
tropical
subtropical
plants—species
naturally
exposed
extreme
temperatures,
salinity,
drought,
other
stressors—while
drawing
parallels
with
similar
mechanisms
observed
arid
temperate
ecosystems.
By
integrating
molecular
biology
ecology,
this
synthesis
highlights
how
provide
valuable
models
understanding
strategies
applicable
across
broader
taxa.
underscores
the
potential
of
epigenetic
inform
conservation
agricultural
innovations
aimed
at
bolstering
face
climate
change.
RNA Biology,
Journal Year:
2024,
Volume and Issue:
21(1), P. 1 - 12
Published: March 25, 2024
The
accurate
classification
of
non-coding
RNA
(ncRNA)
sequences
is
pivotal
for
advanced
genome
annotation
and
analysis,
a
fundamental
aspect
genomics
that
facilitates
understanding
ncRNA
functions
regulatory
mechanisms
in
various
biological
processes.
While
traditional
machine
learning
approaches
have
been
employed
distinguishing
ncRNA,
these
often
necessitate
extensive
feature
engineering.
Recently,
deep
algorithms
provided
advancements
classification.
This
study
presents
BioDeepFuse,
hybrid
framework
integrating
convolutional
neural
networks
(CNN)
or
bidirectional
long
short-term
memory
(BiLSTM)
with
handcrafted
features
enhanced
accuracy.
employs
combination
k-mer
one-hot,
dictionary,
extraction
techniques
input
representation.
Extracted
features,
when
embedded
into
the
network,
enable
optimal
utilization
spatial
sequential
nuances
sequences.
Using
benchmark
datasets
real-world
samples
from
bacterial
organisms,
we
evaluated
performance
BioDeepFuse.
Results
exhibited
high
accuracy
classification,
underscoring
robustness
our
tool
addressing
complex
sequence
data
challenges.
effective
melding
CNN
BiLSTM
external
heralds
promising
directions
future
research,
particularly
refining
classifiers
deepening
insights
ncRNAs
cellular
processes
disease
manifestations.
In
addition
to
its
original
application
context
methodologies
integrated
can
potentially
render
BioDeepFuse
broader
domains.
Plant Communications,
Journal Year:
2024,
Volume and Issue:
5(7), P. 100927 - 100927
Published: April 27, 2024
Long
non-coding
RNAs
(lncRNAs)
have
emerged
as
integral
gene-expression
regulators
underlying
plant
growth,
development,
and
adaptation.
To
adapt
to
the
heterogeneous
dynamic
rhizosphere,
plants
use
interconnected
regulatory
mechanisms
optimally
fine-tune
gene-expression-governing
interactions
with
soil
biota,
well
nutrient
acquisition
heavy
metal
tolerance.
Recently,
high-throughput
sequencing
has
enabled
identification
of
lncRNAs
responsive
rhizosphere
biotic
abiotic
cues.
Here,
we
examine
lncRNA
biogenesis,
classification,
mode
action,
highlighting
functions
in
mediating
adaptation
diverse
factors.
We
then
discuss
studies
that
reveal
significance
target
genes
during
developmental
plasticity
stress
responses
at
rhizobium
interface.
A
comprehensive
understanding
specific
lncRNAs,
their
targets,
intricacies
functional
interaction
networks
will
provide
crucial
insights
into
how
these
transcriptomic
switches
shifting
signals.
Looking
ahead,
foresee
single-cell
dissection
cell-type-specific
dynamics
enhance
our
precise
modulation
enable
Overcoming
future
challenges
through
multi-omics
genetic
approaches
more
fully
roles
governing
belowground
environment.
