bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Dec. 21, 2023
ABSTRACT
Living
organisms
must
maintain
the
integrity
of
their
genome,
and
plants
are
not
exempt.
In
plants,
recognition
DNA
damage
converges
at
transcription
factor
SOG1,
a
functional
homolog
animal
p53
protein.
SOG1
directly
controls
expression
hundreds
genes
orchestrates
sophisticated
network
signaling
pathways
termed
DNA-damage
response
(DDR).
Only
recently,
several
long
non-coding
RNA
(lncRNA)
loci
were
identified
to
be
upregulated
by
damage,
only
handful
have
been
confirmed
actively
contribute
DDR.
this
study,
we
focused
on
one
locus
annotated
as
lncRNA
found
that
it
is
strongly
quickly
upon
direct
target
SOG1.
Combining
in
silico
experimental
analyses,
demonstrate
was
wrongly
fact
gene
coding
for
short
protein
targets
peroxisomes.
Consequently,
renamed
S
HORT
P
EROXISOMAL
ROTEIN
INDUCED
IN
D
NA-
AMAGE
R
ESPONSE1
(
SPPiDDR1
).
SPPiDDRs
well
conserved
present
multiple
copies
across
dicot
genomes,
with
Arabidopsis
containing
two
additional
copies,
SPPiDDR2
SPPiDDR3
.
The
AtSPPiDDR
paralogs
differ
transcriptional
level,
being
least
active.
both
also
induced
salt,
stress
treatment
known
indirectly
induce
via
oxidative
stress.
We
show
these
act
redundantly
inhibit
plant
growth
salt
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.
Plants,
Journal Year:
2024,
Volume and Issue:
13(8), P. 1137 - 1137
Published: April 18, 2024
Generally,
lncPEPs
(peptides
encoded
by
long
non-coding
RNAs)
have
been
identified
in
many
plant
species
of
several
families
and
some
animal
species.
Importantly,
molecular
mechanisms
the
miPEPs
primary
microRNAs,
pri-miRNAs)
are
often
poorly
understood
different
flowering
plants.
Requirement
for
additional
studies
these
directions
is
highlighted
alternative
findings
concerning
positive
regulation
pri-miRNA/miRNA
expression
synthetic
Further
extensive
also
needed
to
understand
full
set
their
roles
eukaryotic
organisms.
This
review
mainly
aims
consider
available
data
on
regulatory
functions
miPEPs.
Studies
chemically
synthesized
analyzing
fine
functional
activities
reviewed.
Brief
description
identify
lncORFs
(open
reading
frames
protein
products
provided.
The Plant Journal,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Sept. 10, 2024
SUMMARY
Plant
long
noncoding
RNAs
(lncRNAs)
exhibit
features
such
as
tissue‐specific
expression,
spatiotemporal
regulation,
and
stress
responsiveness.
Although
diverse
studies
support
the
regulatory
role
of
lncRNAs
in
model
plants,
our
knowledge
about
crops
is
limited.
We
employ
a
custom
pipeline
on
dataset
over
1000
RNA‐seq
samples
across
nine
representative
species
family
Cucurbitaceae
to
predict
91
209
nonredundant
lncRNAs.
The
were
characterized
according
three
confidence
levels
classified
by
their
genomic
context
into
intergenic,
natural
antisense,
intronic,
sense‐overlapping.
Compared
with
protein‐coding
genes,
were,
average,
expressed
at
low
displayed
significantly
higher
specificity
when
considering
tissue,
developmental
stages,
evolutionary
analysis
indicates
positional
conservation
than
sequence
conservation,
probably
linked
conserved
modular
motifs
within
syntenic
Moreover,
positive
correlation
between
expression
intergenic/natural
antisense
closest/parental
gene
was
observed.
For
those
decreases
distance
neighboring
gene,
supporting
that
potential
cis‐regulatory
effect
short‐range.
Furthermore,
showed
NAT‐lncRNA
differentially
coordinated
way
cognate
sense
genes.
These
genes
code
for
proteins
associated
phloem
development,
thus
providing
insights
involvement
some
identified
process.
expect
this
extensive
inventory
will
constitute
valuable
resource
further
research
lines
focused
elucidating
mechanisms
mediated
cucurbits.
Life,
Journal Year:
2024,
Volume and Issue:
14(9), P. 1144 - 1144
Published: Sept. 11, 2024
Long
non-coding
RNAs
(lncRNAs)
are
involved
in
numerous
biological
processes
and
serve
crucial
regulatory
functions
both
animals
plants.
Nevertheless,
there
is
limited
understanding
of
lncRNAs
their
patterns
expression
roles
sharks.
In
the
current
study,
we
systematically
identified
characterized
blue
shark
(
The Plant Journal,
Journal Year:
2024,
Volume and Issue:
120(1), P. 370 - 386
Published: Aug. 15, 2024
SUMMARY
Accurate
quantification
of
gene
and
transcript‐specific
expression,
with
the
underlying
knowledge
precise
transcript
isoforms,
is
crucial
to
understanding
many
biological
processes.
Analysis
RNA
sequencing
data
has
benefited
from
development
alignment‐free
algorithms
which
enhance
precision
speed
expression
analysis.
However,
such
require
a
reference
transcriptome.
Here
we
generate
dataset
(LsRTDv1)
for
lettuce
(cv.
Saladin),
combining
long‐
short‐read
publicly
available
transcriptome
annotations,
filtering
keep
only
transcripts
high‐confidence
splice
junctions
transcriptional
start
end
sites.
LsRTDv1
identifies
novel
genes
(mostly
long
non‐coding
RNAs)
increases
number
isoforms
per
in
genome
1.4
2.7.
We
show
that
significantly
mapping
rate
RNA‐seq
time‐series
experiment
(mock‐
Botrytis
cinerea
‐inoculated)
enables
detection
are
differentially
alternatively
spliced
response
infection
as
well
changes.
valuable
resource
investigation
alternative
splicing
regulation
lettuce.
