Research Square (Research Square),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Aug. 19, 2022
Abstract
Background:
Long
non-coding
RNAs
(lncRNAs),
as
important
regulators,
play
roles
in
plant
growth
and
development.
The
expression
epigenetic
regulation
of
lncRNAs
remain
uncharacterized
generally
seeds,
especially
the
transient
endosperm
dicotyledons.
Results:
In
this
study,
we
identified
11,840
candidate
12
day-after-pollination
sunflower
by
analyzing
RNA-seq
data.
These
were
evenly
distributed
all
chromosomes
had
specific
features
that
distinct
from
mRNAs
including
tissue-specificity
expression,
shorter
fewer
exons.
By
GO
analysis
protein
coding
genes
showing
strong
correlation
with
lncRNAs,
revealed
these
potential
function
many
biological
processes
seed
Additionally,
genome-wide
DNA
methylation
analyses
level
at
transcription
start
sites
was
negatively
correlated
gene
levels
lncRNAs.
Finally,
36
imprinted
32
maternally
expressed
four
paternally
CG
CHG
context,
upstream
body
regions
slightly
lower
than
embryo
tissues,
which
indicated
maternal
demethylation
potentially
induce
bias
endosperm.
Conclusion:
Our
findings
not
only
characterized
on
a
scale
development
endosperm,
but
also
provide
novel
insights
into
parental
effects
dicotyledonous
seeds.
Frontiers in Plant Science,
Journal Year:
2024,
Volume and Issue:
15
Published: May 30, 2024
With
the
rapid
advances
in
next-generation
sequencing
technology,
numerous
non-protein-coding
transcripts
have
been
identified,
including
long
noncoding
RNAs
(lncRNAs),
which
are
functional
comprising
more
than
200
nucleotides.
Although
lncRNA-mediated
regulatory
processes
extensively
investigated
animals,
there
has
considerably
less
research
on
plant
lncRNAs.
Nevertheless,
multiple
studies
major
crops
showed
lncRNAs
involved
crucial
processes,
growth
and
development,
reproduction,
stress
responses.
This
review
summarizes
progress
lncRNA
roles
several
crops,
presents
key
strategies
for
exploring
discusses
current
challenges
future
prospects.
The
insights
provided
this
will
enhance
our
comprehension
of
functions
with
potential
implications
improving
crop
genetics
breeding.
Insects,
Journal Year:
2024,
Volume and Issue:
15(12), P. 950 - 950
Published: Nov. 30, 2024
Background:
Transposable
elements
(TEs)
and
noncoding
sequences
are
major
components
of
the
genome,
yet
their
functional
contributions
to
long
RNAs
(lncRNAs)
not
well
understood.
Although
many
lncRNAs
originating
from
TEs
(TE-lncRNAs)
have
been
identified
across
various
organisms,
characteristics
regulatory
roles,
particularly
in
insects,
remain
largely
unexplored.
This
study
integrated
multi-omics
data
investigate
TE-lncRNAs
D.
melanogaster,
focusing
on
influence
transposons
different
omics
levels.
Results:
We
16,118
overlapping
with
lncRNA
that
constitute
2119
(40.4%
all
lncRNAs)
using
256
public
RNA-seq
samples
15
lncRNA-seq
Drosophila
S2
cells
treated
heavy
metals.
Of
these,
67.2%
contain
more
than
one
TE.
The
LTR/Gypsy
family
was
most
common
transposon
insertion.
Transposons
preferred
insert
into
promoters,
transcription
starting
sites,
intronic
regions,
especially
chromosome
ends.
Compared
lncRNAs,
showed
longer
lengths,
a
lower
conservation,
levels
but
higher
specificity
expression.
Multi-omics
analysis
revealed
positive
correlations
between
insertions
chromatin
openness
at
pre-transcriptional
level.
Notably,
total
516
provided
transcriptional
factor
binding
sites
through
insertions.
network
key
rewired
by
transposons,
potentially
recruiting
other
factors
exert
functions
under
metal
stress.
Additionally,
99
were
associated
m6A
methylation
modification
115
candidate
small
open
reading
frames
Conclusions:
Our
demonstrated
contribute
regulation
lncRNAs.
only
promote
also
facilitate
post-transcriptional
epigenetic
regulation.
Scientific Reports,
Journal Year:
2023,
Volume and Issue:
13(1)
Published: Sept. 12, 2023
Abstract
Over
the
past
decade,
long
non-coding
RNA
(lncRNA),
which
lacks
protein-coding
potential,
has
emerged
as
an
essential
regulator
of
genome.
The
present
study
examined
13,599
lncRNAs
in
Arabidopsis
thaliana
,
11,565
Oryza
sativa
and
32,397
Zea
mays
for
their
characteristic
features
explored
associated
genomic
epigenomic
features.
We
found
were
distributed
throughout
chromosomes
Helitron
family
transposable
elements
(TEs)
enriched,
while
terminal
inverted
repeat
depleted
lncRNA
transcribing
regions.
Our
analyses
determined
that
regions
show
rare
or
weak
signals
most
epigenetic
marks
except
H3K9me2
cytosine
methylation
all
three
plant
species.
LncRNAs
showed
preferential
localization
nucleus
cytoplasm;
however,
distribution
ratio
cytoplasm
varies
among
studied
identified
several
conserved
endogenous
target
mimic
sites
plants.
233,
301,
273
unique
miRNAs,
potentially
targeting
A.
O.
Z.
respectively.
revealed
interact
with
lncRNAs,
genes
are
involved
a
diverse
array
biological
molecular
processes.
miRNA-targeted
displayed
strong
affinity
transcription
factors,
including
ERF
BBR-BPC,
mutually
plants,
advocating
functions.
Overall,
exhibit
characteristics
govern
growth
development
Research Square (Research Square),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Aug. 19, 2022
Abstract
Background:
Long
non-coding
RNAs
(lncRNAs),
as
important
regulators,
play
roles
in
plant
growth
and
development.
The
expression
epigenetic
regulation
of
lncRNAs
remain
uncharacterized
generally
seeds,
especially
the
transient
endosperm
dicotyledons.
Results:
In
this
study,
we
identified
11,840
candidate
12
day-after-pollination
sunflower
by
analyzing
RNA-seq
data.
These
were
evenly
distributed
all
chromosomes
had
specific
features
that
distinct
from
mRNAs
including
tissue-specificity
expression,
shorter
fewer
exons.
By
GO
analysis
protein
coding
genes
showing
strong
correlation
with
lncRNAs,
revealed
these
potential
function
many
biological
processes
seed
Additionally,
genome-wide
DNA
methylation
analyses
level
at
transcription
start
sites
was
negatively
correlated
gene
levels
lncRNAs.
Finally,
36
imprinted
32
maternally
expressed
four
paternally
CG
CHG
context,
upstream
body
regions
slightly
lower
than
embryo
tissues,
which
indicated
maternal
demethylation
potentially
induce
bias
endosperm.
Conclusion:
Our
findings
not
only
characterized
on
a
scale
development
endosperm,
but
also
provide
novel
insights
into
parental
effects
dicotyledonous
seeds.