The genome awakens: transposon-mediated gene regulation
Trends in Plant Science,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 1, 2025
Language: Английский
Towards an unbiased characterization of genetic polymorphism
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: May 30, 2024
Our
view
of
genetic
polymorphism
is
shaped
by
methods
that
provide
a
limited
and
reference-biased
picture.
Long-read
sequencing
technologies,
which
are
starting
to
nearly
complete
genome
sequences
for
population
samples,
should
solve
the
problem—except
characterizing
making
sense
non-SNP
variation
difficult
even
with
perfect
sequence
data.
Here,
we
analyze
27
genomes
Arabidopsis
thaliana
in
an
attempt
address
these
issues,
illustrate
what
can
be
learned
analyzing
whole-genome
data
unbiased
manner.
Estimated
sizes
range
from
135
155
Mb,
differences
almost
entirely
due
centromeric
rDNA
repeats.
The
completely
assembled
chromosome
arms
comprise
roughly
120
Mb
all
accessions,
but
full
structural
variants,
many
caused
insertions
transposable
elements
(TEs)
subsequent
partial
deletions
such
insertions.
Even
only
pan-genome
coordinate
system
includes
resulting
ends
up
being
40%
larger
than
size
any
one
genome.
analysis
reveals
incompletely
annotated
mobile-ome:
our
ability
predict
actually
moving
poor,
detect
several
novel
TE
families.
In
contrast
this,
genic
portion,
or
“gene-ome”,
highly
conserved.
By
annotating
each
using
accession-specific
transcriptome
data,
find
13%
genes
segregating
most
transcriptionally
silenced.
Finally,
show
short-read
previously
massively
underestimated
kinds,
including
SNPs—mostly
regions
where
short
reads
could
not
mapped
reliably,
also
were
incorrectly.
We
demonstrate
SNP-calling
errors
biased
choice
reference
genome,
RNA-seq
BS-seq
results
strongly
affected
mapping
rather
assayed
individual.
conclusion,
while
pose
tremendous
analytical
challenges,
they
will
ultimately
revolutionize
understanding
evolution.
Language: Английский
Cis-regulatory effects of carrot miniature inverted-repeat transposable elements on the expression of genes controlled by LHY/RVE transcription factors
Research Square (Research Square),
Journal Year:
2025,
Volume and Issue:
unknown
Published: May 7, 2025
Abstract
Background
Transposable
elements
constitute
a
large
portion
of
plant
genomes
and,
due
to
their
ability
change
genomic
localization,
they
largely
contribute
genome
evolution
and
adaptability.
Miniature
inverted-repeat
transposable
(MITEs),
small
size
localization
near
genes,
seem
be
major
source
potential
functional
variability.
Effects
imposed
by
MITE
on
the
expression
associated
genes
through
redistributing
cis-regulatory
have
been
postulated,
but
our
knowledge
in
this
area
still
remains
limited.
Results
We
showed
that
MITEs
carrot
are
enriched
with
binding
sites
for
LHY/RVE
transcription
factors.
Experimental
validation
using
DcLHY-DAP-seq
not
only
confirmed
enrichment
DcLHY
within
MITEs,
also
demonstrated
from
DcTourist_15
family
likely
play
key
role
these
factor
sites.
insertional
polymorphisms
correspond
changes
both
control
conditions
response
heat
stress.
In
addition
placing
individual
under
DcLHY/RVE
factors,
copies
were
found
promoters
involved
sulfur
metabolism
cysteine
biosynthesis.
The
rice
OsLHY
suggests
phenomenon
MITE-driven
rewiring
regulation
may
more
widespread
across
kingdom.
Conclusions
Carrot
particularly
those
family,
drive
genome,
especially
context
stress
responsiveness,
as
possibly
fine-tune
gene
factors
family.
Language: Английский
Plant Mobile Domain protein-DNA motif modules counteract Polycomb silencing to stabilize gene expression
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Sept. 28, 2024
Abstract
In
plants
and
animals,
Polycomb
group
(PcG)
proteins
are
crucial
for
development,
regulating
gene
expression
through
H3K27me3
deposition
subsequent
silencing.
While
silencing
target
specification
is
increasingly
understood,
it
remains
unclear
how
certain
genes
with
apparent
silencing-attracting
features
escape
this
process.
Here,
we
show
that
the
plant
mobile
domain
C
(PMD-C)
containing
MAINTENANCE
OF
MERISTEMS
(MAIN),
MAIN-LIKE
1
(MAIL1)
MAIL2
oppose
at
numerous
actively
transcribed
in
Arabidopsis.
Mutations
MAIN
,
MAIL1
or
result
PcG-dependent
ectopic
deposition,
often
associated
transcriptional
repression.
We
MAIL1,
which
functions
concert
MAIN,
distinct
sets
associate
chromatin
specific
DNA
sequence
motifs.
demonstrate
integrity
of
these
motif
sequences
essential
promoting
antagonizing
deposition.
Our
results
unveil
a
novel
system
opposing
involving
PMD-C
protein-DNA
modules,
expanding
our
understanding
eukaryotic
regulation
mechanisms.
Language: Английский