Transposable elements as essential elements in the control of gene expression
Mobile DNA,
Год журнала:
2023,
Номер
14(1)
Опубликована: Авг. 18, 2023
Abstract
Interspersed
repetitions
called
transposable
elements
(TEs),
commonly
referred
to
as
mobile
elements,
make
up
a
significant
portion
of
the
genomes
higher
animals.
TEs
contribute
in
controlling
expression
genes
locally
and
even
far
away
at
transcriptional
post-transcriptional
levels,
which
is
one
their
functional
effects
on
gene
function
genome
evolution.
There
are
different
mechanisms
through
control
genes.
First,
offer
cis-regulatory
regions
with
inherent
regulatory
features
for
own
expression,
making
them
potential
factors
host
Promoter
enhancer
contain
sites
generated
from
TE,
binding
variety
trans-acting
factors.
Second,
miRNAs
long
non-coding
RNAs
(lncRNAs)
have
been
shown
that
encode
RNAs,
revealing
TE
origin
these
RNAs.
Furthermore,
it
was
sequences
essential
RNAs'
actions,
include
target
mRNA.
By
being
member
RNA
sequences,
therefore
play
roles.
Additionally,
has
suggested
TE-derived
both
evolutionary
novelty
regulation.
systems
arising
frequently
tissue-specific
functions.
The
objective
this
review
discuss
TE-mediated
regulation,
particular
emphasis
processes,
contributions
various
types,
differential
roles
tissue
based
mostly
recent
studies
humans.
Язык: Английский
Hallmarks of ageing in human skeletal muscle and implications for understanding the pathophysiology of sarcopenia in women and men
Clinical Science,
Год журнала:
2023,
Номер
137(22), С. 1721 - 1751
Опубликована: Ноя. 1, 2023
Abstract
Ageing
is
a
complex
biological
process
associated
with
increased
morbidity
and
mortality.
Nine
classic,
interdependent
hallmarks
of
ageing
have
been
proposed
involving
genetic
biochemical
pathways
that
collectively
influence
trajectories
susceptibility
to
pathology
in
humans.
skeletal
muscle
undergoes
profound
morphological
physiological
changes
loss
strength,
mass,
function,
condition
known
as
sarcopenia.
The
aetiology
sarcopenia
whilst
research
this
area
growing
rapidly,
there
relative
paucity
human
studies,
particularly
older
women.
Here,
we
evaluate
how
the
nine
classic
ageing:
genomic
instability,
telomere
attrition,
epigenetic
alterations,
proteostasis,
deregulated
nutrient
sensing,
mitochondrial
dysfunction,
cellular
senescence,
stem
cell
exhaustion,
altered
intercellular
communication
contribute
pathophysiology
We
also
highlight
five
novel
particular
significance
inflammation,
neural
extracellular
matrix
reduced
vascular
perfusion,
ionic
dyshomeostasis,
discuss
are
interconnected.
Their
clinical
relevance
translational
potential
considered.
Язык: Английский
SUMOylation of TRIM28 is positively modulated by the BTB/POZ domain of Kaiso
Molecular Biology Reports,
Год журнала:
2025,
Номер
52(1)
Опубликована: Янв. 23, 2025
Язык: Английский
Massively parallel assessment of gene regulatory activity at human cortical structure associated variants
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 8, 2025
Abstract
Genetic
association
studies
have
identified
hundreds
of
largely
non-coding
loci
associated
with
inter-individual
differences
in
the
structure
human
cortex,
though
specific
genetic
variants
that
impact
regulatory
activity
are
unknown.
We
implemented
a
Massively
Parallel
Reporter
Assay
(MPRA)
to
measure
9,092
cortical
DNA
neural
progenitor
cells
during
Wnt
stimulation
and
at
baseline.
918
potential
from
150
(76%
studied),
which
>50%
showed
allelic
effects.
modified
subset
functioned
as
condition-dependent
enhancers.
Regulatory
MPRA
was
induced
by
Alu
elements
were
hypothesized
contribute
expansion.
The
regionally
disrupt
motifs
is
likely
mediated
through
levels
transcription
factor
expression
development,
further
clarifying
molecular
mechanisms
altering
structure.
Язык: Английский
Reactivation of retrotransposable elements is associated with environmental stress and ageing
Nature Reviews Genetics,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 2, 2025
Язык: Английский
X chromosome-wide association study of quantitative biomarkers from the Alzheimer’s Disease Neuroimaging Initiative study
Frontiers in Aging Neuroscience,
Год журнала:
2023,
Номер
15
Опубликована: Ноя. 14, 2023
Introduction
Alzheimer’s
disease
(AD)
is
a
complex
neurodegenerative
with
high
heritability.
Compared
to
autosomes,
higher
proportion
of
disorder-associated
genes
on
X
chromosome
are
expressed
in
the
brain.
However,
only
few
studies
focused
identification
susceptibility
loci
for
AD
chromosome.
Methods
Using
data
from
Disease
Neuroimaging
Initiative
Study,
we
conducted
an
chromosome-wide
association
study
between
16
quantitative
biomarkers
and
19,692
single
nucleotide
polymorphisms
(SNPs)
based
both
cross-sectional
longitudinal
studies.
Results
We
identified
15
SNPs
statistically
significantly
associated
different
AD.
For
study,
six
(rs5927116,
rs4596772,
rs5929538,
rs2213488,
rs5920524,
rs5945306)
located
or
near
DMD
,
TBX22
LOC101928437
TENM1
SPANXN1
ZFP92
which
have
been
reported
be
schizophrenia
neuropsychiatric
diseases
literature.
four
(rs4829868,
rs5931111,
rs6540385,
rs763320)
included
two
RAC1P4
AFF2
demonstrated
brain
development
intellectual
disability
literature,
while
functional
annotations
other
five
novel
(rs12157031,
rs428303,
rs5953487,
rs10284107,
rs5955016)
not
found.
Discussion
were
found
Follow-up
molecular
genetics
needed
verify
whether
they
indeed
related
The
findings
this
article
expand
our
understanding
role
exploring
susceptibility,
introduce
new
insights
into
behind
AD,
may
provide
mechanistic
clue
further
AD-related
Язык: Английский
Mouse retrotransposons: sequence structure, evolutionary age, genomic distribution and function
Genes & Genetic Systems,
Год журнала:
2023,
Номер
98(6), С. 337 - 351
Опубликована: Ноя. 21, 2023
Retrotransposons
are
transposable
elements
that
transposed
via
transcription
and
reverse
transcription.
Their
copies
have
accumulated
in
the
genome
of
mammals,
occupying
approximately
40%
mammalian
genomic
mass.
These
often
involved
numerous
phenomena,
such
as
chromatin
spatial
organization,
gene
expression,
development
disease,
been
recognized
a
driving
force
evolution.
Different
organisms
gained
specific
retrotransposon
subfamilies
retrotransposed
copies,
hundreds
Mus-specific
with
diverse
sequences
locations.
Despite
this
complexity,
basic
information
is
still
necessary
for
present-day
epigenomic
studies.
Herein,
we
describe
characteristics
each
subfamily
retrotransposons
terms
sequence
structure,
phylogenetic
relationships,
evolutionary
age,
preference
A
or
B
compartments
chromatin.
Язык: Английский
Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 10, 2024
CCR4-NOT
regulates
multiple
steps
in
gene
regulation,
including
transcription,
mRNA
decay,
protein
ubiquitylation,
and
translation.
It
has
been
well
studied
budding
yeast;
however,
relatively
less
is
known
about
its
regulation
functions
mammals.
To
characterize
the
of
human
complex,
we
developed
a
rapid
auxin-induced
degron
system
to
deplete
CNOT1
(the
scaffold
complex)
CNOT4
(E3
ubiquitin
ligase)
cell
culture.
Transcriptome-wide
measurements
gene-expression
revealed
that
depleting
changed
several
thousand
transcripts,
wherein
most
mRNAs
were
increased
resulted
global
decrease
decay
rates.
In
contrast
what
was
observed
CNOT1-depleted
cells,
depletion
only
modestly
RNA
steady-state
levels
and,
surprisingly,
led
acceleration
decay.
further
investigate
role
used
transient
transcriptome
sequencing
(TT-seq)
measure
ongoing
synthesis.
Depletion
either
subunit
synthesis
genes.
genome,
reduction
KRAB-Zinc-Finger-proteins
(KZNFs)
genes,
especially
those
clustered
on
chromosome
19,
observed.
KZNFs
are
transcriptional
repressors
retro-transposable
elements
(rTEs),
consistent
with
decreased
expression,
significant
activation
rTEs,
mainly
Long
interspersed
Nuclear
Elements
(LINEs).
Our
data
reveal
expression
silences
retrotransposons
across
genome
by
maintaining
KZNF
expression.
These
establish
as
regulator
have
identified
novel
mammalian-specific
function
suppression
rTEs.
Язык: Английский
Quantifying the arms race between LINE-1 and KRAB-zinc finger genes through TECookbook
NAR Genomics and Bioinformatics,
Год журнала:
2023,
Номер
5(3)
Опубликована: Июль 5, 2023
To
defend
against
the
invasion
of
transposons,
hundreds
KRAB-zinc
finger
genes
(ZNFs)
evolved
to
recognize
and
silence
various
repeat
families
specifically.
However,
most
elements
reside
in
human
genome
with
high
copy
numbers,
making
ChIP-seq
reads
ZNFs
targeting
these
repeats
predominantly
multi-mapping
reads.
This
complicates
downstream
data
analysis
signal
quantification.
better
visualize
quantify
arms
race
between
transposons
ZNFs,
R
package
TECookbook
has
been
developed
lift
into
reference
coordinates
proper
normalization
extract
all
putative
ZNF
binding
sites
from
defined
loci
for
analysis.
In
conjunction
specificity
profiles
derived
Язык: Английский