Essays in Biochemistry,
Journal Year:
2019,
Volume and Issue:
63(6), P. 677 - 689
Published: Oct. 11, 2019
Transposable
elements
dominate
the
mammalian
genome,
but
their
contribution
to
genetic
and
epigenetic
regulation
has
been
largely
overlooked.
This
was
in
part
due
technical
limitations,
which
made
study
of
repetitive
sequences
at
single
copy
resolution
difficult.
The
advancement
next-generation
sequencing
assays
last
decade
greatly
enhanced
our
understanding
transposable
element
function.
In
some
instances,
specific
are
thought
have
co-opted
into
regulatory
roles
during
both
mouse
human
development,
while
disease
such
potential
can
contribute
malignancy.
DNA
methylation
is
arguably
best
characterised
regulator
activity.
associated
with
repression,
acts
limit
genotoxic
potential.
developmental
contexts,
erasure
a
burst
expression.
Developmental
enables
transposon
activation,
ensuring
survival
propagation
throughout
host
also
allows
access
encoded
within
elements.
Here
I
discuss
elements,
describing
its
function
dynamic
murine
development.
Annual Review of Genetics,
Journal Year:
2020,
Volume and Issue:
54(1), P. 539 - 561
Published: Sept. 21, 2020
Transposable
elements
(TEs)
are
mobile
DNA
sequences
that
propagate
within
genomes.
Through
diverse
invasion
strategies,
TEs
have
come
to
occupy
a
substantial
fraction
of
nearly
all
eukaryotic
genomes,
and
they
represent
major
source
genetic
variation
novelty.
Here
we
review
the
defining
features
each
group
explore
their
evolutionary
origins
relationships.
We
discuss
how
unique
biology
different
influences
propagation
distribution
across
Environmental
factors
acting
at
level
host
species
further
modulate
activity,
diversification,
fate
TEs,
producing
dramatic
in
TE
content
observed
eukaryotes.
argue
cataloging
diversity
dissecting
idiosyncratic
behavior
individual
crucial
expanding
our
comprehension
impact
on
genomes
evolution
species.
Genome biology,
Journal Year:
2021,
Volume and Issue:
22(1)
Published: May 10, 2021
Abstract
Endogenous
retroviruses
(ERVs)
are
emerging
as
promising
therapeutic
targets
in
cancer.
As
remnants
of
ancient
retroviral
infections,
ERV-derived
regulatory
elements
coordinate
expression
from
gene
networks,
including
those
underpinning
embryogenesis
and
immune
cell
function.
ERV
activation
can
promote
an
interferon
response,
a
phenomenon
termed
viral
mimicry.
Although
is
associated
with
cancer,
provisionally
autoimmune
neurodegenerative
diseases,
ERV-mediated
inflammation
being
explored
way
to
sensitize
tumors
immunotherapy.
Here
we
review
co-option
development
innate
immunity,
the
aberrant
contribution
ERVs
tumorigenesis,
wider
biomedical
potential
therapies
directed
at
ERVs.
Molecular Biology and Evolution,
Journal Year:
2024,
Volume and Issue:
41(4)
Published: April 1, 2024
Transposable
elements
(TEs)
are
major
components
of
eukaryotic
genomes
and
implicated
in
a
range
evolutionary
processes.
Yet,
TE
annotation
characterization
remain
challenging,
particularly
for
nonspecialists,
since
existing
pipelines
typically
complicated
to
install,
run,
extract
data
from.
Current
methods
automated
also
subject
issues
that
reduce
overall
quality,
(i)
fragmented
overlapping
annotations,
leading
erroneous
estimates
count
coverage,
(ii)
repeat
models
represented
by
short
sections
total
length,
with
poor
capture
5'
3'
ends.
To
address
these
issues,
we
present
Earl
Grey,
fully
pipeline
designed
user-friendly
curation
TEs
genome
assemblies.
Using
nine
simulated
an
Drosophila
melanogaster,
show
Grey
outperforms
current
widely
used
methodologies
ameliorating
the
mentioned
above
while
scoring
highly
benchmarking
classification
being
robust
across
genomic
contexts.
provides
comprehensive
toolkit
researchers
paper-ready
summary
figures
outputs
standard
formats
compatible
other
bioinformatics
tools.
has
modular
format,
great
scope
inclusion
additional
modules
focused
on
further
quality
control
tailored
analyses
future
releases.
