bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 13, 2024
Abstract
Global
health
and
food
supply
are
endangered
by
an
increasing
frequency
of
antifungal
resistance
in
pathogenic
fungi.
Wild-type
fission
yeast,
Schizosaccharomyces
pombe
,
can
gain
to
insults
such
as
caffeine
compounds
through
reversible
epimutations.
Resistant
epimutants
exhibit
histone
H3K9
methylation-dependent
heterochromatin
islands
at
various
chromosomal
locations,
reducing
expression
underlying
genes.
Two
genes
whose
island-induced
repression
causes
encode
mitochondrial
proteins:
the
LYR
domain
protein
Cup1
Cox1
translation
regulator
Ppr4.
Genetic
mutations,
cup1-tt
ppr4Δ
that
phenocopy
their
respective
epimutants,
cause
dysfunction,
including
respiratory
deficiency,
poor
growth
on
non-glucose
carbon
sources,
elevated
reactive
oxygen
species.
RNA-Seq
analyses
indicate
cells
activate
mitonuclear
retrograde
pathway
Pap1
transcription
factor-dependent
oxidative
stress
response
pathways.
Both
mutants
show
increased
nuclear
localisation
its
recruitment
promoters
encoding
oxidoreductases
membrane
transporters,
causing
efflux
activity.
cup1
ppr4
also
dysfunction
phenotypes
efflux,
explaining
how
heterochromatin-island
epimutations
drug
resistance.
Thus,
wild-type
harness
impose
bypass
external
insults.
As
has
been
linked
several
fungi,
similar
likely
contribute
development
fungal
pathogens.
Trends in Microbiology,
Год журнала:
2024,
Номер
32(12), С. 1229 - 1240
Опубликована: Июнь 5, 2024
Recent
studies
of
dynamic
interactions
between
epigenetic
modifications
a
host
organism
and
the
composition
or
activity
its
associated
gut
microbiota
suggest
an
opportunity
for
to
shape
microbiome
through
alterations
that
lead
changes
in
gene
expression
noncoding
RNA
activity.
We
use
insights
from
microbiota-induced
review
potential
epigenetically
regulate
microbiome,
which
bidirectional
'epigenome–microbiome
axis'
emerges.
This
axis
embeds
environmentally
induced
variation,
may
influence
adaptive
evolution
host–microbe
interactions.
furthermore
present
our
perspective
on
how
epigenome–microbiome
can
be
understood
investigated
within
holo-omic
framework
with
applications
applied
health
food
sciences.
Anthropogenic
activities
are
responsible
for
a
wide
array
of
environmental
disturbances
that
threaten
biodiversity.
Climate
change,
encompassing
temperature
increases,
ocean
acidification,
increased
salinity,
droughts,
and
floods
caused
by
frequent
extreme
weather
events,
represents
one
the
most
significant
alterations.
These
drastic
challenges
pose
ecological
constraints,
with
over
million
species
expected
to
disappear
in
coming
years.
Therefore,
organisms
must
adapt
or
face
potential
extinctions.
Adaptations
can
occur
not
only
through
genetic
changes
but
also
non-genetic
mechanisms,
which
often
confer
faster
acclimatization
wider
variability
ranges
than
their
counterparts.
Among
these
mechanisms
epigenetics
defined
as
study
molecules
perpetuate
alternative
gene
activity
states
context
same
DNA
sequence.
Epigenetics
has
received
attention
past
decades,
epigenetic
sensitive
cues,
epimutations
spread
populations
mutations.
Epimutations
be
neutral,
deleterious,
adaptative
transmitted
subsequent
generations,
making
them
crucial
factors
both
long-
short-term
responses
fluctuations,
such
climate
change.
In
this
review,
we
compile
existing
evidence
involvement
adaptation
change
discuss
derived
perspectives
remaining
field
epigenetics.
Proceedings of the National Academy of Sciences,
Год журнала:
2025,
Номер
122(11)
Опубликована: Март 10, 2025
Genetic
assimilation
is
a
process
by
which
trait
originally
driven
the
environment
becomes
independent
of
initial
cue
and
expressed
constitutively
in
population.
More
than
seven
decades
have
passed
since
Waddington's
pioneering
demonstration
acquisition
morphological
traits
through
genetic
assimilation,
but
underlying
mechanism
remains
unknown.
Here,
we
address
this
gap
performing
combined
genomic
analyses
experiments
using
ectopic
veins
(EV)
phenocopy
Drosophila
as
model.
Our
study
reveals
EV
both
outbred
inbred
fly
natural
populations,
despite
their
limited
diversity.
We
identified
key
changes
expression
developmental
genes
pinpointed
selected
alleles
involved
assimilation.
The
mainly
selection
regulatory
already
present
ancestral
including
downregulation
receptor
tyrosine
kinase
gene
Cad96Ca
insertion
transposable
element
its
3'
untranslated
region.
variation
at
locus
population
maintained
large
chromosomal
inversion.
In
evolution
results
from
polygenic
response
shaped
selective
environment.
support
model
for
multiple
preexisting
population,
rather
stress-induced
or
epigenetic
variation,
drives
populations.
Evolutionary Applications,
Год журнала:
2024,
Номер
17(6)
Опубликована: Май 29, 2024
Spreading
of
bacterial
and
fungal
strains
that
are
resistant
to
antimicrobials
poses
a
serious
threat
the
well-being
humans,
animals,
plants.
Antimicrobial
resistance
has
been
mainly
investigated
in
clinical
settings.
However,
throughout
their
evolutionary
history
microorganisms
wild
have
encountered
antimicrobial
substances,
forcing
them
evolve
strategies
combat
action.
It
is
well
known
many
these
based
on
genetic
mechanisms,
but
do
not
fully
explain
important
aspects
response
such
as
rapid
development
resistance,
reversible
phenotypes,
hetero-resistance.
Consequently,
attention
turned
toward
epigenetic
pathways
may
offer
additional
insights
into
mechanisms.
The
aim
this
review
explore
mechanisms
confer
focusing
those
might
be
relevant
for
wild.
First,
we
examine
presence
natural
Then
describe
documented
bacteria
fungi
associated
with
discuss
innovative
editing
techniques
establish
causality
context.
Finally,
relevance
dynamics
wild,
emphasizing
critical
role
priming
adaptation
process.
We
underscore
necessity
incorporating
non-genetic
our
understanding
evolution.
These
invaluable
within
ecosystems.
Evolutionary Applications,
Год журнала:
2024,
Номер
17(7)
Опубликована: Июль 1, 2024
Abstract
The
epigenome
is
the
suite
of
interacting
chemical
marks
and
molecules
that
helps
to
shape
patterns
development,
phenotypic
plasticity
gene
regulation,
in
part
due
its
responsiveness
environmental
stimuli.
There
increasing
interest
understanding
functional
evolutionary
importance
this
sensitivity
under
ecologically
realistic
conditions.
Observations
epigenetic
variation
abounds
natural
populations
have
prompted
speculation
it
may
facilitate
responses
rapid
perturbations,
such
as
those
occurring
climate
change.
A
frequent
point
contention
whether
variants
reflect
genetic
or
are
independent
it.
genome
often
appear
tightly
linked
interdependent.
While
many
changes
genetically
determined,
converse
also
true,
with
DNA
sequence
influenced
by
presence
marks.
Understanding
how
epigenome,
environment
interact
one
another
therefore
an
essential
step
explaining
broader
consequences
epigenomic
variation.
Drawing
on
results
from
experimental
comparative
studies
carried
out
diverse
plant
animal
species,
we
synthesize
our
current
these
factors
populations,
a
focus
identifying
similarities
differences
between
taxonomic
groups.
We
describe
main
components
they
vary
within
taxa.
review
interacts
features
determinants,
role
transposable
elements
(TEs)
integrating
environment.
And
look
at
recent
investigating
interactions.
Although
differentiation
nature
likely
result
drift
selection
stochastic
epimutations,
there
growing
evidence
significant
fraction
can
be
stably
inherited
could
contribute
evolution
independently
Non-genetic
information
can
be
inherited
across
generations
in
a
process
known
as
transgenerational
epigenetic
inheritance
(TEI).
In
Drosophila,
hemizygosity
of
the
Fab-7
regulatory
element
triggers
histone
mark
H3K27me3
at
homologous
locus
on
another
chromosome,
resulting
heritable
differences
eye
color.
Here,
by
mutating
transcription
factor
binding
sites
within
element,
we
demonstrate
importance
proteins
pleiohomeotic
and
GAGA
establishment
maintenance
TEI.
We
show
that
these
function
recruiting
polycomb
repressive
complex
2
mediating
interchromosomal
chromatin
contacts
between
its
locus,
respectively.
Using
an
vivo
synthetic
biology
system
to
induce
them,
then
alone
establish
TEI,
providing
mechanism
which
one
memory
distant
trans
through
contacts.
Why
did
inanimate
materials
evolve
into
complex
organisms
and
societies
on
Earth?
This
is
a
fundamental
scientific
question
that
has
captivated
humans
for
millennia.
Here
we
propose
the
Carbon-Based
Evolutionary
Theory
(CBET)
to
provide
novel,
direct,
explicit
answers
this
question.
The
CBET
identifies
three
key
mechanisms
based
some
principles
of
physics
chemistry
(e.g.,
laws
thermodynamics)
features
Earth
carbon-based
entities
(CBEs):
driving
force
mechanism
provides
energy,
structural
generates
new
functions,
natural
selection
accumulates
orderliness,
all
evolution
CBEs.
These
lead
progression
from
chemical
biological
social
evolution,
marked
by
escalating
hierarchy
CBEs
increase
in
quantity,
diversity,
orderliness
high-hierarchy
clarifies
roots
multiple
pivotal
seemingly
paradoxical
management
notions,
such
as
inclusiveness
competition,
altruism
selfishness,
freedom
restriction,
well
inherited
advantages
acquired
strengths.
It
advocates
balanced,
harmonious,
peaceful
development
human
society
integration
countries
single
harmonious
collective.
unifies
biology
with
could
be
basic
theory
shared
sciences
sciences.
also
significant
rational
society.
Why
did
unordered,
simple
substances
on
Earth
evolve
into
orderly,
complex,
and
diverse
organisms
social
organizations?
This
is
a
fundamental
scientific
question
that
has
captivated
humans
for
millennia.
Here
we
propose
the
Carbon-Based
Evolutionary
Theory
(CBET)
to
provide
novel,
direct,
explicit,
relatively
comprehensive
answers
this
question.
The
CBET
identifies
three
key
mechanisms
based
some
well-known
principles
of
physics
chemistry
(e.g.,
laws
thermodynamics)
features
carbon-based
(CBSs):
driving
force
mechanism
provides
energy,
structure-function
generates
new
functions,
natural
selection
accumulates
orderliness,
all
evolution
CBSs.
These
lead
progression
from
chemical
biological
evolution,
marked
by
escalating
hierarchy
CBSs
increase
in
quantity,
diversity,
orderliness
high-hierarchy
clarifies
roots
multiple
pivotal
seemingly
paradoxical
notions,
such
as
inclusiveness
versus
elimination,
collaboration
competition,
altruism
selfishness,
freedom
restriction.
It
advocates
balanced,
harmonious,
peaceful
development
human
society
well
integration
countries
single
harmonious
collective.
unifies
biology
with
could
be
basic
theory
shared
sciences
sciences.
also
significant
rational
society.
Why
and
how
did
unordered,
simple
substances
on
Earth
evolve
into
orderly,
complex,
diverse
organisms
social
organizations?
This
is
a
fundamental
scientific
question
that
has
captivated
humans
for
millennia.
Here
we
propose
the
Carbon-Based
Evolutionary
Theory
(CBET)
to
provide
novel,
explicit,
relatively
comprehensive
answers
this
question.
The
CBET
identifies
three
key
mechanisms
based
some
principles
of
classical
physics
chemistry
(e.g.,
laws
thermodynamics
organic
chemistry)
features
carbon-based
materials
(CBMs):
driving
force
mechanism,
structure-function
natural
selection
which
underpin
evolution
CBMs
with
energy,
functions,
orderliness,
respectively.
These
are
shared
by
phases
CBMs:
chemical
evolution,
biological
evolution.
They
escalate
hierarchy
augment
quantity,
diversity,
orderliness
high-hierarchy
CBMs.
clarifies
roots
multiple
pivotal
seemingly
paradoxical
notions,
such
as
inclusiveness
versus
elimination,
collaboration
competition,
altruism
selfishness,
freedom
restriction.
It
advocates
balanced,
harmonious,
peaceful
development
human
society.
unifies
biology
could
be
basic
theory
sciences
sciences.
also
significant
in
rational
Why
and
how
did
simple
unordered
substances
on
Earth
evolve
into
complex,
orderly,
diverse
organisms
social
organizations?
Here
we
propose
the
Carbon-Based
Evolutionary
Theory
(CBET)
to
provide
an
explicit
comprehensive
answer
this
fundamental
scientific
question.
The
CBET
is
based
integration
of
principles
physics
chemistry
(e.g.,
laws
thermodynamics),
features
having
abundant
water
energy),
carbon-based
materials
(CBMs)
using
rational
logic
evidence
from
a
panoramic
view.
reveals
driving
force
mechanism,
structure-function
natural
selection
which
underpin
evolution
with
energy
supply,
function
generation,
structural
optimization,
respectively.
These
three
mechanisms
escalate
hierarchy
CBMs,
augment
quantity,
diversity,
orderliness
high-hierarchy
lead
chemical,
biological,
evolution.
uncovers
roots
multiple
pivotal
seemingly
paradoxical
notions,
such
as
inclusiveness
versus
elimination,
cooperation
competition,
altruism
selfishness.
It
advocates
for
balanced,
harmonious,
peaceful
development
human
society.
could
unify
biology
chemistry,
bridge
sciences
sciences,
guide