bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Май 9, 2022
SUMMARY
RNA
interference
systems
depend
on
the
synthesis
of
small
precursors
whose
sequences
define
target
spectrum
these
silencing
pathways.
The
Drosophila
Heterochromatin
Protein
1
(HP1)
variant
Rhino
permits
transcription
PIWI-interacting
(piRNA)
within
transposon-rich
heterochromatic
loci
in
germline
cells.
Current
models
propose
that
Rhino’s
specific
chromatin
occupancy
at
piRNA
source
is
determined
by
histone
marks
and
maternally
inherited
piRNAs,
but
also
imply
existence
other,
undiscovered
specificity
cues.
Here,
we
identify
a
member
diverse
family
zinc
finger
associated
domain
(ZAD)-C
2
H
proteins,
Kipferl,
as
critical
cofactor
ovaries.
By
binding
to
guanosine-rich
DNA
motifs
interacting
with
chromodomain,
Kipferl
recruits
stabilizes
it
chromatin.
In
kipferl
mutant
flies,
lost
from
most
its
instead
accumulates
pericentromeric
satellite
arrays,
resulting
decreased
levels
transposon
targeting
piRNAs
impaired
fertility.
Our
findings
reveal
sequence,
addition
H3K9me3
mark,
determines
identity
provide
insight
into
how
might
be
caught
crossfire
genetic
conflicts.
Proceedings of the National Academy of Sciences,
Год журнала:
2025,
Номер
122(2)
Опубликована: Янв. 7, 2025
From
RNA
interference
to
chromatin
silencing,
diverse
genome
defense
pathways
silence
selfish
genetic
elements
safeguard
integrity.
Despite
their
diversity,
different
share
a
modular
organization,
where
numerous
specificity
factors
identify
targets
and
common
effectors
them.
In
the
PIWI-interacting
(piRNA)
pathway,
target
RNAs
are
first
identified
by
complementary
base
pairing
with
piRNAs
then
silenced
PIWI-clade
nucleases.
Such
binary
architecture
allows
systems
be
readily
adaptable,
new
can
captured
via
innovation
of
factors.
Thus,
our
current
understanding
against
lineage-specific
genes
has
been
largely
limited
factor
innovations,
while
it
remains
poorly
understood
whether
other
types
innovations
required.
Here,
we
describe
type
innovation,
which
escalates
capacity
control
recently
expanded
gene
in
Drosophila
melanogaster
.
Through
targeted
RNAi
screen
for
repressors
Stellate
—a
evolved
meiotic
driver—we
factor,
Trailblazer.
Trailblazer
is
transcription
that
promotes
expression
two
nucleases,
Aub
AGO3,
match
abundance.
Recent
DNA-binding
domain
enabled
elevate
AGO3
expression,
thereby
escalating
silencing
piRNA
pathway
tame
fertility.
As
copy-number
expansion
recurrent
feature
across
tree
life,
envision
augmenting
quantitatively
repeatedly
employed
strategy
evolution.
RNA
interference
systems
depend
on
the
synthesis
of
small
precursors
whose
sequences
define
target
spectrum
these
silencing
pathways.
The
Drosophila
Heterochromatin
Protein
1
(HP1)
variant
Rhino
permits
transcription
PIWI-interacting
(piRNA)
within
transposon-rich
heterochromatic
loci
in
germline
cells.
Current
models
propose
that
Rhino’s
specific
chromatin
occupancy
at
piRNA
source
is
determined
by
histone
marks
and
maternally
inherited
piRNAs,
but
also
imply
existence
other,
undiscovered
specificity
cues.
Here,
we
identify
a
member
diverse
family
zinc
finger
associated
domain
(ZAD)-C
2
H
proteins,
Kipferl,
as
critical
cofactor
ovaries.
By
binding
to
guanosine-rich
DNA
motifs
interacting
with
chromodomain,
Kipferl
recruits
stabilizes
it
chromatin.
In
kipferl
mutant
flies,
lost
from
most
its
instead
accumulates
pericentromeric
Satellite
arrays,
resulting
decreased
levels
transposon
targeting
piRNAs
impaired
fertility.
Our
findings
reveal
sequence,
addition
H3K9me3
mark,
determines
identity
provide
insight
into
how
might
be
caught
crossfire
genetic
conflicts.
Many
animal
species
employ
sperm
nuclear
basic
proteins
(SNBPs)
or
protamines
to
package
genomes
tightly.
SNBPs
vary
across
lineages
and
evolve
rapidly
in
mammals.
We
used
a
phylogenomic
approach
investigate
SNBP
diversification
Drosophila
species.
found
that
most
genes
melanogaster
under
positive
selection
except
for
essential
male
fertility.
Unexpectedly,
evolutionarily
young
are
more
likely
be
critical
fertility
than
ancient,
conserved
genes.
For
example,
CG30056
is
dispensable
despite
being
one
of
three
universally
retained
19
independent
gene
amplification
events
occurred
preferentially
on
sex
chromosomes.
Conversely,
the
montium
group
lost
otherwise-conserved
genes,
coincident
with
an
X-Y
chromosomal
fusion.
Furthermore,
became
linked
chromosomes
via
fusions
were
degenerate
relocate
back
autosomes.
hypothesize
autosomal
suppress
meiotic
drive,
whereas
sex-chromosomal
expansions
lead
drive.
render
by
making
X-versus-Y
drive
obsolete
costly.
Thus,
genetic
conflicts
between
may
rapid
evolution
during
spermatogenesis
Genome Research,
Год журнала:
2023,
Номер
33(8), С. 1325 - 1339
Опубликована: Авг. 1, 2023
Cys2-His2
zinc
finger
genes
(ZNFs)
form
the
largest
family
of
transcription
factors
in
metazoans.
ZNF
evolution
is
highly
dynamic
and
characterized
by
rapid
expansion
contraction
numerous
subfamilies
across
animal
phylogeny.
The
forces
mechanisms
underlying
remain
poorly
understood,
but
there
growing
evidence
that,
tetrapods,
targeting
repression
lineage-specific
transposable
elements
(TEs)
plays
a
critical
role
Krüppel-associated
box
(KZNF)
subfamily.
Currently,
it
unknown
whether
this
function
coevolutionary
relationship
unique
to
KZNFs
or
broader
feature
metazoan
ZNFs.
Here,
we
present
that
genomic
conflict
with
TEs
has
been
central
driver
diversification
ZNFs
animals.
Sampling
from
3221
genome
assemblies,
show
copy
number
retroelements
correlates
at
least
750
million
years
evolution.
Using
computational
predictions,
preferentially
bind
diverse
species.
We
further
investigate
subfamily
found
cyprinid
fish,
which
conserved
sequence
dubbed
fish
N-terminal
finger–associated
(FiNZ)
domain.
Zebrafish
possess
approximately
700
FiNZ-ZNFs,
many
are
evolving
adaptively
under
positive
selection.
Like
mammalian
KZNFs,
most
zebrafish
FiNZ-ZNFs
expressed
onset
zygotic
activation,
blocking
their
translation
using
morpholinos
during
early
embryogenesis
results
derepression
transcriptionally
active
TEs.
Together,
these
data
suggest
intimately
connected
TE
throughout
Annual Review of Genomics and Human Genetics,
Год журнала:
2024,
Номер
25(1), С. 1 - 25
Опубликована: Апрель 11, 2024
Transposable
elements
(TEs)
are
genomic
parasites
found
in
nearly
all
eukaryotes,
including
humans.
This
evolutionary
success
of
TEs
is
due
to
their
replicative
activity,
involving
insertion
into
new
locations.
TE
activity
varies
at
multiple
levels,
from
between
taxa
within
individuals.
The
rapidly
accumulating
evidence
the
influence
on
human
health,
as
well
rapid
growth
tools
study
it,
motivated
an
evaluation
what
we
know
about
thus
far.
Here,
discuss
why
varies,
and
consequences
this
variation,
perspective.
By
studying
nonhuman
organisms
context
theories,
can
shed
light
factors
that
affect
activity.
While
usually
deleterious,
some
have
lasting
impacts
by
conferring
benefits
host
or
affecting
other
processes.
Contrary
to
dogma,
evolutionarily
young
and
dynamic
genes
can
encode
essential
functions.
We
find
that
ZAD-ZNF
genes,
which
the
most
abundant
class
of
insect
transcription
factors,
are
more
likely
functions
in
Drosophila
melanogaster
than
ancient,
conserved
genes.
focus
on
Nicknack
gene,
is
young,
poorly
retained
species,
evolves
under
strong
positive
selection.
Yet
we
it
necessary
for
larval
development
D.
melanogaster.
show
encodes
a
heterochromatin-localizing
protein
like
its
paralog
Oddjob
,
also
an
yet
gene.
divergent
simulans
still
localize
heterochromatin
rescue
viability
female
but
not
male
Nicknack-
null
.
Our
findings
suggest
innovation
rapidly
changing
might
generally
explain
essentiality
many
insects.
Heterochromatin
is
a
key
architectural
feature
of
eukaryotic
genomes
crucial
for
silencing
repetitive
elements.
During
Drosophila
embryonic
cellularization,
heterochromatin
rapidly
appears
over
sequences,
but
the
molecular
details
how
established
are
poorly
understood.
Here,
we
map
genome-wide
distribution
H3K9me3-dependent
in
individual
embryos
miranda
at
precisely
staged
developmental
time
points.
We
find
that
canonical
H3K9me3
enrichment
prior
to
cellularization
and
matures
into
stable
broad
domains
through
development.
Intriguingly,
initial
nucleation
sites
appear
as
early
stage
3
transposable
elements
(TEs)
progressively
broaden,
consistent
with
spreading
neighboring
nucleosomes.
The
earliest
limited
specific
regions
small
number
recently
active
retrotransposon
families
often
promoter
5’
LTR
retrotransposons,
while
late
develop
broadly
across
entirety
most
TEs.
Interestingly,
nucleating
TEs
strongly
associated
abundant
maternal
piRNAs
show
zygotic
transcription.
These
results
support
model
piRNA-associated
co-transcriptional
also
suggesting
additional
mechanisms
site-restricted
pre-cellular
embryos.
PLoS Genetics,
Год журнала:
2021,
Номер
17(7), С. e1009654 - e1009654
Опубликована: Июль 9, 2021
It
is
a
conventionally
held
dogma
that
the
genetic
basis
underlying
development
conserved
in
long
evolutionary
time
scale.
Ample
experiments
based
on
mutational,
biochemical,
functional,
and
complementary
knockdown/knockout
approaches
have
revealed
unexpectedly
important
role
of
recently
evolved
new
genes
Drosophila.
The
recent
progress
genome-wide
experimental
testing
gene
effects
improvements
computational
identification
(<
40
million
years
ago,
Mya)
open
door
to
investigate
evolution
essentiality
with
phylogenetically
high
resolution.
These
advancements
also
raised
interesting
issues
techniques
concepts
related
phenotypic
effect
analyses
genes,
particularly
those
originated.
Here
we
reported
our
these
issues,
including
reproducibility
efficiency
knockdown
experiment
difference
between
RNAi
libraries
effects.
We
further
analyzed
large
data
from
knockdowns
11,354
(~75%
Drosophila
melanogaster
total
genes),
702
(~66%
species
aged
<
Mya),
revealing
similarly
proportion
(~32.2%)
essential
originated
various
Sophophora
subgenus
lineages
distant
ancestors
beyond
genus.
transcriptional
compensation
CRISPR
knockout
were
detected
for
highly
similar
duplicate
copies.
Knockout
few
young
analogous
functions
development.
Taken
together,
provide
valuable
detection
general
strong
evidence
concept
quickly
viability
during