Cell,
Год журнала:
2024,
Номер
187(14), С. 3541 - 3562.e51
Опубликована: Июль 1, 2024
Analyses
of
ancient
DNA
typically
involve
sequencing
the
surviving
short
oligonucleotides
and
aligning
to
genome
assemblies
from
related,
modern
species.
Here,
we
report
that
skin
a
female
woolly
mammoth
(†Mammuthus
primigenius)
died
52,000
years
ago
retained
its
architecture.
We
use
PaleoHi-C
map
chromatin
contacts
assemble
genome,
yielding
28
chromosome-length
scaffolds.
Chromosome
territories,
compartments,
loops,
Barr
bodies,
inactive
X
chromosome
(Xi)
superdomains
persist.
The
active
compartments
in
more
closely
resemble
Asian
elephant
than
other
tissues.
Our
analyses
uncover
new
biology.
Differences
compartmentalization
reveal
genes
whose
transcription
was
potentially
altered
mammoths
vs.
elephants.
Mammoth
Xi
has
tetradic
architecture,
not
bipartite
like
human
mouse.
hypothesize
that,
shortly
after
this
mammoth's
death,
sample
spontaneously
freeze-dried
Siberian
cold,
leading
glass
transition
preserved
subfossils
chromosomes
at
nanometer
scale.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Янв. 17, 2024
Abstract
Frogs
are
an
ecologically
diverse
and
phylogenetically
ancient
group
of
anuran
amphibians
that
include
important
vertebrate
cell
developmental
model
systems,
notably
the
genus
Xenopus
.
Here
we
report
a
high-quality
reference
genome
sequence
for
western
clawed
frog,
tropicalis
,
along
with
draft
chromosome-scale
sequences
three
distantly
related
emerging
frog
species,
Eleutherodactylus
coqui
Engystomops
pustulosus
Hymenochirus
boettgeri
Frog
chromosomes
have
remained
remarkably
stable
since
Mesozoic
Era,
limited
Robertsonian
(i.e.,
arm-preserving)
translocations
end-to-end
fusions
found
among
smaller
chromosomes.
Conservation
synteny
includes
conservation
centromere
locations,
marked
by
centromeric
tandem
repeats
associated
Cenp-a
binding
surrounded
pericentromeric
LINE/L1
elements.
This
work
explores
structure
across
frogs,
using
dense
meiotic
linkage
map
X.
chromatin
conformation
capture
(Hi-C)
data
all
species.
Abundant
satellite
occupy
unusually
long
(~20
megabase)
terminal
regions
each
chromosome
coincide
high
rates
recombination.
Both
embryonic
differentiated
cells
show
reproducible
associations
telomeres,
reflecting
Rabl-like
configuration.
Our
comparative
analyses
reveal
13
conserved
ancestral
from
which
contemporary
genomes
were
constructed.
Genome
structural
variations
within
species
are
rare.
How
selective
constraints
preserve
gene
order
and
chromosome
structure
is
a
central
question
in
evolutionary
biology
that
remains
unsolved.
Our
sequencing
of
several
genomes
the
appendicularian
tunicate
Oikopleura
dioica
around
globe
reveals
extreme
genome
scrambling
caused
by
thousands
chromosomal
rearrangements,
although
showing
no
obvious
morphological
differences
between
these
animals.
The
breakpoint
accumulation
rate
an
magnitude
higher
than
ascidian
tunicates,
nematodes,
Drosophila,
or
mammals.
Chromosome
arms
sex-specific
regions
appear
to
be
primary
unit
macrosynteny
conservation.
At
microsyntenic
level,
did
not
operon
structures,
suggesting
absence
pressure
maintain
them.
uncoupling
with
conservation
O.
suggests
presence
previously
unnoticed
cryptic
provides
new
biological
system
challenges
our
previous
vision
speciation
which
similar
animals
always
share
structures.
Cold Spring Harbor Perspectives in Biology,
Год журнала:
2021,
Номер
14(7), С. a041268 - a041268
Опубликована: Авг. 16, 2021
This
work
reviews
nuclear
compartments,
defined
broadly
to
include
distinct
structures,
bodies,
and
chromosome
domains.
It
first
summarizes
original
cytological
observations
before
comparing
concepts
of
compartments
emerging
from
microscopy
versus
genomic
approaches
then
introducing
new
multiplexed
imaging
that
promise
in
the
future
meld
both
approaches.
I
discuss
how
previous
models
radial
distribution
chromosomes
or
binary
division
genome
into
A
B
are
now
being
refined
by
recognition
more
complex
compartmentalization.
The
poorly
understood
question
these
established
maintained
is
discussed,
including
through
modern
perspective
phase
separation,
moving
on
address
possible
functions
using
role
speckles
modulating
gene
expression
as
an
example.
Finally,
review
concludes
with
a
discussion
questions
for
this
field.
Proceedings of the National Academy of Sciences,
Год журнала:
2022,
Номер
119(22)
Опубликована: Май 26, 2022
Significance
DNA
functions
in
living
cells
are
crucially
affected
by
the
three-dimensional
genome
structure
and
dynamics.
We
analyze
whole
of
human
developing
a
polymer
model
interphase
nuclei.
The
reveals
essential
importance
unfolding
process
chromosomes
from
condensed
mitotic
state
for
describing
nuclei;
through
process,
heterogeneous
repulsive
interactions
among
chromatin
chains
induce
phase
separation
chromatin,
which
quantitatively
explains
experimentally
observed
various
genomic
data.
can
use
this
as
platform
to
relationship
structure,
dynamics,
functions.
Nucleic Acids Research,
Год журнала:
2022,
Номер
50(8), С. 4258 - 4271
Опубликована: Апрель 14, 2022
Abstract
The
link
between
genomic
structure
and
biological
function
is
yet
to
be
consolidated,
it
is,
however,
clear
that
physical
manipulation
of
the
genome,
driven
by
activity
a
variety
proteins,
crucial
step.
To
understand
consequences
forces
underlying
genome
organization,
we
build
coarse-grained
polymer
model
featuring
three
fundamentally
distinct
classes
interactions:
lengthwise
compaction,
i.e.,
compaction
chromosomes
along
its
contour,
self-adhesion
among
epigenetically
similar
segments,
adhesion
chromosome
segments
nuclear
envelope
or
lamina.
We
postulate
these
types
interactions
sufficiently
represent
concerted
action
different
proteins
organizing
architecture
show
an
interplay
can
recapitulate
architectural
variants
observed
across
tree
life.
elucidates
how
arising
from
drive
drastic,
predictable,
changes
in
global
architecture,
makes
testable
predictions.
posit
precise
control
over
vivo
key
regulation
architecture.
Annual Review of Animal Biosciences,
Год журнала:
2022,
Номер
10(1), С. 17 - 37
Опубликована: Фев. 15, 2022
Tardigrades
are
ubiquitous
meiofauna
that
especially
renowned
for
their
exceptional
extremotolerance
to
various
adverse
environments,
including
pressure,
temperature,
and
even
ionizing
radiation.
This
is
achieved
through
a
reversible
halt
of
metabolism
triggered
by
desiccation,
phenomenon
called
anhydrobiosis.
Recent
establishment
genome
resources
two
tardigrades,
Hypsibius
exemplaris
Ramazzottius
varieornatus,
accelerated
research
uncover
the
molecular
mechanisms
behind
anhydrobiosis,
leading
discovery
many
tardigrade-unique
proteins.
review
focuses
on
history,
methods,
discoveries,
current
state
challenges
regarding
tardigrade
genomics,
with
an
emphasis
anhydrobiology.
Remaining
questions
future
perspectives
prospective
approaches
fully
elucidate
machinery
this
complex
discussed.
Abstract
Background
The
three-dimensional
(3D)
architecture
of
the
genome
has
a
highly
ordered
and
hierarchical
nature,
which
influences
regulation
essential
nuclear
processes
at
basis
gene
expression,
such
as
transcription.
While
organization
heterochromatin
euchromatin
can
underlie
differences
in
expression
that
determine
evolutionary
among
species,
way
3D
is
affected
by
forces
within
major
lineages
remains
unclear.
Here,
we
report
comprehensive
comparison
genomes,
using
high
resolution
Hi-C
data
fibroblast
cells
fish,
chickens,
10
mammalian
species.
Results
This
analysis
shows
correlation
between
size
chromosome
length
affects
territory
(CT)
upper
hierarchy
architecture,
whereas
lower
features,
including
local
transcriptional
availability
DNA,
are
selected
through
evolution
vertebrates.
Furthermore,
conservation
topologically
associating
domains
(TADs)
appears
strongly
associated
with
modularity
profiles
across
Additionally,
LINE
SINE
transposable
elements
likely
contribute
to
organization,
respectively,
during
architecture.
Conclusions
Our
uncovers
organizational
features
appear
functional
genes
These
findings
guide
ongoing
investigations
extending
our
understanding
mechanisms
shaping
