Annals of the Rheumatic Diseases,
Journal Year:
2024,
Volume and Issue:
83(8), P. 1048 - 1059
Published: March 13, 2024
Osteoarthritis
is
a
complex
disease
with
huge
public
health
burden.
Genome-wide
association
studies
(GWAS)
have
identified
hundreds
of
osteoarthritis-associated
sequence
variants,
but
the
effector
genes
underpinning
these
signals
remain
largely
elusive.
Understanding
chromosome
organisation
in
three-dimensional
(3D)
space
essential
for
identifying
long-range
contacts
between
distant
genomic
features
(e.g.,
and
regulatory
elements),
tissue-specific
manner.
Here,
we
generate
first
whole
genome
conformation
analysis
(Hi-C)
map
primary
osteoarthritis
chondrocytes
identify
novel
candidate
disease.
Science,
Journal Year:
2022,
Volume and Issue:
375(6580), P. 566 - 570
Published: Feb. 3, 2022
Past
studies
offer
contradictory
claims
for
the
role
of
genome
organization
in
regulation
gene
activity.
Here,
we
show
through
high-resolution
chromosome
conformation
analysis
that
Nature Genetics,
Journal Year:
2021,
Volume and Issue:
53(4), P. 487 - 499
Published: April 1, 2021
Abstract
The
relationship
between
chromatin
organization
and
gene
regulation
remains
unclear.
While
disruption
of
domains
domain
boundaries
can
lead
to
misexpression
developmental
genes,
acute
depletion
regulators
genome
has
a
relatively
small
effect
on
expression.
It
is
therefore
uncertain
whether
expression
state
drive
or
changes
in
facilitate
cell-type-specific
activation
Here,
using
the
dorsoventral
patterning
Drosophila
melanogaster
embryo
as
model
system,
we
provide
evidence
for
independence
We
define
tissue-specific
enhancers
link
them
patterns
single-cell
RNA-seq.
Surprisingly,
despite
states
expression,
largely
maintained
across
tissues.
Our
results
indicate
that
conformation
not
necessary
but
rather
acts
scaffold
facilitating
when
become
active.
PLoS Computational Biology,
Journal Year:
2024,
Volume and Issue:
20(5), P. e1012067 - e1012067
Published: May 6, 2024
Chromosome
conformation
capture
(3C)
technologies
reveal
the
incredible
complexity
of
genome
organization.
Maps
increasing
size,
depth,
and
resolution
are
now
used
to
probe
architecture
across
cell
states,
types,
organisms.
Larger
datasets
add
challenges
at
each
step
computational
analysis,
from
storage
memory
constraints
researchers’
time;
however,
analysis
tools
that
meet
these
increased
resource
demands
have
not
kept
pace.
Furthermore,
existing
offer
limited
support
for
customizing
specific
use
cases
or
new
biology.
Here
we
introduce
cooltools
(
https://github.com/open2c/cooltools
),
a
suite
enables
flexible,
scalable,
reproducible
high-resolution
contact
frequency
data.
Cooltools
leverages
widely-adopted
cooler
format
which
handles
access
datasets.
provides
paired
command
line
interface
(CLI)
Python
application
programming
(API),
respectively
facilitate
workflows
on
high-performance
computing
clusters
in
interactive
environments.
In
short,
effective
latest
largest
folding
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Nov. 1, 2022
Abstract
Chromosome
conformation
capture
(3C)
technologies
reveal
the
incredible
complexity
of
genome
organization.
Maps
increasing
size,
depth,
and
resolution
are
now
used
to
probe
architecture
across
cell
states,
types,
organisms.
Larger
datasets
add
challenges
at
each
step
computational
analysis,
from
storage
memory
constraints
researchers’
time;
however,
analysis
tools
that
meet
these
increased
resource
demands
have
not
kept
pace.
Furthermore,
existing
offer
limited
support
for
customizing
specific
use
cases
or
new
biology.
Here
we
introduce
cooltools
(
https://github.com/open2c/cooltools
),
a
suite
enables
flexible,
scalable,
reproducible
high-resolution
contact
frequency
data.
Cooltools
leverages
widely-adopted
cooler
format
which
handles
access
datasets.
provides
paired
command
line
interface
(CLI)
Python
application
programming
(API),
respectively
facilitate
workflows
on
high-performance
computing
clusters
in
interactive
environments.
In
short,
effective
latest
largest
folding
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Feb. 15, 2023
Abstract
The
field
of
3D
genome
organization
produces
large
amounts
sequencing
data
from
Hi-C
and
a
rapidly-expanding
set
other
chromosome
conformation
protocols
(3C+).
Massive
heterogeneous
3C+
require
high-performance
flexible
processing
sequenced
reads
into
contact
pairs.
To
meet
these
challenges,
we
present
pairtools
–
suite
tools
for
extraction
data.
Pairtools
provides
modular
command-line
interface
(CLI)
that
can
be
flexibly
chained
pipelines.
both
crucial
core
as
well
auxiliary
building
feature-rich
pipelines,
including
pair
manipulation,
filtration,
quality
control.
Benchmarking
against
popular
pipelines
shows
advantages
analysis.
Finally,
protocol-specific
multi-way
contacts,
haplotype-resolved
single-cell
Hi-C.
combination
CLI
tight
integration
with
Python
analysis
libraries
makes
versatile
foundation
broad
range
PLoS Computational Biology,
Journal Year:
2024,
Volume and Issue:
20(5), P. e1012164 - e1012164
Published: May 29, 2024
The
field
of
3D
genome
organization
produces
large
amounts
sequencing
data
from
Hi-C
and
a
rapidly-expanding
set
other
chromosome
conformation
protocols
(3C+).
Massive
heterogeneous
3C+
require
high-performance
flexible
processing
sequenced
reads
into
contact
pairs.
To
meet
these
challenges,
we
present
pairtools
–a
suite
tools
for
extraction
data.
Pairtools
provides
modular
command-line
interface
(CLI)
that
can
be
flexibly
chained
pipelines.
core
operations
provided
by
are
parsing
of.sam
alignments
pairs,
sorting
removal
PCR
duplicates.
In
addition,
auxiliary
building
feature-rich
pipelines,
including
pair
manipulation,
filtration,
quality
control.
Benchmarking
against
popular
pipelines
shows
advantages
analysis.
Finally,
protocol-specific
restriction-based
protocols,
haplotype-resolved
contacts,
single-cell
Hi-C.
combination
CLI
tight
integration
with
Python
analysis
libraries
makes
versatile
foundation
broad
range
