Finding functional microproteins
Trends in Genetics,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
Язык: Английский
Genome modeling and design across all domains of life with Evo 2
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 21, 2025
Abstract
All
of
life
encodes
information
with
DNA.
While
tools
for
sequencing,
synthesis,
and
editing
genomic
code
have
transformed
biological
research,
intelligently
composing
new
systems
would
also
require
a
deep
understanding
the
immense
complexity
encoded
by
genomes.
We
introduce
Evo
2,
foundation
model
trained
on
9.3
trillion
DNA
base
pairs
from
highly
curated
atlas
spanning
all
domains
life.
train
2
7B
40B
parameters
to
an
unprecedented
1
million
token
context
window
single-nucleotide
resolution.
learns
sequence
alone
accurately
predict
functional
impacts
genetic
variation—from
noncoding
pathogenic
mutations
clinically
significant
BRCA1
variants—without
task-specific
finetuning.
Applying
mechanistic
interpretability
analyses,
we
reveal
that
autonomously
breadth
features,
including
exon–intron
boundaries,
transcription
factor
binding
sites,
protein
structural
elements,
prophage
regions.
Beyond
its
predictive
capabilities,
generates
mitochondrial,
prokaryotic,
eukaryotic
sequences
at
genome
scale
greater
naturalness
coherence
than
previous
methods.
Guiding
via
inference-time
search
enables
controllable
generation
epigenomic
structure,
which
demonstrate
first
scaling
results
in
biology.
make
fully
open,
parameters,
training
code,
inference
OpenGenome2
dataset,
accelerate
exploration
design
complexity.
Язык: Английский
Evaluation of Cas13d as a tool for genetic interaction mapping
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Фев. 14, 2025
Abstract
Mapping
genetic
interactions
(GIs)
is
crucial
for
understanding
network
complexity.
In
this
study,
we
investigate
the
utility
of
Cas13d,
a
CRISPR
system
targeting
RNA,
GI
mapping
and
compare
it
to
Cas9
Cas12a,
two
DNA
nucleases
commonly
used
mapping.
We
find
that
Cas13d
induces
faster
target
gene
perturbation
generates
more
uniform
cell
populations
with
double
perturbations
than
or
Cas12a.
then
encounter
gRNA-gRNA
interference
when
concatenating
gRNAs
different
genes
into
one
gRNA
array,
which
overcome
by
dual
promoter
expression
strategy.
Moreover,
three
same
are
able
maximize
Cas13d-mediated
knockdown
effects.
Combining
these
strategies
enhances
proliferation
phenotypes
while
reducing
library
size
facilitates
reproducible
quantification
GIs
in
oncogenic
signaling
pathways.
Our
study
highlights
potential
mapping,
promising
advancements
therapeutically
relevant
drug
response
Язык: Английский
Emerging Roles of Long Non‐Coding RNAs in Cardiovascular Diseases
Journal of Cellular and Molecular Medicine,
Год журнала:
2025,
Номер
29(5)
Опубликована: Март 1, 2025
Cardiovascular
diseases
(CVDs)
are
the
leading
cause
of
morbidity
and
mortality
worldwide.
Over
past
decade,
studies
have
demonstrated
that
circulating
long
non-coding
RNAs
(lncRNAs)-recognised
for
their
stability
ease
detection-serve
as
crucial
regulators
potential
biomarkers
in
multiple
diseases.
LncRNAs
regulate
key
processes,
including
endothelial
function,
vascular
remodelling,
myocardial
hypertrophy,
all
which
influence
CVD
progression.
Additionally,
lncRNAs
display
cell-,
tissue-,
disease-specific
expression
patterns,
making
them
ideal
therapeutic
targets
or
tools.
This
review
presents
a
comprehensive
overview
current
understanding
CVDs,
examining
mechanisms
action
recent
research
advances.
It
also
addresses
use
diagnostic
prognostic
markers,
well
applications
RNA
therapeutics
novel
treatment
strategies.
Язык: Английский
Long noncoding RNA as an emerging regulator of endoderm differentiation: progress and perspectives
Cell Regeneration,
Год журнала:
2025,
Номер
14(1)
Опубликована: Март 26, 2025
Abstract
Accumulated
studies
have
demonstrated
that
long
noncoding
RNAs
(lncRNAs)
play
crucial
regulatory
roles
in
diverse
biological
processes,
such
as
embryonic
development
and
cell
differentiation.
Comprehensive
transcriptome
analysis
identifies
extensive
lncRNAs,
gradually
elucidating
their
functions
across
various
contexts.
Recent
highlighted
the
essential
role
of
lncRNAs
definitive
endoderm
differentiation,
underscoring
importance
early
development.
In
this
review,
we
analyzed
features
overlapping,
proximal,
desert
classified
by
genomic
location,
pluripotent
stem
cells
(PSCs)
differentiation
derivatives.
Furthermore,
focus
on
lineage
review
latest
advancements
lncRNA
identification
distinct
mechanisms.
By
consolidating
current
knowledge,
aim
to
provide
a
clearer
perspective
how
contribute
different
manners.
Язык: Английский
High throughput CRISPR approaches: New solutions for challenging problems
TrAC Trends in Analytical Chemistry,
Год журнала:
2025,
Номер
unknown, С. 118245 - 118245
Опубликована: Март 1, 2025
Язык: Английский
Next-Generation Sequencing: a powerful multi-purpose tool in cell line development for biologics production
Computational and Structural Biotechnology Journal,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 1, 2025
Within
the
biopharmaceutical
industry,
cell
line
development
(CLD)
process
generates
recombinant
mammalian
lines
for
expression
of
therapeutic
proteins.
Analytical
methods
extensive
characterisation
protein
product
are
well
established;
however,
over
recent
years,
next-generation
sequencing
(NGS)
technologies
have
rapidly
become
an
integral
part
CLD
workflow.
NGS
can
be
used
different
applications
to
characterise
genome,
epigenome
and
transcriptome
lines.
The
resulting
datasets,
especially
when
integrated
with
systems
biology
models,
give
comprehensive
insights
that
applied
optimize
lines,
media,
fermentation
processes.
also
provides
monitor
genetic
variability
during
CLD.
High
coverage
experiments
indeed
ensure
integrity
plasmids,
identify
integration
sites,
verify
monoclonality
This
review
summarises
role
in
advancing
production
safety
efficacy
Язык: Английский
Unveiling roles of non‐coding RNAs in cancer through advanced technologies
Quantitative Biology,
Год журнала:
2025,
Номер
13(4)
Опубликована: Апрель 20, 2025
Язык: Английский
CRISPRi Screen Uncovers lncRNA Regulators of Human Monocyte Growth
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 25, 2024
Abstract
Long
noncoding
RNAs
are
emerging
as
critical
regulators
of
biological
processes.
While
there
over
20,000
lncRNAs
annotated
in
the
human
genome
we
do
not
know
function
for
majority.
Here
performed
a
high-throughput
CRISPRi
screen
to
identify
those
that
important
viability
monocytes
using
cell
line
THP1.
We
identified
total
38
hits
from
and
validated
characterized
two
top
intergenic
hits.
The
first
is
lncRNA
neighboring
macrophage
transcription
factor
IRF8
(
RP11-542M13
.
2
hereafter
referred
long
RNA
regulator
monocyte
proliferation,
LNCRMP
)
second
called
OLMALINC
(oligodendrocyte
maturation-associated
intervening
non-coding
RNA)
was
previously
found
be
oligodendrocyte
maturation.
Transcriptional
repression
severely
limited
their
proliferation
capabilities.
RNA-seq
analysis
knockdown
lines
showed
regulated
proapoptotic
pathways
while
impacted
genes
associated
with
cycle.
Data
supports
both
functioning
cis
regulate
proteins
also
essential
THP1
growth.
This
research
highlights
importance
screening
powerful
tool
quickly
discovering
functional
(lncRNAs)
play
vital
role
regulating
viability.
Язык: Английский