Recent progress in single-cell transcriptomic studies in plants
Plant Biotechnology Reports,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 3, 2025
Язык: Английский
Bioinformatics and AI/ML approaches using multi-omics data to accelerate diagnosis and delivery of precision care for patients with rare diseases
Methods in cell biology,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
Язык: Английский
Direct RNA sequencing in plants: practical applications and future perspectives
Plant Communications,
Год журнала:
2024,
Номер
5(11), С. 101064 - 101064
Опубликована: Авг. 18, 2024
The
transcriptome
serves
as
a
bridge
that
links
genomic
variation
to
phenotypic
diversity.
A
vast
number
of
studies
using
next-generation
RNA
sequencing
(RNA-seq)
over
the
last
2
decades
have
emphasized
essential
roles
plant
in
response
developmental
and
environmental
conditions,
providing
numerous
insights
into
dynamic
changes,
evolutionary
traces,
elaborate
regulation
transcriptome.
With
substantial
improvement
accuracy
throughput,
direct
(DRS)
has
emerged
new
powerful
platform
for
precise
detection
native
full-length
transcripts,
overcoming
many
limitations
such
read
length
PCR
bias
are
inherent
short-read
RNA-seq.
Here,
we
review
recent
advances
dissecting
complexity
diversity
transcriptomes
DRS
main
technological
approach,
covering
aspects
metabolism,
including
novel
isoforms,
poly(A)
tails,
modification,
propose
comprehensive
workflow
processing
data.
Many
challenges
application
plants,
need
machine
learning
tools
tailored
transcriptomes,
remain
be
overcome,
together
outline
future
biological
questions
can
addressed
by
DRS,
allele-specific
modification.
This
technology
provides
convenient
support
on
which
connection
distinct
features
is
tightly
built,
sustainably
refining
our
understanding
functions
Язык: Английский
Deciphering the Cell-Specific Transcript Heterogeneity and Alternative Splicing during the Early Embryonic Development of Zebrafish
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 8, 2024
Abstract
Cell
fate
determination
during
early
embryonic
development
is
a
complex
process
modulated
by
gene
expression.
The
intricate
interplay
of
transcriptional
and
post-transcriptional
regulation
integral
to
the
developmental
trajectory
embryogenesis,
yet
how
RNA
processing
may
contribute
programming
largely
elusive.
Leveraging
recent
technological
advances
in
single-molecule
nanopore
sequencing,
we
developed
single-cell
long-read
transcriptome
sequencing
technology,
allowing
clear
view
transcript
diversity
zebrafish
embryogenesis
pre-
post-zygotic
genome
activation
(ZGA).
A
closer
examination
dynamic
usage
potential
alternative
splicing
revealed
that
abundant
stage-specific
transcripts
with
differential
coding
potentials
are
involved
distinct
biological
functions.
Specifically,
identified
two
cell
populations
at
onset
ZGA
based
on
isoform
instead
profiling,
which
followed
divergent
trajectories
toward
ectoderm
presumptive
ectoderm.
These
cells
were
characterized
regulations
linked
RNA-binding
proteins,
including
SNRPA
SFPQ.
Altogether,
using
strategy,
work
has
cell-specific
dynamics
contributing
embryogenesis.
Язык: Английский
Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs
Frontiers in Genetics,
Год журнала:
2024,
Номер
15
Опубликована: Дек. 2, 2024
The
advent
of
long-read
(LR)
sequencing
technologies
has
provided
a
direct
opportunity
to
determine
the
structure
transcripts
with
potential
for
end-to-end
full-length
RNAs.
LR
methods
that
have
been
described
date
include
commercial
offerings
from
Oxford
Nanopore
Technologies
(ONT)
and
Pacific
Biosciences.
These
kits
are
based
on
selection
polyadenylated
(polyA+)
RNAs
and/or
oligo-dT
priming
reverse
transcription.
Thus,
these
approaches
do
not
allow
comprehensive
interrogation
transcriptome
due
their
exclusion
non-polyadenylated
(polyA-)
In
addition,
polyA
+
specificity
also
results
in
3'-biased
measurements
PolyA+
especially
when
RNA
input
is
partially
degraded.
To
address
limitations
current
protocols,
we
modified
rRNA
depletion
protocols
used
short-read
sequencing:
one
approach
representing
ligation-based
method
other
template-switch
cDNA
synthesis-based
append
ONT-specific
adaptor
sequences
by
removing
any
deliberate
fragmentation/shearing
RNA/cDNA.
Here,
present
comparisons
poly+
RNA-specific
versions
two
including
ONT
PCR-cDNA
Barcoding
kit.
displayed
higher
proportions
(30%-50%)
intronic
content
compared
polyA-specific
(5%-8%).
enabled
∼20-50%
detection
expressed
genes.
Other
metrics
were
favourable
better
coverage
long
transcripts,
accuracy
reproducibility
expression
measurements.
Overall,
indicate
depletion-based
here
characterization
While
resulting
reads
enough
help
decipher
transcript
structures,
future
endeavors
warranted
improve
proportion
individual
spanning
transcripts.
Язык: Английский
scTrends: A living review of commercial single-cell and spatial 'omic technologies
Cell Genomics,
Год журнала:
2024,
Номер
4(12), С. 100723 - 100723
Опубликована: Дек. 1, 2024
Understanding
the
rapidly
evolving
landscape
of
single-cell
and
spatial
omic
technologies
is
crucial
for
advancing
biomedical
research
drug
development.
We
provide
a
living
review
both
mature
emerging
commercial
platforms,
highlighting
key
methodologies
trends
shaping
field.
This
spans
from
foundational
such
as
microfluidics
plate-based
methods
to
newer
approaches
like
combinatorial
indexing;
on
side,
we
consider
next-generation
sequencing
imaging-based
transcriptomics.
Finally,
highlight
that
may
fundamentally
expand
scope
data
generation
within
pharmaceutical
research,
creating
opportunities
discover
validate
novel
mechanisms.
Overall,
this
serves
critical
resource
navigating
commercialization
application
in
academic
research.
Язык: Английский