Following the Birth, Life, and Death of mRNAs in Single Cells

Single-molecule imaging reveals translation-dependent destabilization of mRNAs

(2023) Pratik Dave et al.   MOLECULAR CELL

SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding

(2022) Sofia A. Quinodoz et al.   Nature Protocols

Large-scale two-photon calcium imaging in freely moving mice

(2022) Weijian Zong et al.   CELL

Transcriptional coupling of distant regulatory genes in living embryos

(2022) Michal Levo et al.   NATURE

Single-molecule imaging of microRNA-mediated gene silencing in cells

(2022) Hotaka Kobayashi et al.   Nature Communications

Nuclear speckles – a driving force in gene expression

(2022) Gabriel P. Faber et al.   JOURNAL OF CELL SCIENCE

Real-time visualization of mRNA synthesis during memory formation in live mice

(2022) Byung Hun Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Imaging translational control by Argonaute with single-molecule resolution in live cells

(2022) Charlotte A. Cialek et al.   Nature Communications

ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ

(2022) Ian Dardani et al.   NATURE METHODS

HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging

(2022) Adham Safieddine et al.   Nature Protocols

RNA export through the nuclear pore complex is directional

(2022) Asaf Ashkenazy-Titelman et al.   Nature Communications

An improved imaging system that corrects MS2-induced RNA destabilization

(2022) Weihan Li et al.   NATURE METHODS

Structure of a transcribing RNA polymerase II–U1 snRNP complex

(2021) Suyang Zhang et al.   SCIENCE

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics

(2021) Murat Sunbul et al.   NATURE BIOTECHNOLOGY

RNA Peach and Mango: Orthogonal two-color fluorogenic aptamers distinguish nearly identical ligands.

(2021) Kristen Y. S. Kong et al.   RNA

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

(2021) Shahar Alon et al.   SCIENCE

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection

(2021) Yihan Wan et al.   CELL

p53 mediates target gene association with nuclear speckles for amplified RNA expression

(2021) Katherine A. Alexander et al.   MOLECULAR CELL

Differential regulation of local mRNA dynamics and translation following long-term potentiation and depression

(2021) Paul G. Donlin-Asp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Imaging translation dynamics in live embryos reveals spatial heterogeneities

(2021) Jeremy Dufourt et al.   SCIENCE

smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods

(2021) Llilians Calvo et al.   Communications Biology

Probing steps in DNA transcription using single-molecule methods

(2021) Chun-Ying Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tutorial: practical considerations for tissue clearing and imaging

(2021) Kurt R. Weiss et al.   Nature Protocols

Imaging Organization of RNA Processing within the Nucleus

(2021) Jeetayu Biswas et al.   Cold Spring Harbor Perspectives in Biology

Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics

(2021) Virginia L. Pimmett et al.   Nature Communications

EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization

(2021) Yuhan Wang et al.   CELL

Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters

(2020) Tatjana Trcek et al.   MOLECULAR CELL

Live cell imaging of single RNA molecules with fluorogenic Mango II arrays

(2020) Adam D. Cawte et al.   Nature Communications

Speculating on the Roles of Nuclear Speckles: How RNA‐Protein Nuclear Assemblies Affect Gene Expression

(2020) Sarah E. Hasenson et al.   BIOESSAYS

Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo

(2020) Caroline Hoppe et al.   DEVELOPMENTAL CELL

Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins

(2020) Joseph Dopie et al.   JOURNAL OF CELL BIOLOGY

Highly specific multiplexed RNA imaging in tissues with split-FISH

(2020) Jolene Jie Lin Goh et al.   NATURE METHODS

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

(2020) Daniel Gyllborg et al.   NUCLEIC ACIDS RESEARCH

SON and SRRM2 are essential for nuclear speckle formation

(2020) İbrahim Avşar Ilik et al.   eLife

Single-Molecule Imaging Reveals Translation of mRNAs Localized to Stress Granules

(2020) Daniel Mateju et al.   CELL

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

(2020) Liguo Zhang et al.   GENOME RESEARCH

Enhancer-promoter communication: hubs or loops?

(2020) Bomyi Lim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Late Endosomes Act as mRNA Translation Platforms and Sustain Mitochondria in Axons

(2019) Jean-Michel Cioni et al.   CELL

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons

(2019) Sarah A. Middleton et al.   BMC BIOLOGY

Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting

(2019) Benjamin T Donovan et al.   EMBO JOURNAL

Single-Molecule Imaging Uncovers Rules Governing Nonsense-Mediated mRNA Decay

(2019) Tim A. Hoek et al.   MOLECULAR CELL

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

(2019) Jocelyn Y. Kishi et al.   NATURE METHODS

Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding

(2019) Sanne Boersma et al.   CELL

Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells

(2019) Jieru Li et al.   CELL

Genome organization around nuclear speckles

(2019) Yu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Large distances separate coregulated genes in living Drosophila embryos

(2019) Tyler Heist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo

(2019) Ning Zhao et al.   Nature Communications

Multiplexed detection of RNA using MERFISH and branched DNA amplification

(2019) Chenglong Xia et al.   Scientific Reports

RNA Granules Hitchhike on Lysosomes for Long-Distance Transport, Using Annexin A11 as a Molecular Tether

(2019) Ya-Cheng Liao et al.   CELL

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Live-cell imaging of single mRNA dynamics using split superfolder green fluorescent proteins with minimal background

(2019) Sung Young Park et al.   RNA

Availability of splicing factors in the nucleoplasm can regulate the release of mRNA from the gene after transcription

(2019) Hodaya Hochberg-Laufer et al.   PLoS Genetics

Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems

(2019) Liang-Zhong Yang et al.   MOLECULAR CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

Visualizing transcription factor dynamics in living cells

(2018) Zhe Liu et al.   JOURNAL OF CELL BIOLOGY

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

A transgenic mouse for imaging activity-dependent dynamics of endogenous Arc mRNA in live neurons

(2018) Sulagna Das et al.   Science Advances

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing

(2018) Takayuki Nojima et al.   MOLECULAR CELL

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells

(2017) Ivana Horvathova et al.   MOLECULAR CELL

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

An improved MS2 system for accurate reporting of the mRNA life cycle

(2017) Evelina Tutucci et al.   NATURE METHODS

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

(2017) Xiaoyin Chen et al.   NUCLEIC ACIDS RESEARCH

Enzymatic production of single-molecule FISH and RNA capture probes

(2017) Imre Gaspar et al.   RNA

A Fluorescence in Situ Hybridization Method To Quantify mRNA Translation by Visualizing Ribosome–mRNA Interactions in Single Cells

(2017) Kelly S. Burke et al.   ACS Central Science

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells

(2016) Chong Wang et al.   CELL

Dynamics of Translation of Single mRNA Molecules In Vivo

(2016) Xiaowei Yan et al.   CELL

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

(2016) David A. Nelles et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

(2016) Sheel Shah et al.   DEVELOPMENT

Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

(2016) Xavier Pichon et al.   JOURNAL OF CELL BIOLOGY

smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability

(2016) Nikolay Tsanov et al.   NUCLEIC ACIDS RESEARCH

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

(2016) Kevin M. Harlen et al.   Cell Reports

Mapping translation 'hot-spots' in live cells by tracking single molecules of mRNA and ribosomes

(2016) Zachary B Katz et al.   eLife

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences

(2015) Bin Wu et al.   GENES & DEVELOPMENT

Bursty Gene Expression in the Intact Mammalian Liver

(2015) Keren Bahar Halpern et al.   MOLECULAR CELL

High-performance probes for light and electron microscopy

(2015) Sarada Viswanathan et al.   NATURE METHODS

A general method to improve fluorophores for live-cell and single-molecule microscopy

(2015) Jonathan B Grimm et al.   NATURE METHODS

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system

(2015) J. F. Garcia et al.   RNA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

An RNA biosensor for imaging the first round of translation from single cells to living animals

(2015) J. M. Halstead et al.   SCIENCE

Expansion microscopy

(2015) F. Chen et al.   SCIENCE

Drosophila germ granules are structured and contain homotypic mRNA clusters

(2015) Tatjana Trcek et al.   Nature Communications

RNA Mango Aptamer-Fluorophore: A Bright, High-Affinity Complex for RNA Labeling and Tracking

(2014) Elena V. Dolgosheina et al.   ACS Chemical Biology

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation

(2014) Nimish Khanna et al.   CURRENT BIOLOGY

Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

(2014) Grigory S. Filonov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Programmable RNA recognition and cleavage by CRISPR/Cas9

(2014) Mitchell R. O’Connell et al.   NATURE

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Axonal Transport of TDP-43 mRNA Granules Is Impaired by ALS-Causing Mutations

(2014) Nael H. Alami et al.   NEURON

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

(2014) J. P. Bothma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structural Basis of Pathogenic Subgenomic Flavivirus RNA (sfRNA) Production

(2014) E. G. Chapman et al.   SCIENCE

Visualization of Dynamics of Single Endogenous mRNA Labeled in Live Mouse

(2014) H. Y. Park et al.   SCIENCE

The embryo as a laboratory: quantifying transcription in Drosophila

(2014) Thomas Gregor et al.   TRENDS IN GENETICS

Background free imaging of single mRNAs in live cells using split fluorescent proteins

(2014) Bin Wu et al.   Scientific Reports

Kinetic competition during the transcription cycle results in stochastic RNA processing

(2014) Antoine Coulon et al.   eLife

Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos

(2013) Tanguy Lucas et al.   CURRENT BIOLOGY

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning

(2013) Hernan G. Garcia et al.   CURRENT BIOLOGY

A multispectral LED array for the reduction of background autofluorescence in brain tissue

(2013) Haison Duong et al.   JOURNAL OF NEUROSCIENCE METHODS

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

(2013) Nico Battich et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Single-molecule analysis of gene expression using two-color RNA labeling in live yeast

(2012) Sami Hocine et al.   NATURE METHODS

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

A transgenic mouse for in vivo detection of endogenous labeled mRNA

(2011) Timothée Lionnet et al.   NATURE METHODS

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

(2011) D. R. Larson et al.   SCIENCE

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

(2011) Yehuda Brody et al.   PLOS BIOLOGY

Hsp70 gene association with nuclear speckles is Hsp70 promoter specific

(2010) Yan Hu et al.   JOURNAL OF CELL BIOLOGY

In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport

(2010) David Grünwald et al.   NATURE

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells

(2010) Amir Mor et al.   NATURE CELL BIOLOGY

Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells

(2010) Antony K. Chen et al.   NUCLEIC ACIDS RESEARCH

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

A role for TREX components in the release of spliced mRNA from nuclear speckle domains

(2010) Anusha P. Dias et al.   Nature Communications

High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis

(2009) J. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Vivo Imaging of oskar mRNA Transport Reveals the Mechanism of Posterior Localization

(2008) Vitaly L. Zimyanin et al.   CELL

The dynamics of fluorescently labeled endogenous gurken mRNA in Drosophila

(2008) A. M. Jaramillo et al.   JOURNAL OF CELL SCIENCE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY