4.5 Review

The alternative life of RNA-sequencing meets single molecule approaches

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Imaging mRNA and protein interactions within neurons

Carolina Eliscovich et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Multidisciplinary Sciences

Activity-dependent spatially localized miRNA maturation in neuronal dendrites

Sivakumar Sambandan et al.

SCIENCE (2017)

Review Neurosciences

mTOR and MAPK: from localized translation control to epilepsy

Helena F. Pernice et al.

BMC NEUROSCIENCE (2016)

Article Biochemistry & Molecular Biology

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

Chong Wang et al.

Article Biochemistry & Molecular Biology

Dynamics of Translation of Single mRNA Molecules In Vivo

Xiaowei Yan et al.

Article Biochemistry & Molecular Biology

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins

Aoife C. McMahon et al.

Article Biochemistry & Molecular Biology

Dynamic Axonal Translation in Developing and Mature Visual Circuits

Toshiaki Shigeoka et al.

Article Biochemistry & Molecular Biology

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

Zhipeng Lu et al.

Editorial Material Biochemistry & Molecular Biology

RNA Transport: From Head to Toe in Radial Glial Cells

Janina Ehses et al.

CURRENT BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Dynamic mRNA Transport and Local Translation in Radial Glial Progenitors of the Developing Brain

Louis-Jan Pilaz et al.

CURRENT BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Distal Alternative Last Exons Localize mRNAs to Neural Projections

J. Matthew Taliaferro et al.

MOLECULAR CELL (2016)

Article Biochemistry & Molecular Biology

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

Jong Ghut Ashley Aw et al.

MOLECULAR CELL (2016)

Article Biochemistry & Molecular Biology

Global Mapping of Human RNA-RNA Interactions

Eesha Sharma et al.

MOLECULAR CELL (2016)

Article Neurosciences

Evolving insights into RNA modifications and their functional diversity in the brain

Sarah Nainar et al.

NATURE NEUROSCIENCE (2016)

Article Biochemistry & Molecular Biology

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

Nikolay Tsanov et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Alternative splicing affects the subcellular localization of Drosha

Steffen Link et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Glutamate-induced RNA localization and translation in neurons

Young J. Yoon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

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

Tatsuya Morisaki et al.

SCIENCE (2016)

Article Multidisciplinary Sciences

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

Naomi Habib et al.

SCIENCE (2016)

Review Cell Biology

Evolution and Biological Roles of Alternative 3′UTRs

Christine Mayr

TRENDS IN CELL BIOLOGY (2016)

Article Multidisciplinary Sciences

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

Benjamin Lacar et al.

NATURE COMMUNICATIONS (2016)

Article Biochemistry & Molecular Biology

CLIPing Staufen to secondary RNA structures: Size and location matter!

Sandra M. Fernandez Moya et al.

BIOESSAYS (2015)

Article Biochemistry & Molecular Biology

Quantifying Protein-mRNA Interactions in Single Live Cells

Bin Wu et al.

Article Cell & Tissue Engineering

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

Jaehoon Shin et al.

CELL STEM CELL (2015)

Review Biochemistry & Molecular Biology

Advances and Applications of Single-Cell Sequencing Technologies

Yong Wang et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

L. Velten et al.

Molecular Systems Biology (2015)

Article Multidisciplinary Sciences

Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization

Binyamin D. Berkovits et al.

NATURE (2015)

Article Multidisciplinary Sciences

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

Yoichiro Sugimoto et al.

NATURE (2015)

Review Cell Biology

Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes

Soren Lykke-Andersen et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Multidisciplinary Sciences

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

James M. Halstead et al.

SCIENCE (2015)

Article Biotechnology & Applied Microbiology

High-throughput characterization of protein-RNA interactions

Kate B. Cook et al.

BRIEFINGS IN FUNCTIONAL GENOMICS (2015)

Review Cell Biology

In the right place at the right time: visualizing and understanding mRNA localization

Adina R. Buxbaum et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

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

Marvin E. Tanenbaum et al.

Article Multidisciplinary Sciences

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

Barbara Treutlein et al.

NATURE (2014)

Article Biochemical Research Methods

Quantitative single-cell RNA-seq with unique molecular identifiers

Saiful Islam et al.

NATURE METHODS (2014)

Review Cell Biology

Regulation of microRNA biogenesis

Minju Ha et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2014)

Article Multidisciplinary Sciences

Visualization of Dynamics of Single Endogenous mRNA Labeled in Live Mouse

Hye Yoon Park et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

Diego Adhemar Jaitin et al.

SCIENCE (2014)

Review Neurosciences

The multifunctional Staufen proteins: conserved roles from neurogenesis to synaptic plasticity

Jacki E. Heraud-Farlow et al.

TRENDS IN NEUROSCIENCES (2014)

Article Genetics & Heredity

Brain-expressed 3′UTR extensions strengthen miRNA cross-talk between ion channel/transporter encoding mRNAs

Claudia C. Wehrspaun et al.

FRONTIERS IN GENETICS (2014)

Article Biochemistry & Molecular Biology

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

Aleksandra Helwak et al.

Article Multidisciplinary Sciences

RNA-sequencing from single nuclei

Rashel V. Grindberg et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Cell Biology

Computational biology of RNA interactions

Christoph Dieterich et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2013)

Article Biochemistry & Molecular Biology

Introns in UTRs: Why we should stop ignoring them

Alicia A. Bicknell et al.

BIOESSAYS (2012)

Review Neurosciences

RNA-binding proteins involved in RNA localization and their implications in neuronal diseases

Marco Tolino et al.

EUROPEAN JOURNAL OF NEUROSCIENCE (2012)

Article Biochemistry & Molecular Biology

Extensive alternative polyadenylation during zebrafish development

Igor Ulitsky et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

Hidenori Tani et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

Iakes Ezkurdia et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Multidisciplinary Sciences

Identification of a cis-acting element that localizes mRNA to synapses

Elliott J. Meer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Cleavage factor Im is a key regulator of 3′ UTR length

Andreas R. Gruber et al.

RNA BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

Minna-Liisa Aenkoe et al.

GENOME BIOLOGY (2012)

Article Biochemistry & Molecular Biology

SAM68 Regulates Neuronal Activity-Dependent Alternative Splicing of Neurexin-1

Takatoshi Iijima et al.

Review Biochemistry & Molecular Biology

Mechanisms of dendritic mRNA transport and its role in synaptic tagging

Michael Doyle et al.

EMBO JOURNAL (2011)

Article Biochemistry & Molecular Biology

Independent localization of MAP2, CaMKIIα and β-actin RNAs in low copy numbers

Martin Mikl et al.

EMBO REPORTS (2011)

Article Cell Biology

Regulation of alternative splicing by the core spliceosomal machinery

Arneet L. Saltzman et al.

GENES & DEVELOPMENT (2011)

Review Biochemistry & Molecular Biology

Signaling Role of Cdc42 in Regulating Mammalian Physiology

Jaime Melendez et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2011)

Article Biochemistry & Molecular Biology

Identification of Neuronal RNA Targets of TDP-43-containing Ribonucleoprotein Complexes

Chantelle F. Sephton et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2011)

Review Biochemistry & Molecular Biology

Mechanisms and Consequences of Alternative Polyadenylation

Dafne Campigli Di Giammartino et al.

MOLECULAR CELL (2011)

Article Multidisciplinary Sciences

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

Grzegorz Kudla et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Neural-specific elongation of 3′ UTRs during Drosophila development

Valerie Hilgers et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Editorial Material Biochemistry & Molecular Biology

Assembly, disassembly and recycling The dynamics of exon junction complexes

Fulvia Bono et al.

RNA BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

Christine Vogel et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Multidisciplinary Sciences

Distinct 3′UTRs differentially regulate activity-dependent translation of brain-derived neurotrophic factor (BDNF)

Anthony G. Lau et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Biochemistry & Molecular Biology

Pre-mRNA Processing Reaches Back to Transcription and Ahead to Translation

Melissa J. Moore et al.

Article Biochemistry & Molecular Biology

CD47 Is Upregulated on Circulating Hematopoietic Stem Cells and Leukemia Cells to Avoid Phagocytosis

Siddhartha Jaiswal et al.

Article Biochemical Research Methods

mRNA-Seq whole-transcriptome analysis of a single cell

Fuchou Tang et al.

NATURE METHODS (2009)

Article Biochemistry & Molecular Biology

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

Gene W. Yeo et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Multidisciplinary Sciences

Synapse- and Stimulus-Specific Local Translation During Long-Term Neuronal Plasticity

Dan Ohtan Wang et al.

SCIENCE (2009)

Review Multidisciplinary Sciences

Subcellular mRNA Localization in Animal Cells and Why It Matters

Christine E. Holt et al.

SCIENCE (2009)

Article Multidisciplinary Sciences

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Nicholas T. Ingolia et al.

SCIENCE (2009)

Review Cell Biology

To localize or not to localize: mRNA fate is in 3′UTR ends

Catia Andreassi et al.

TRENDS IN CELL BIOLOGY (2009)

Article Biochemical Research Methods

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

Daniel Ramskold et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

Myriam Heiman et al.

Article Multidisciplinary Sciences

Alternative isoform regulation in human tissue transcriptomes

Eric T. Wang et al.

NATURE (2008)

Article Multidisciplinary Sciences

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

Donny D. Licatalosi et al.

NATURE (2008)

Review Biochemistry & Molecular Biology

Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?

Nicholas J. McGlincy et al.

TRENDS IN BIOCHEMICAL SCIENCES (2008)

Article Biochemistry & Molecular Biology

The signal sequence coding region promotes nuclear export of mRNA

Alexander F. Palazzo et al.

PLOS BIOLOGY (2007)

Article Neurosciences

Identification of process-localized mRNAs from cultured rodent hippocampal neurons

Michael M. Poon et al.

JOURNAL OF NEUROSCIENCE (2006)

Article Biotechnology & Applied Microbiology

Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light

NG Gurskaya et al.

NATURE BIOTECHNOLOGY (2006)

Article Biochemical Research Methods

CLIP: A method for identifying protein-RNA interaction sites in living cells

J Ule et al.

METHODS (2005)

Review Cell Biology

The role of the Rho GTPases in neuronal development

EE Govek et al.

GENES & DEVELOPMENT (2005)

Review Biochemistry & Molecular Biology

AU-rich elements and associated factors: are there unifying principles?

C Barreau et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Multidisciplinary Sciences

Nuclear export of microRNA precursors

E Lund et al.

SCIENCE (2004)

Article Biotechnology & Applied Microbiology

An unappreciated role for RNA surveillance

RT Hillman et al.

GENOME BIOLOGY (2004)

Article Biochemistry & Molecular Biology

A quantitative analysis of intron effects on mammalian gene expression

A Nott et al.

Review Genetics & Heredity

Alternative splicing:: multiple control mechanisms and involvement in human disease

JF Cáceres et al.

TRENDS IN GENETICS (2002)

Article Biochemistry & Molecular Biology

SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs

A Sureau et al.

EMBO JOURNAL (2001)

Review Genetics & Heredity

Alternative splicing: increasing diversity in the proteomic world

BR Graveley

TRENDS IN GENETICS (2001)