RNA-Centric Methods: Toward the Interactome of Specific RNA Transcripts

Proximity dependent biotinylation: key enzymes and adaptation to proteomics approaches

(2020) Payman Samavarchi-Tehrani et al.   MOLECULAR & CELLULAR PROTEOMICS

Massively parallel Cas13 screens reveal principles for guide RNA design

(2020) Hans-Hermann Wessels et al.   NATURE BIOTECHNOLOGY

Split-TurboID enables contact-dependent proximity labeling in cells

(2020) Kelvin F. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

CRISPR-assisted detection of RNA–protein interactions in living cells

(2020) Wenkai Yi et al.   NATURE METHODS

Photoactivatable RNA N 6 ‐Methyladenosine Editing with CRISPR‐Cas13

(2020) Jie Zhao et al.   Small

RNA–protein interaction mapping via MS2- or Cas13-based APEX targeting

(2020) Shuo Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

(2019) Rayner M. L. Queiroz et al.   NATURE BIOTECHNOLOGY

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

(2019) Erika C. Urdaneta et al.   Nature Communications

Directed Evolution of Split APEX2 Peroxidase

(2019) Yisu Han et al.   ACS Chemical Biology

Current approaches for RNA labelling to identify RNA-binding proteins

(2019) Darren Gemmill et al.   Biochemistry and Cell Biology

Defining the RNA interactome by total RNA‐associated protein purification

(2019) Vadim Shchepachev et al.   Molecular Systems Biology

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

(2019) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

Programmable RNA-Guided RNA Effector Proteins Built from Human Parts

(2019) Simone Rauch et al.   CELL

β-Actin mRNA interactome mapping by proximity biotinylation

(2019) Joyita Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In-cell identification and measurement of RNA-protein interactions

(2019) Antoine Graindorge et al.   Nature Communications

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

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

Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5′ UTR of tumor-associated mRNAs

(2018) Tatsuo Serikawa et al.   BIOCHIMIE

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m 6 A Modification

(2018) Hengyou Weng et al.   Cell Stem Cell

Molecular Mechanisms of RNA Targeting by Cas13-containing Type VI CRISPR–Cas Systems

(2018) Mitchell R. O'Connell   JOURNAL OF MOLECULAR BIOLOGY

Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein

(2018) Winston X. Yan et al.   MOLECULAR CELL

RNA–protein interaction detection in living cells

(2018) Muthukumar Ramanathan et al.   NATURE METHODS

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Expanding RNA binding specificity and affinity of engineered PUF domains

(2018) Yang-Yang Zhao et al.   NUCLEIC ACIDS RESEARCH

Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

(2018) Matthew M. Makowski et al.   Nature Communications

Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts

(2018) Barbara Herdy et al.   NUCLEIC ACIDS RESEARCH

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

(2018) Jakob Trendel et al.   CELL

Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

(2018) Stephanie Fanucchi et al.   NATURE GENETICS

Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture

(2018) Joel I. Perez-Perri et al.   Nature Communications

Split-BioID: a proximity biotinylation assay for dimerization-dependent protein interactions

(2017) Sofie De Munter et al.   FEBS LETTERS

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

Diversity and evolution of class 2 CRISPR–Cas systems

(2017) Sergey Shmakov et al.   NATURE REVIEWS MICROBIOLOGY

Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation

(2017) Simão T da Rocha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes

(2017) Isabel Myriam Schopp et al.   Nature Communications

Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation

(2017) Simão T da Rocha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry

(2017) Rachel A. Knoener et al.   Scientific Reports

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs

(2016) Eric J Strobel et al.   CURRENT OPINION IN BIOTECHNOLOGY

Identification of RNA-binding Proteins in Macrophages by Interactome Capture

(2016) Anke Liepelt et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive Identification of RNA-Binding Domains in Human Cells

(2016) Alfredo Castello et al.   MOLECULAR CELL

Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection

(2016) Alexandra East-Seletsky et al.   NATURE

Comparison of Cas9 activators in multiple species

(2016) Alejandro Chavez et al.   NATURE METHODS

The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions

(2016) Benedikt M. Beckmann et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

(2016) Omar O. Abudayyeh et al.   SCIENCE

Urb-RIP – An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins

(2016) Kyle A. Cottrell et al.   PLoS One

Identification of lncRNA MEG3 Binding Protein Using MS2-Tagged RNA Affinity Purification and Mass Spectrometry

(2015) Shanshan Liu et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

A Quantitative Proteomics Tool To Identify DNA–Protein Interactions in Primary Cells or Blood

(2015) Nina C. Hubner et al.   JOURNAL OF PROTEOME RESEARCH

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

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

(2014) Marvin E. Tanenbaum et al.   CELL

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Mass spectrometry-based identification of proteins interacting with nucleic acids

(2013) A. Tacheny et al.   Journal of Proteomics

RNA-protein analysis using a conditional CRISPR nuclease

(2013) H. Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

MS2-TRAP (MS2-tagged RNA affinity purification): Tagging RNA to identify associated miRNAs

(2012) Je-Hyun Yoon et al.   METHODS

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Split-protein systems: beyond binary protein–protein interactions

(2011) Sujan S Shekhawat et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Efficient detection of RNA-protein interactions using tethered RNAs

(2011) H. Iioka et al.   NUCLEIC ACIDS RESEARCH

Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3’ UTR structures

(2011) Alex Michael Ward et al.   RNA Biology

Unbiased RNA-protein interaction screen by quantitative proteomics

(2009) F. Butter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS