Context-dependent control of alternative splicing by RNA-binding proteins

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Both Decreased and Increased SRPK1 Levels Promote Cancer by Interfering with PHLPP-Mediated Dephosphorylation of Akt

(2014) Pingping Wang et al.   MOLECULAR CELL

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L

(2014) Oliver Rossbach et al.   RNA Biology

HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism

(2014) Sebastien M. Weyn-Vanhentenryck et al.   Cell Reports

The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation

(2014) Qin Li et al.   eLife

Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

Direct Conversion of Fibroblasts to Neurons by Reprogramming PTB-Regulated MicroRNA Circuits

(2013) Yuanchao Xue et al.   CELL

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

Regulation of splicing by SR proteins and SR protein-specific kinases

(2013) Zhihong Zhou et al.   CHROMOSOMA

Stress granules as crucibles of ALS pathogenesis

(2013) Yun R. Li et al.   JOURNAL OF CELL BIOLOGY

Transcriptome-Wide RNA Interaction Profiling Reveals Physical and Functional Targets of hnRNP L in Human T Cells

(2013) G. Shankarling et al.   MOLECULAR AND CELLULAR BIOLOGY

RBM5, 6, and 10 Differentially Regulate NUMB Alternative Splicing to Control Cancer Cell Proliferation

(2013) Elias G. Bechara et al.   MOLECULAR CELL

Competition between Pre-mRNAs for the Splicing Machinery Drives Global Regulation of Splicing

(2013) Elizabeth M. Munding et al.   MOLECULAR CELL

HnRNP L and HnRNP A1 Induce Extended U1 snRNA Interactions with an Exon to Repress Spliceosome Assembly

(2013) Ni-Ting Chiou et al.   MOLECULAR CELL

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

(2013) Shatakshi Pandit et al.   MOLECULAR CELL

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

(2013) Hong Han et al.   NATURE

Hidden specificity in an apparently nonspecific RNA-binding protein

(2013) Ulf-Peter Guenther et al.   NATURE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS

(2013) Hong Joo Kim et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Cas9 as a versatile tool for engineering biology

(2013) Prashant Mali et al.   NATURE METHODS

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

(2013) Michael T Lovci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43

(2013) E. S. Arnold et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation

(2013) M. P. Hall et al.   RNA

Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins

(2012) Eric T. Wang et al.   CELL

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies

(2012) Tina W. Han et al.   CELL

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

(2012) Alfredo Castello et al.   CELL

Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2

(2012) Niroshika Keppetipola et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain

(2012) D. D. Licatalosi et al.   GENES & DEVELOPMENT

Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

(2012) K. A. Dittmar et al.   MOLECULAR AND CELLULAR BIOLOGY

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation

(2012) Rui Xiao et al.   MOLECULAR CELL

LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor Abundance

(2012) Melissa L. Wilbert et al.   MOLECULAR CELL

The Akt-SRPK-SR Axis Constitutes a Major Pathway in Transducing EGF Signaling to Regulate Alternative Splicing in the Nucleus

(2012) Zhihong Zhou et al.   MOLECULAR CELL

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

(2012) Clotilde Lagier-Tourenne et al.   NATURE NEUROSCIENCE

PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2

(2012) Sika Zheng et al.   NATURE NEUROSCIENCE

A complex network of factors with overlapping affinities represses splicing through intronic elements

(2012) Yang Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules

(2012) Yang Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Muscleblind-like 2-Mediated Alternative Splicing in the Developing Brain and Dysregulation in Myotonic Dystrophy

(2012) Konstantinos Charizanis et al.   NEURON

Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability

(2012) Gulayse Ince-Dunn et al.   NEURON

Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms

(2012) S. Erkelenz et al.   RNA

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins

(2012) Stephanie C. Huelga et al.   Cell Reports

An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors

(2012) Idit Kosti et al.   PLoS Computational Biology

Intrinsic Disorder in the Human Spliceosomal Proteome

(2012) Iga Korneta et al.   PLoS Computational Biology

Muscle-Specific Splicing Factors ASD-2 and SUP-12 Cooperatively Switch Alternative Pre-mRNA Processing Patterns of the ADF/Cofilin Gene in Caenorhabditis elegans

(2012) Genta Ohno et al.   PLoS Genetics

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

(2012) Minna-Liisa Änkö et al.   GENOME BIOLOGY

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

(2011) Takatoshi Iijima et al.   CELL

RNA structure and the mechanisms of alternative splicing

(2011) C Joel McManus et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Regulation of alternative splicing by the core spliceosomal machinery

(2011) A. L. Saltzman et al.   GENES & DEVELOPMENT

Quantitative evaluation of all hexamers as exonic splicing elements

(2011) Shengdong Ke et al.   GENOME RESEARCH

Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor

(2011) Kensuke Ninomiya et al.   JOURNAL OF CELL BIOLOGY

U1 snRNA Directly Interacts with Polypyrimidine Tract-Binding Protein during Splicing Repression

(2011) Shalini Sharma et al.   MOLECULAR CELL

The Ewing Sarcoma Protein Regulates DNA Damage-Induced Alternative Splicing

(2011) Maria Paola Paronetto et al.   MOLECULAR CELL

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

Frequent pathway mutations of splicing machinery in myelodysplasia

(2011) Kenichi Yoshida et al.   NATURE

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assembly

(2011) S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of activation and repression by the alternative splicing factors RBFOX1/2

(2011) S. Sun et al.   RNA

DEGRADE, MOVE, REGROUP: signaling control of splicing proteins

(2011) Florian Heyd et al.   TRENDS IN BIOCHEMICAL SCIENCES

Pre-mRNA splicing: where and when in the nucleus

(2011) Joonhee Han et al.   TRENDS IN CELL BIOLOGY

Evolution of SR protein and hnRNP splicing regulatory factors

(2011) Anke Busch et al.   Wiley Interdisciplinary Reviews-RNA

An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis

(2010) Michael J. Moore et al.   CELL

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged

(2010) C. J. David et al.   GENES & DEVELOPMENT

SR Proteins Induce Alternative Exon Skipping through Their Activities on the Flanking Constitutive Exons

(2010) J. Han et al.   MOLECULAR AND CELLULAR BIOLOGY

Phosphorylation-Dependent Regulation of PSF by GSK3 Controls CD45 Alternative Splicing

(2010) Florian Heyd et al.   MOLECULAR CELL

Context-Dependent Regulatory Mechanism of the Splicing Factor hnRNP L

(2010) Laura B. Motta-Mena et al.   MOLECULAR CELL

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy

(2010) Hongqing Du et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

(2010) Miriam Llorian et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing

(2010) Margherita Corioni et al.   NUCLEIC ACIDS RESEARCH

The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events

(2010) Claude C. Warzecha et al.   RNA Biology

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

(2010) C. Zhang et al.   SCIENCE

Developments in RNA Splicing and Disease

(2010) M. G. Poulos et al.   Cold Spring Harbor Perspectives in Biology

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

Regulation of Vertebrate Nervous System Alternative Splicing and Development by an SR-Related Protein

(2009) John A. Calarco et al.   CELL

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

SRp38 Regulates Alternative Splicing and Is Required for Ca2+ Handling in the Embryonic Heart

(2009) Ying Feng et al.   DEVELOPMENTAL CELL

Regulation of SR protein phosphorylation and alternative splicing by modulating kinetic interactions of SRPK1 with molecular chaperones

(2009) X.-Y. Zhong et al.   GENES & DEVELOPMENT

Interaction of Akt-phosphorylated SRPK2 with 14-3-3 Mediates Cell Cycle and Cell Death in Neurons

(2009) Sung-Wuk Jang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An Overview of the Introns-First Theory

(2009) David Penny et al.   JOURNAL OF MOLECULAR EVOLUTION

Cooperative-Binding and Splicing-Repressive Properties of hnRNP A1

(2009) H. L. Okunola et al.   MOLECULAR AND CELLULAR BIOLOGY

ESRP1 and ESRP2 Are Epithelial Cell-Type-Specific Regulators of FGFR2 Splicing

(2009) Claude C. Warzecha et al.   MOLECULAR CELL

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

(2009) Yuanchao Xue et al.   MOLECULAR CELL

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

(2009) Gene W Yeo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Splice site strength–dependent activity and genetic buffering by poly-G runs

(2009) Xinshu Xiao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Autoregulation of Fox protein expression to produce dominant negative splicing factors

(2009) A. Damianov et al.   RNA

RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

(2009) Randy S. Daughters et al.   PLoS Genetics

The SR protein family of splicing factors: master regulators of gene expression

(2008) Jennifer C. Long et al.   BIOCHEMICAL JOURNAL

SMN Deficiency Causes Tissue-Specific Perturbations in the Repertoire of snRNAs and Widespread Defects in Splicing

(2008) Zhenxi Zhang et al.   CELL

Dynamic Regulation of Alternative Splicing by Silencers that Modulate 5′ Splice Site Competition

(2008) Yang Yu et al.   CELL

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

The Heterogeneous Nuclear Ribonucleoprotein L Is an Essential Component in the Ca2+/Calmodulin-dependent Protein Kinase IV-regulated Alternative Splicing through Cytidine-Adenosine Repeats

(2008) Jiankun Yu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

hnRNP H and hnRNP F Complex with Fox2 To Silence Fibroblast Growth Factor Receptor 2 Exon IIIc

(2008) D. M. Mauger et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2008) Donny D. Licatalosi et al.   NATURE

Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome

(2008) Shalini Sharma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The splicing factor SC35 has an active role in transcriptional elongation

(2008) Shengrong Lin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A cell-based screen for splicing regulators identifies hnRNP LL as a distinct signal-induced repressor of CD45 variable exon 4

(2008) J. D. Topp et al.   RNA

Regulation of CD45 Alternative Splicing by Heterogeneous Ribonucleoprotein, hnRNPLL

(2008) S. Oberdoerffer et al.   SCIENCE