What is the switch for coupling transcription and splicing? RNA Polymerase II C‐terminal domain phosphorylation, phase separation and beyond

Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome

(2019) Chuangye Yan et al.   Cold Spring Harbor Perspectives in Biology

The C-Terminal Domain of RNA Polymerase II Is a Multivalent Targeting Sequence that Supports Drosophila Development with Only Consensus Heptads

(2019) Feiyue Lu et al.   MOLECULAR CELL

The circular RNome of primary breast cancer

(2019) Marcel Smid et al.   GENOME RESEARCH

Yeast Ataxin-2 Forms an Intracellular Condensate Required for the Inhibition of TORC1 Signaling during Respiratory Growth

(2019) Yu-San Yang et al.   CELL

Redox State Controls Phase Separation of the Yeast Ataxin-2 Protein via Reversible Oxidation of Its Methionine-Rich Low-Complexity Domain

(2019) Masato Kato et al.   CELL

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization

(2018) Maike M.K. Hansen et al.   CELL

Short cryptic exons mediate recursive splicing in Drosophila

(2018) Brian Joseph et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Short cryptic exons mediate recursive splicing in Drosophila

(2018) Brian Joseph et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Luminal breast cancer-specific circular RNAs uncovered by a novel tool for data analysis

(2018) Lucia Coscujuela Tarrero et al.   Oncotarget

Interactome analyses revealed that the U1 snRNP machinery overlaps extensively with the RNAP II machinery and contains multiple ALS/SMA-causative proteins

(2018) Binkai Chi et al.   Scientific Reports

The Biogenesis, Functions, and Challenges of Circular RNAs

(2018) Xiang Li et al.   MOLECULAR CELL

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The temporal landscape of recursive splicing during Pol II transcription elongation in human cells

(2018) Xiao-Ou Zhang et al.   PLoS Genetics

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

(2018) Lorea Blazquez et al.   MOLECULAR CELL

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

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

(2017) Jingyi Fei et al.   JOURNAL OF CELL SCIENCE

Translation of CircRNAs

(2017) Nagarjuna Reddy Pamudurti et al.   MOLECULAR CELL

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis

(2017) Ivano Legnini et al.   MOLECULAR CELL

The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting

(2017) Dongming Liang et al.   MOLECULAR CELL

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

(2017) Lydia Herzel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nuclear speckles: molecular organization, biological function and role in disease

(2017) Lukasz Galganski et al.   NUCLEIC ACIDS RESEARCH

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly

(2017) An-Yun Chang et al.   Cell Reports

Dephosphorylating eukaryotic RNA polymerase II

(2016) Joshua E. Mayfield et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Phase separation in biology; functional organization of a higher order

(2016) Diana M. Mitrea et al.   Cell Communication and Signaling

Higher‐order oligomerization promotes localization of SPOP to liquid nuclear speckles

(2016) Melissa R Marzahn et al.   EMBO JOURNAL

Droplet organelles?

(2016) Edward M Courchaine et al.   EMBO JOURNAL

The RNA Polymerase II CTD: The Increasing Complexity of a Low-Complexity Protein Domain

(2016) Célia Jeronimo et al.   JOURNAL OF MOLECULAR BIOLOGY

Heptad-Specific Phosphorylation of RNA Polymerase II CTD

(2016) Roland Schüller et al.   MOLECULAR CELL

Lessons from non-canonical splicing

(2016) Christopher R. Sibley et al.   NATURE REVIEWS GENETICS

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Targeted Intron Retention and Excision for Rapid Gene Regulation in Response to Neuronal Activity

(2016) Oriane Mauger et al.   NEURON

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans

(2016) Jeong H. Ahn et al.   PLoS Genetics

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

SnapShot: Spliceosome Dynamics III

(2015) Markus C. Wahl et al.   CELL

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

(2015) Paul L. Boutz et al.   GENES & DEVELOPMENT

Molecular Basis of Transcription-Coupled Pre-mRNA Capping

(2015) Fuensanta W. Martinez-Rucobo et al.   MOLECULAR CELL

Chromatin-wide Profiling of DYRK1A Reveals a Role as a Gene-Specific RNA Polymerase II CTD Kinase

(2015) Chiara Di Vona et al.   MOLECULAR CELL

Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II

(2015) Kathleen A. Burke et al.   MOLECULAR CELL

Recursive splicing in long vertebrate genes

(2015) Christopher R. Sibley et al.   NATURE

Genome-wide identification of zero nucleotide recursive splicing in Drosophila

(2015) Michael O. Duff et al.   NATURE

Phosphorylation-mediated RNA/peptide complex coacervation as a model for intracellular liquid organelles

(2015) William M. Aumiller et al.   Nature Chemistry

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP

(2015) Yong Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exon-intron circular RNAs regulate transcription in the nucleus

(2015) Zhaoyong Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Short intronic repeat sequences facilitate circular RNA production

(2014) Dongming Liang et al.   GENES & DEVELOPMENT

TFIIH Phosphorylation of the Pol II CTD Stimulates Mediator Dissociation from the Preinitiation Complex and Promoter Escape

(2014) Koon Ho Wong et al.   MOLECULAR CELL

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR CELL

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Kin28 regulates the transient association of Mediator with core promoters

(2014) Célia Jeronimo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation

(2014) Friederike Itzen et al.   NUCLEIC ACIDS RESEARCH

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

(2014) Reut Shalgi et al.   Cell Reports

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

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

(2013) Zhihong Zhou et al.   CHROMOSOMA

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

Nascent-Seq Indicates Widespread Cotranscriptional RNA Editing in Drosophila

(2012) Joseph Rodriguez et al.   MOLECULAR CELL

Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II

(2012) Stéphane Larochelle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Serine-7 but not serine-5 phosphorylation primes RNA polymerase II CTD for P-TEFb recognition

(2012) Nadine Czudnochowski et al.   Nature Communications

Intrinsic Disorder in the Human Spliceosomal Proteome

(2012) Iga Korneta et al.   PLoS Computational Biology

Exon and intron definition in pre-mRNA splicing

(2012) Laura De Conti et al.   Wiley Interdisciplinary Reviews-RNA

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex

(2011) C. J. David et al.   GENES & DEVELOPMENT

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

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

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

(2010) J. Y. Ip et al.   GENOME RESEARCH

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation

(2010) Stefania Millevoi et al.   NUCLEIC ACIDS RESEARCH

Nuclear Speckles

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

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

DNA Damage Regulates Alternative Splicing through Inhibition of RNA Polymerase II Elongation

(2009) Manuel J. Muñoz et al.   CELL

TFIIH-Associated Cdk7 Kinase Functions in Phosphorylation of C-Terminal Domain Ser7 Residues, Promoter-Proximal Pausing, and Termination by RNA Polymerase II

(2009) K. Glover-Cutter et al.   MOLECULAR AND CELLULAR BIOLOGY

Rtr1 Is a CTD Phosphatase that Regulates RNA Polymerase II during the Transition from Serine 5 to Serine 2 Phosphorylation

(2009) Amber L. Mosley et al.   MOLECULAR CELL

7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development

(2009) M. Barboric et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-transcriptional splicing of constitutive and alternative exons

(2009) A. Pandya-Jones et al.   RNA

Molecular evolution of the RNA polymerase II CTD

(2008) Rob D. Chapman et al.   TRENDS IN GENETICS