Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase

(2020) Li-Tao Guo et al.   JOURNAL OF MOLECULAR BIOLOGY

A potential mechanism underlying U1 snRNP inhibition of the cleavage step of mRNA 3’ processing

(2020) Yanhui Deng et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation

(2019) Sebastian M. Fica et al.   SCIENCE

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Quality and quantity control of gene expression by nonsense-mediated mRNA decay

(2019) Tatsuaki Kurosaki et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Complex of U1 snRNP with Cleavage and Polyadenylation Factors Controls Telescripting, Regulating mRNA Transcription in Human Cells

(2019) Byung Ran So et al.   MOLECULAR CELL

Nascent RNA and the Coordination of Splicing with Transcription

(2019) Karla M. Neugebauer   Cold Spring Harbor Perspectives in Biology

RNA Splicing by the Spliceosome

(2019) Max E. Wilkinson et al.   Annual Review of Biochemistry

Mechanistic insights into mRNA 3′-end processing

(2019) Ananthanarayanan Kumar et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler et al.   MOLECULAR CELL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling

(2018) Weijun Chen et al.   CELL

Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution

(2018) Jordan E. Burke et al.   CELL

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

(2018) Lydia Herzel et al.   GENOME RESEARCH

Short-hairpin RNA against aberrant HBB[IVSI-110(G>A)] mRNA restores β-globin levels in a novel cell model and acts as mono- and combination therapy for β-thalassemia in primary hematopoietic stem cells

(2018) Petros Patsali et al.   HAEMATOLOGICA

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

(2018) Yong Zhu et al.   MOLECULAR CELL

Short-hairpin RNA against aberrant HBB[IVSI-110(G>A)] mRNA restores β-globin levels in a novel cell model and acts as mono- and combination therapy for β-thalassemia in primary hematopoietic stem cells

(2018) Petros Patsali et al.   HAEMATOLOGICA

Numerous recursive sites contribute to accuracy of splicing in long introns in flies

(2018) Athma A. Pai et al.   PLoS Genetics

Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response

(2018) Athma A. Pai et al.   Wiley Interdisciplinary Reviews-RNA

Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5′ Pause Release, Termination, and Transcription Elongation Rate

(2018) Ryan M. Sheridan 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

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

(2017) Vahid Aslanzadeh et al.   GENOME RESEARCH

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

(2017) Hagen Tilgner et al.   GENOME RESEARCH

SR Proteins: Binders, Regulators, and Connectors of RNA

(2017) Sunjoo Jeong   MOLECULES AND CELLS

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

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

Alternative splicing as a regulator of development and tissue identity

(2017) Francisco E. Baralle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Widespread intra-dependencies in the removal of introns from human transcripts

(2017) Seong Won Kim et al.   NUCLEIC ACIDS RESEARCH

Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

(2017) Anna Vilborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Control of Gene Expression in Senescence through Transcriptional Read-Through of Convergent Protein-Coding Genes

(2017) Lisa Muniz et al.   Cell Reports

RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit

(2017) Laura Milligan et al.   eLife

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

Co-transcriptional splicing and the CTD code

(2016) Noélia Custódio et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

(2016) Michaela Müller-McNicoll et al.   GENES & DEVELOPMENT

Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts

(2016) Nicola Meola et al.   MOLECULAR CELL

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

(2016) P. Eser et al.   Molecular Systems Biology

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

The roles of RNA processing in translating genotype to phenotype

(2016) Kassie S. Manning et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

RNA structure in splicing: An evolutionary perspective

(2016) Chien-Ling Lin et al.   RNA Biology

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

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

(2015) Takayuki Nojima et al.   CELL

Widespread Inducible Transcription Downstream of Human Genes

(2015) Anna Vilborg et al.   MOLECULAR CELL

Recursive splicing in long vertebrate genes

(2015) Christopher R. Sibley et al.   NATURE

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The fission yeast MTREC complex targets CUTs and unspliced pre-mRNAs to the nuclear exosome

(2015) Yang Zhou et al.   Nature Communications

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

(2015) Ana R Grosso et al.   eLife

Global transcriptome analyses of human and murine terminal erythroid differentiation

(2014) X. An et al.   BLOOD

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

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation

(2014) Keerthi T. Chathoth et al.   MOLECULAR CELL

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Kinetic competition during the transcription cycle results in stochastic RNA processing

(2014) Antoine Coulon et al.   eLife

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

(2013) Hannes Braberg et al.   CELL

Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation

(2013) Ignacio E Schor et al.   EMBO JOURNAL

Splicing-coupled 3′ end formation requires a terminal splice acceptor site, but not intron excision

(2013) Lee Davidson et al.   NUCLEIC ACIDS RESEARCH

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus

(2012) Guramrit Singh et al.   CELL

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes

(2011) Sandra Bento Martins et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pause locally, splice globally

(2011) Fernando Carrillo Oesterreich et al.   TRENDS IN CELL BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

Splicing-Dependent RNA Polymerase Pausing in Yeast

(2010) Ross D. Alexander et al.   MOLECULAR CELL

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

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

RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae

(2010) R. D. Alexander et al.   RNA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Co-transcriptional splicing of constitutive and alternative exons

(2009) A. Pandya-Jones et al.   RNA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

“Nought May Endure but Mutability”: Spliceosome Dynamics and the Regulation of Splicing

(2008) Duncan J. Smith et al.   MOLECULAR CELL

In vivo selection of genetically modified erythroblastic progenitors leads to long-term correction of  -thalassemia

(2008) A. Miccio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE