U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes

Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential

(2022) Hanneke Vlaming et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci

(2022) Chad B. Stein et al.   MOLECULAR CELL

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

(2021) Kirsten A. Reimer et al.   MOLECULAR CELL

Structure of a transcribing RNA polymerase II–U1 snRNP complex

(2021) Suyang Zhang et al.   SCIENCE

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

(2021) Amit Blumberg et al.   BMC BIOLOGY

Efficient RNA polymerase II pause release requires U2 snRNP function

(2021) Livia Caizzi et al.   MOLECULAR CELL

Gene Size Matters: An Analysis of Gene Length in the Human Genome

(2021) Inês Lopes et al.   Frontiers in Genetics

Pharmacologic modulation of RNA splicing enhances anti-tumor immunity

(2021) Sydney X. Lu et al.   CELL

RNA polymerase II speed: a key player in controlling and adapting transcriptome composition

(2021) Lisa Muniz et al.   EMBO JOURNAL

Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo

(2021) Kristina Žumer et al.   MOLECULAR CELL

Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination

(2021) Ashwin Narain et al.   MOLECULAR CELL

Using TTchem-seq for profiling nascent transcription and measuring transcript elongation

(2020) Lea H. Gregersen et al.   Nature Protocols

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

Intron and gene size expansion during nervous system evolution

(2020) Matthew J. McCoy et al.   BMC GENOMICS

Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

(2020) Tomasz W. Turowski et al.   MOLECULAR CELL

Structural Biology of RNA Polymerase II Transcription: 20 Years On

(2020) Sara Osman et al.   Annual Review of Cell and Developmental Biology

U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene Regulation

(2019) Christopher C. Venters et al.   Cold Spring Harbor Perspectives in Biology

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation

(2019) Malgorzata Krajewska et al.   Nature Communications

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

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Transcriptional Control by Premature Termination: A Forgotten Mechanism

(2019) Kinga Kamieniarz-Gdula et al.   TRENDS IN GENETICS

Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma

(2019) Hiromichi Suzuki et al.   NATURE

The U1 spliceosomal RNA is recurrently mutated in multiple cancers

(2019) Shimin Shuai et al.   NATURE

RNA Splicing by the Spliceosome

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

Exon-Mediated Activation of Transcription Starts

(2019) Ana Fiszbein et al.   CELL

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

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

(2018) Lydia Herzel et al.   GENOME RESEARCH

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

(2018) Anthony C. Chiu et al.   MOLECULAR CELL

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

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

CDK12 regulates DNA repair genes by suppressing intronic polyadenylation

(2018) Sara J. Dubbury et al.   NATURE

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

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

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

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation

(2017) Andrew Routh et al.   NUCLEIC ACIDS RESEARCH

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast motif matching revisited: high-order PWMs, SNPs and indels

(2016) Janne H. Korhonen et al.   BIOINFORMATICS

Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases

(2016) Aleksandr B. Sahakyan et al.   BMC GENOMICS

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

(2016) Fernando Carrillo Oesterreich et al.   CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

The reciprocal regulation between splicing and 3′-end processing

(2016) Daisuke Kaida   Wiley Interdisciplinary Reviews-RNA

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

(2015) Minho Chae et al.   BMC BIOINFORMATICS

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

(2015) Takayuki Nojima et al.   CELL

GC skew defines distinct RNA polymerase pause sites in CpG island promoters

(2015) Wendy A. Kellner et al.   GENOME RESEARCH

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

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

(2014) A. Veloso et al.   GENOME RESEARCH

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

(2014) Iris Jonkers et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) H. Kwak et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

(2012) B. Zamft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

(2011) D. Blazek et al.   GENES & DEVELOPMENT

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The architecture of RNA polymerase fidelity

(2010) Craig D Kaplan   BMC BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A 5′ Splice Site Enhances the Recruitment of Basal Transcription Initiation Factors In Vivo

(2008) Christian Kroun Damgaard et al.   MOLECULAR CELL

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA

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

(2008) Leighton J. Core et al.   SCIENCE