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

Essential histone chaperones collaborate to regulate transcription and chromatin integrity

(2021) Olga Viktorovskaya et al.   GENES & DEVELOPMENT

Yeast Spt6 Reads Multiple Phosphorylation Patterns of RNA Polymerase II C-Terminal Domain In Vitro

(2020) Pavel Brázda et al.   JOURNAL OF MOLECULAR BIOLOGY

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

(2020) Pabitra K. Parua et al.   Nature Communications

SPT6-driven error-free DNA repair safeguards genomic stability of glioblastoma cancer stem-like cells

(2020) Elisabeth Anne Adanma Obara et al.   Nature Communications

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

(2019) Apoorva Baluapuri et al.   MOLECULAR CELL

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications

(2019) Célia Jeronimo et al.   Cell Reports

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

The pause-initiation limit restricts transcription activation in human cells

(2019) Saskia Gressel et al.   Nature Communications

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism

(2019) Michael A. Cortazar et al.   MOLECULAR CELL

Dissecting newly transcribed and old RNA using GRAND-SLAM

(2018) Christopher Jürges et al.   BIOINFORMATICS

Estimating pseudocounts and fold changes for digital expression measurements

(2018) Florian Erhard   BIOINFORMATICS

Acetylation-Dependent Recruitment of the FACT Complex and Its Role in Regulating Pol II Occupancy Genome-Wide inSaccharomyces cerevisiae

(2018) Rakesh Pathak et al.   GENETICS

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Casein kinase 2 mediated phosphorylation of Spt6 modulates histone dynamics and regulates spurious transcription

(2018) Emmanuelle Gouot et al.   NUCLEIC ACIDS RESEARCH

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

(2018) Matthias Muhar et al.   SCIENCE

Acetylation-Dependent Recruitment of the FACT Complex and Its Role in Regulating Pol II Occupancy Genome-Wide inSaccharomyces cerevisiae

(2018) Rakesh Pathak et al.   GENETICS

A Cdk9–PP1 switch regulates the elongation–termination transition of RNA polymerase II

(2018) Pabitra K. Parua et al.   NATURE

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

(2018) Seychelle M. Vos et al.   NATURE

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Spt6 Is Required for the Fidelity of Promoter Selection

(2018) Stephen M. Doris et al.   MOLECULAR CELL

Structure of transcribing RNA polymerase II-nucleosome complex

(2018) Lucas Farnung et al.   Nature Communications

Casein Kinase II Phosphorylation of Spt6 Enforces Transcriptional Fidelity by Maintaining Spn1-Spt6 Interaction

(2018) Raghuvar Dronamraju et al.   Cell Reports

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

(2017) Margarita Schlackow et al.   MOLECULAR CELL

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes

(2017) Nicole Uwimana et al.   NUCLEIC ACIDS RESEARCH

Histone Marks in the ‘Driver’s Seat’: Functional Roles in Steering the Transcription Cycle

(2017) Leah A. Gates et al.   TRENDS IN BIOCHEMICAL SCIENCES

A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription

(2017) Matthew A Sdano et al.   eLife

Histone chaperones FACT and Spt6 prevent histone variants from turning into histone deviants

(2016) Célia Jeronimo et al.   BIOESSAYS

Integrated genome browser: visual analytics platform for genomics

(2016) Nowlan H. Freese et al.   BIOINFORMATICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Regulation of chaperone binding and nucleosome dynamics by key residues within the globular domain of histone H3

(2016) Sarah J. Hainer et al.   Epigenetics & Chromatin

The Biogenesis of Nascent Circular RNAs

(2016) Yang Zhang et al.   Cell Reports

Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors

(2016) Toyoaki Natsume et al.   Cell Reports

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

(2016) Julio C. Morales et al.   PLoS Genetics

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

(2015) Takayuki Nojima et al.   CELL

The Abundant Histone Chaperones Spt6 and FACT Collaborate to Assemble, Inspect, and Maintain Chromatin Structure in Saccharomyces cerevisiae

(2015) L. McCullough et al.   GENETICS

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

(2015) Nova Fong et al.   MOLECULAR CELL

The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations

(2015) Célia Jeronimo et al.   MOLECULAR CELL

Widespread Inducible Transcription Downstream of Human Genes

(2015) Anna Vilborg et al.   MOLECULAR CELL

Histone exchange, chromatin structure and the regulation of transcription

(2015) Swaminathan Venkatesh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Chromatin-remodeling and the initiation of transcription

(2015) Yahli Lorch et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Widespread disruption of host transcription termination in HSV-1 infection

(2015) Andrzej J. Rutkowski et al.   Nature Communications

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles

(2014) Susanne Walz et al.   NATURE

Transcribing through the nucleosome

(2014) Sheila S. Teves et al.   TRENDS IN BIOCHEMICAL SCIENCES

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

(2014) Gilad Fuchs et al.   GENOME BIOLOGY

Gene promoters dictate histone occupancy within genes

(2013) Roberto Perales et al.   EMBO JOURNAL

Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast

(2013) C. M. DeGennaro et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Spt6 prevents transcription-coupled loss of posttranslationally modified histone H3

(2013) Hiroaki Kato et al.   Scientific Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

Crystal Structures of the S. cerevisiae Spt6 Core and C-Terminal Tandem SH2 Domain

(2011) Devin Close et al.   JOURNAL OF MOLECULAR BIOLOGY

Control of Chromatin Structure by Spt6: Different Consequences in Coding and Regulatory Regions

(2010) I. Ivanovska et al.   MOLECULAR AND CELLULAR BIOLOGY

Spt6 enhances the elongation rate of RNA polymerase II in vivo

(2009) M Behfar Ardehali et al.   EMBO JOURNAL

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Crystal Structure and RNA Binding of the Tex Protein from Pseudomonas aeruginosa

(2008) Sean J. Johnson et al.   JOURNAL OF MOLECULAR BIOLOGY

Roles for Ctk1 and Spt6 in Regulating the Different Methylation States of Histone H3 Lysine 36

(2008) M. L. Youdell et al.   MOLECULAR AND CELLULAR BIOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

A RECQ5-RNA polymerase II association identified by targeted proteomic analysis of human chromatin

(2008) O. Aygun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY