Chromatin, DNA structure and alternative splicing

Modifications of RNA polymerase II CTD: Connections to the histone code and cellular function

(2015) Rakesh Srivastava et al.   BIOTECHNOLOGY ADVANCES

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

(2015) Takayuki Nojima et al.   CELL

A Distinct Triplex DNA Unwinding Activity of ChlR1 Helicase

(2015) Manhong Guo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Getting up to speed with transcription elongation by RNA polymerase II

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

Transcription blockage by stable H-DNA analogs in vitro

(2015) Shristi Pandey et al.   NUCLEIC ACIDS RESEARCH

A positioned +1 nucleosome enhances promoter-proximal pausing

(2015) Silvia Jimeno-González et al.   NUCLEIC ACIDS RESEARCH

Pack, unpack, bend, twist, pull, push: the physical side of gene expression

(2014) Christophe Lavelle   CURRENT OPINION IN GENETICS & DEVELOPMENT

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

(2014) Manju Bansal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability

(2014) Stephan Hamperl et al.   DNA REPAIR

FANCJ promotes DNA synthesis through G-quadruplex structures

(2014) P. Castillo Bosch et al.   EMBO JOURNAL

Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells

(2014) D. Schiavone et al.   EMBO JOURNAL

G-quadruplex formation enhances splicing efficiency of PAX9 intron 1

(2014) Mariana Martins Ribeiro et al.   HUMAN GENETICS

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD

(2014) Lucas T Gray et al.   Nature Chemical Biology

Histone core modifications regulating nucleosome structure and dynamics

(2014) Peter Tessarz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification and characterization of RNA guanine-quadruplex binding proteins

(2014) Annekathrin von Hacht et al.   NUCLEIC ACIDS RESEARCH

New concepts in DNA methylation

(2014) Albert Jeltsch et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2014) Iris Jonkers et al.   eLife

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability

(2013) Boris P. Belotserkovskii et al.   CHEMICAL REVIEWS

Alternative splicing: a pivotal step between eukaryotic transcription and translation

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

Associations between intronic non-B DNA structures and exon skipping

(2013) Z. T.-Y. Tsai et al.   NUCLEIC ACIDS RESEARCH

Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss

(2013) Maxim Y. Sheinin et al.   Nature Communications

RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription

(2012) Martin Heidemann et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

(2012) Lacramioara Bintu et al.   CELL

The RNA polymerase II CTD coordinates transcription and RNA processing

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

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer

(2012) Laura D Nelson et al.   Molecular Cancer

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

(2012) Pierre Close et al.   NATURE

DNA secondary structures: stability and function of G-quadruplex structures

(2012) Matthew L. Bochman et al.   NATURE REVIEWS GENETICS

Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks

(2012) Boris P. Belotserkovskii et al.   NUCLEIC ACIDS RESEARCH

Overcoming the nucleosome barrier during transcript elongation

(2012) Steven J. Petesch et al.   TRENDS IN GENETICS

Heterogeneous Nuclear Ribonucleoprotein K and Nucleolin as Transcriptional Activators of the Vascular Endothelial Growth Factor Promoter through Interaction with Secondary DNA Structures

(2011) Diana J. Uribe et al.   BIOCHEMISTRY

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila

(2011) Y. L. Khodor et al.   GENES & DEVELOPMENT

Functional characterization of the AFF (AF4/FMR2) family of RNA-binding proteins: insights into the molecular pathology of FRAXE intellectual disability

(2011) Mireille Melko et al.   HUMAN MOLECULAR GENETICS

TCERG1 Regulates Alternative Splicing of the Bcl-x Gene by Modulating the Rate of RNA Polymerase II Transcription

(2011) M. Montes et al.   MOLECULAR AND CELLULAR BIOLOGY

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

DNA secondary structures and epigenetic determinants of cancer genome evolution

(2011) Subhajyoti De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Potential in vivo roles of nucleic acid triple-helices

(2011) Fabian A. Buske et al.   RNA Biology

G-quadruplex structures in TP53 intron 3: role in alternative splicing and in production of p53 mRNA isoforms

(2010) Virginie Marcel et al.   CARCINOGENESIS

Making sense of G-quadruplex and i-motif functions in oncogene promoters

(2010) Tracy A. Brooks et al.   FEBS Journal

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

(2010) A. K. Ramani et al.   GENOME RESEARCH

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

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

First come, first served revisited: Factors affecting the same alternative splicing event have different effects on the relative rates of intron removal

(2010) M. de la Mata et al.   RNA

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

The carboxy terminal domain of RNA polymerase II and alternative splicing

(2010) Manuel J. Muñoz et al.   TRENDS IN BIOCHEMICAL SCIENCES

Spliceosome Structure and Function

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

Role of 5′- and 3′-untranslated regions of mRNAs in human diseases

(2009) Sangeeta Chatterjee et al.   BIOLOGY OF THE CELL

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

(2009) Manuel J. Muñoz et al.   CELL

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Control of alternative splicing through siRNA-mediated transcriptional gene silencing

(2009) Mariano Alló et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing

(2009) I. E. Schor 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

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

(2009) C. Hodges et al.   SCIENCE

Genome-Wide Identification of Alternative Splice Forms Down-Regulated by Nonsense-Mediated mRNA Decay in Drosophila

(2009) Kasper Daniel Hansen et al.   PLoS Genetics

Histones: Annotating Chromatin

(2008) Eric I. Campos et al.   Annual Review of Genetics