Chromatin and epigenetic regulation of pre-mRNA processing

The COMPASS Family of Histone H3K4 Methylases: Mechanisms of Regulation in Development and Disease Pathogenesis

(2012) Ali Shilatifard   Annual Review of Biochemistry

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

Histone methylation: a dynamic mark in health, disease and inheritance

(2012) Eric L. Greer et al.   NATURE REVIEWS GENETICS

Vezf1 protein binding sites genome-wide are associated with pausing of elongating RNA polymerase II

(2012) H. Gowher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome positioning: bringing order to the eukaryotic genome

(2012) Vishwanath R. Iyer   TRENDS IN CELL BIOLOGY

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

The changing faces of HP1: From heterochromatin formation and gene silencing to euchromatic gene expression

(2011) So Hee Kwon et al.   BIOESSAYS

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

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

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

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

(2011) Sanjeev Shukla et al.   NATURE

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

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

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone Deacetylase Activity Modulates Alternative Splicing

(2011) Jarmila Hnilicová et al.   PLoS One

Evolution of Exon-Intron Structure and Alternative Splicing

(2011) Tomasz E. Koralewski et al.   PLoS One

Pre-mRNA splicing is a determinant of histone H3K36 methylation

(2011) S. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

(2011) Yehuda Brody et al.   PLOS BIOLOGY

Transcript Elongation by RNA Polymerase II

(2010) Luke A. Selth et al.   Annual Review of Biochemistry

Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers

(2010) Michiel Vermeulen et al.   CELL

The Dnmt3a PWWP Domain Reads Histone 3 Lysine 36 Trimethylation and Guides DNA Methylation

(2010) Arunkumar Dhayalan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Novel Mammalian Complex Containing Sin3B Mitigates Histone Acetylation and RNA Polymerase II Progression within Transcribed Loci

(2010) P. Jelinic et al.   MOLECULAR AND CELLULAR BIOLOGY

Exon Definition Complexes Contain the Tri-snRNP and Can Be Directly Converted into B-like Precatalytic Splicing Complexes

(2010) Marc Schneider et al.   MOLECULAR CELL

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

(2010) Fernando Carrillo Oesterreich et al.   MOLECULAR CELL

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Reciprocal intronic and exonic histone modification regions in humans

(2010) Jason T Huff et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution

(2010) Pawandeep Dhami et al.   PLoS One

Sequence dependence of DNA bending rigidity

(2010) S. Geggier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the DOT1L Network: Implications of Diverse Roles for DOT1L

(2010) Geunyeong Park et al.   PROTEIN JOURNAL

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Contrasting chromatin organization of CpG islands and exons in the human genome

(2010) Jung Kyoon Choi   GENOME BIOLOGY

G+C content dominates intrinsic nucleosome occupancy

(2009) Desiree Tillo et al.   BMC BIOINFORMATICS

Patterns of exon-intron architecture variation of genes in eukaryotic genomes

(2009) Liucun Zhu et al.   BMC GENOMICS

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Heterogeneous Nuclear Ribonucleoprotein L Is a Subunit of Human KMT3a/Set2 Complex Required for H3 Lys-36 Trimethylation Activityin Vivo

(2009) Wen Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ESRP1 and ESRP2 Are Epithelial Cell-Type-Specific Regulators of FGFR2 Splicing

(2009) Claude C. Warzecha et al.   MOLECULAR CELL

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

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

The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes

(2009) Amir B. Cohanim et al.   NUCLEIC ACIDS RESEARCH

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

Epigenetics: molecular mechanisms and implications for disease

(2009) Adam E. Handel et al.   TRENDS IN MOLECULAR MEDICINE

Discovery and Annotation of Functional Chromatin Signatures in the Human Genome

(2009) Gary Hon et al.   PLoS Computational Biology

The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation

(2008) S. M. Yoh et al.   GENES & DEVELOPMENT

Histone Ubiquitination: Triggering Gene Activity

(2008) Vikki M. Weake et al.   MOLECULAR CELL

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome

(2008) Shalini Sharma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

(2008) Z. Wang et al.   RNA

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology