DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

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

(2012) Dev M. Bhatt et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

Transcription factories: genetic programming in three dimensions

(2012) Lucas Brandon Edelman et al.   CURRENT OPINION IN GENETICS & 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

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion

(2012) Thierry Cheutin et al.   PLoS Genetics

Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing

(2012) Madapura M. Pradeepa et al.   PLoS Genetics

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs

(2011) Liuqing Yang et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

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

(2011) Sanjeev Shukla et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

The proteomes of transcription factories containing RNA polymerases I, II or III

(2011) Svitlana Melnik et al.   NATURE METHODS

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

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

Transcription factories in the context of the nuclear and genome organization

(2011) S. V. Razin et al.   NUCLEIC ACIDS RESEARCH

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

Pause locally, splice globally

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

Biogenesis and function of nuclear bodies

(2011) Yuntao S. Mao et al.   TRENDS IN GENETICS

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

(2010) Satu Nahkuri et al.   CELL CYCLE

The transcriptional interactome: gene expression in 3D

(2010) Stefan Schoenfelder et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing

(2010) Schraga Schwartz et al.   EMBO JOURNAL

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

(2010) M. T. Kassouf et al.   GENOME RESEARCH

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

Does CTCF mediate between nuclear organization and gene expression?

(2009) Rolf Ohlsson et al.   BIOESSAYS

Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex

(2009) Sue Mei Tan-Wong et al.   GENES & DEVELOPMENT

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Differential chromatin marking of introns and expressed exons by H3K36me3

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

Nucleosome positioning as a determinant of exon recognition

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

Splicing, transcription, and chromatin: a ménage à trois

(2008) Eric Allemand et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Promoter-driven splicing regulation in fission yeast

(2008) Alberto Moldón et al.   NATURE

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

(2008) Qun Pan et al.   NATURE GENETICS

Dynamic interactions between the promoter and terminator regions of the mammalianBRCA1gene

(2008) Sue Mei Tan-Wong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA