Transcription-driven chromatin repression of Intragenic transcription start sites

Intragenic transcriptional interference regulates the human immune ligand MICA

(2018) Da Lin et al.   EMBO JOURNAL

FACT complex is required for DNA demethylation at heterochromatin during reproduction inArabidopsis

(2018) Jennifer M. Frost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient termination of nuclear lncRNA transcription promotes mitochondrial genome maintenance

(2018) Dorine Jeanne Mariëtte du Mee et al.   eLife

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

(2018) Peter Kindgren et al.   Nature Communications

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

(2017) Tom Smith et al.   GENOME RESEARCH

Determinants of Histone H3K4 Methylation Patterns

(2017) Luis M. Soares et al.   MOLECULAR CELL

H2A.Z Represses Gene Expression by Modulating Promoter Nucleosome Structure and Enhancer Histone Modifications in Arabidopsis

(2017) Xiaozhuan Dai et al.   Molecular Plant

Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis

(2017) Sandra Cortijo et al.   Molecular Plant

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

Is H3K4me1 at enhancers correlative or causative?

(2017) Alvaro Rada-Iglesias   NATURE GENETICS

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

(2017) Wojciech Antosz et al.   PLANT CELL

Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags

(2017) Mutsutomo Tokizawa et al.   PLANT JOURNAL

Integrated molecular mechanism directing nucleosome reorganization by human FACT

(2016) Yasuo Tsunaka et al.   GENES & DEVELOPMENT

Genome-wide analysis of chromatin packing inArabidopsis thalianaat single-gene resolution

(2016) Chang Liu et al.   GENOME RESEARCH

Noncoding Transcription Is a Driving Force for Nucleosome Instability inspt16Mutant Cells

(2016) Jianxun Feng et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome-wide quantification of 5′-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics

(2016) Vicent Pelechano et al.   Nature Protocols

Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference

(2016) Ryan Ard et al.   NUCLEIC ACIDS RESEARCH

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

The Interleaved Genome

(2016) Jane Mellor et al.   TRENDS IN GENETICS

EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling

(2016) Fan Zhang et al.   Nature Communications

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates

(2015) Allen Wang et al.   Cell Stem Cell

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

(2015) Célia Jeronimo et al.   MOLECULAR CELL

Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

(2015) Thomas Wiesner et al.   NATURE

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone exchange, chromatin structure and the regulation of transcription

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

Histone H2A/H2B chaperones: from molecules to chromatin-based functions in plant growth and development

(2015) Wangbin Zhou et al.   PLANT JOURNAL

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

(2014) Ramesh Yelagandula et al.   CELL

Functional Consequences of Splicing of the Antisense Transcript COOLAIR on FLC Transcription

(2014) Sebastian Marquardt et al.   MOLECULAR CELL

Transcript elongation factors: shaping transcriptomes after transcript initiation

(2014) Mieke Van Lijsebettens et al.   TRENDS IN PLANT SCIENCE

Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells

(2014) Nicolas Descostes et al.   eLife

Proteasome-Mediated Processing of Def1, a Critical Step in the Cellular Response to Transcription Stress

(2013) Marcus D. Wilson et al.   CELL

Chromatin Remodeling at DNA Double-Strand Breaks

(2013) Brendan D. Price et al.   CELL

RNA Polymerase II C-Terminal Domain: Tethering Transcription to Transcript and Template

(2013) Jeffry L. Corden   CHEMICAL REVIEWS

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Structural basis of histone H2A–H2B recognition by the essential chaperone FACT

(2013) Maria Hondele et al.   NATURE

Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription

(2013) Sílvia Carvalho et al.   NUCLEIC ACIDS RESEARCH

Regulation of plant translation by upstream open reading frames

(2013) Albrecht G. von Arnim et al.   PLANT SCIENCE

Emerging roles for RNA polymerase II CTD in Arabidopsis

(2013) Mohsen Hajheidari et al.   TRENDS IN PLANT SCIENCE

Facilitates Chromatin Transcription Complex Is an “Accelerator” of Tumor Transformation and Potential Marker and Target of Aggressive Cancers

(2013) Henry Garcia et al.   Cell Reports

A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription

(2013) Harm van Bakel et al.   PLoS Genetics

Catch me if you can

(2013) Maria Hondele et al.   Nucleus

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes

(2012) Swaminathan Venkatesh et al.   NATURE

Site-specific DICER and DROSHA RNA products control the DNA-damage response

(2012) Sofia Francia et al.   NATURE

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production

(2012) Chongyuan Luo et al.   PLANT JOURNAL

A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis

(2012) J. Lloyd et al.   PLANT PHYSIOLOGY

Identification of Mutant Versions of the Spt16 Histone Chaperone That Are Defective for Transcription-Coupled Nucleosome Occupancy in Saccharomyces cerevisiae

(2012) Sarah J. Hainer et al.   G3-Genes Genomes Genetics

HMG Domain Containing SSRP1 Is Required for DNA Demethylation and Genomic Imprinting in Arabidopsis

(2011) Yoko Ikeda et al.   DEVELOPMENTAL CELL

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Histone Chaperone FACT Coordinates Nucleosome Interaction through Multiple Synergistic Binding Events

(2011) Duane D. Winkler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

(2011) Marta Radman-Livaja et al.   PLOS BIOLOGY

Perspectives on the RNA polymerase II core promoter

(2011) James T. Kadonaga   Wiley Interdisciplinary Reviews-Developmental Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Dynamic Changes in Genome-Wide Histone H3 Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana

(2010) Karin van Dijk et al.   BMC PLANT BIOLOGY

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Uniform transitions of the general RNA polymerase II transcription complex

(2010) Andreas Mayer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Histone Chaperone Spt16 Promotes Redeposition of the Original H3-H4 Histones Evicted by Elongating RNA Polymerase

(2009) Adil Jamai et al.   MOLECULAR CELL

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

Silencing of a plant gene by transcriptional interference

(2009) B. Hedtke et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

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

The transcript elongation factor FACT affects Arabidopsis vegetative and reproductive development and genetically interacts with HUB1/2

(2009) Ihab B. Lolas et al.   PLANT JOURNAL

The ASH1 HOMOLOG 2 (ASHH2) Histone H3 Methyltransferase Is Required for Ovule and Anther Development in Arabidopsis

(2009) Paul E. Grini et al.   PLoS One

The FACT Spt16 “peptidase” domain is a histone H3–H4 binding module

(2008) Tobias Stuwe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The functional consequences of alternative promoter use in mammalian genomes

(2008) Ramana V. Davuluri et al.   TRENDS IN GENETICS

Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome

(2008) Vanessa Cheung et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY