Functional characterization of open chromatin in bidirectional promoters of rice

Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription

(2015) Susanne Bornelöv et al.   BMC GENOMICS

Determinants of nucleosome positioning and their influence on plant gene expression

(2015) Ming-Jung Liu et al.   GENOME RESEARCH

Structural and functional analysis of an asymmetric bidirectional promoter inArabidopsis thaliana

(2015) Shi-Juan Liu et al.   Journal of Integrative Plant Biology

Getting up to speed with transcription elongation by RNA polymerase II

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

Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants

(2015) Tao Zhang et al.   PLANT PHYSIOLOGY

Functional Characterization of a Strong Bi-directional Constitutive Plant Promoter Isolated from Cotton Leaf Curl Burewala Virus

(2015) Zainul A. Khan et al.   PLoS One

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells

(2014) Suhn Rhie et al.   BMC GENOMICS

Identification and functional characterization of bidirectional gene pairs and their intergenic regions in maize

(2014) Xiaoqing Liu et al.   BMC GENOMICS

Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming

(2014) A. Abdelsamad et al.   PLANT CELL

Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice

(2014) Yufeng Wu et al.   PLoS Genetics

Identification of regulatory regions of bidirectional genes in cervical cancer

(2013) Guohua Wang et al.   BMC Medical Genomics

Bidirectional promoters in seed development and related hormone/stress responses

(2013) Sofia Kourmpetli et al.   BMC PLANT BIOLOGY

Major cis-regulatory elements for rice bidirectional promoter activity reside in the 5′-untranslated regions

(2013) Surendar Reddy Dhadi et al.   GENE

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Regulation of nucleosome dynamics by histone modifications

(2013) Gabriel E Zentner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An Intergenic Region Shared by At4g35985 and At4g35987 in Arabidopsis thaliana Is a Tissue Specific and Stress Inducible Bidirectional Promoter Analyzed in Transgenic Arabidopsis and Tobacco Plants

(2013) Joydeep Banerjee et al.   PLoS One

A Quantitative Analysis of the Impact on Chromatin Accessibility by Histone Modifications and Binding of Transcription Factors in DNase I Hypersensitive Sites

(2013) Peng Cui et al.   Biomed Research International

The dual lives of bidirectional promoters

(2012) Clay Wakano 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

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

High-resolution mapping of open chromatin in the rice genome

(2011) W. Zhang et al.   GENOME RESEARCH

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes

(2011) Yang Zhang et al.   Plant Methods

Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions

(2010) Wei-Hua Chen et al.   BMC GENOMICS

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Gene regulation by nucleosome positioning

(2010) Lu Bai et al.   TRENDS IN GENETICS

The Role of Nucleosome Positioning in the Evolution of Gene Regulation

(2010) Alexander M. Tsankov et al.   PLOS BIOLOGY

Relating periodicity of nucleosome organization and gene regulation

(2009) Jun Wan et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Searching for bidirectional promoters in Arabidopsis thaliana

(2009) Quan Wang et al.   BMC BIOINFORMATICS

A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes

(2009) Liang Yang et al.   BMC EVOLUTIONARY BIOLOGY

A small intergenic region drives exclusive tissue-specific expression of the adjacent genes in Arabidopsis thaliana

(2009) Hernán G Bondino et al.   BMC MOLECULAR BIOLOGY

Nucleosome positioning: How is it established, and why does it matter?

(2009) Marta Radman-Livaja et al.   DEVELOPMENTAL BIOLOGY

A novel strategy of transcription regulation by intragenic nucleosome ordering

(2009) C. Vaillant et al.   GENOME RESEARCH

c-Myc regulates the coordinated transcription of brain disease-related PDCD10–SERPINI1 bidirectional gene pair

(2009) Ping-Yen Chen et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

(2009) Yong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Genome-wide comparative analysis of putative bidirectional promoters from rice, Arabidopsis and Populus

(2008) Surendar Reddy Dhadi et al.   GENE

Comparative Analysis of Divergent and Convergent Gene Pairs and Their Expression Patterns in Rice, Arabidopsis, and Populus

(2008) N. Krom et al.   PLANT PHYSIOLOGY