Histone modifications facilitate the coexpression of bidirectional promoters in rice

Functional characterization of open chromatin in bidirectional promoters of rice

(2016) Yuan Fang et al.   Scientific Reports

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

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

(2015) Li Lu et al.   Epigenetics

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

Human Promoters Are Intrinsically Directional

(2015) Sascha H.C. Duttke et al.   MOLECULAR CELL

SIFGD: Setaria italica Functional Genomics Database

(2015) Qi You et al.   Molecular Plant

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

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

(2014) Xiaoqing Liu et al.   BMC GENOMICS

SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways

(2014) Juan Yu et al.   BMC GENOMICS

Differential Nuclease Sensitivity Profiling of Chromatin Reveals Biochemical Footprints Coupled to Gene Expression and Functional DNA Elements in Maize

(2014) D. L. Vera et al.   PLANT CELL

A key general stress response motif is regulated non-uniformly by CAMTA transcription factors

(2014) Geoffrey Benn et al.   PLANT JOURNAL

ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis

(2014) Guang Li et al.   PLANT JOURNAL

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

(2014) Yufeng Wu et al.   PLoS Genetics

Divergent transcription is associated with promoters of transcriptional regulators

(2013) Cyrille Lepoivre et al.   BMC GENOMICS

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

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-Wide Prediction of Nucleosome Occupancy in Maize Reveals Plant Chromatin Structural Features at Genes and Other Elements at Multiple Scales

(2013) J. A. Fincher et al.   PLANT PHYSIOLOGY

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

The dual lives of bidirectional promoters

(2012) Clay Wakano et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Expression analysis in response to drought stress in soybean: shedding light on the regulation of metabolic pathway genes

(2012) Fábia Guimarães-Dias et al.   GENETICS AND MOLECULAR BIOLOGY

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

(2012) W. Zhang et al.   PLANT CELL

High-resolution mapping of open chromatin in the rice genome

(2011) W. Zhang et al.   GENOME RESEARCH

Coordinated histone modifications are associated with gene expression variation within and between species

(2011) M. Ha et al.   GENOME RESEARCH

Arabidopsis HsfB1 and HsfB2b Act as Repressors of the Expression of Heat-Inducible Hsfs But Positively Regulate the Acquired Thermotolerance

(2011) M. Ikeda et al.   PLANT PHYSIOLOGY

Functional consequences of bidirectional promoters

(2011) Wu Wei et al.   TRENDS IN GENETICS

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

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

Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in Saccharomyces cerevisiae

(2010) Yangyang Deng et al.   BMC GENOMICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

(2009) Liang Yang et al.   BMC EVOLUTIONARY BIOLOGY

Positive correlation between gene coexpression and positional clustering in the zebrafish genome

(2009) Yen Kaow Ng et al.   BMC GENOMICS

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

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

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

Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells

(2008) Neri Minsky et al.   NATURE CELL BIOLOGY

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

(2008) N. Krom et al.   PLANT PHYSIOLOGY

Genome-Wide Expression Profiling Arabidopsis at the Stage of Golovinomyces cichoracearum Haustorium Formation

(2008) G. Fabro et al.   PLANT PHYSIOLOGY

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE