Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations

(2016) Florian Mattenberger et al.   G3-Genes Genomes Genetics

Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana

(2015) Mala Singh et al.   BMC PLANT BIOLOGY

Genome-Wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families

(2015) Amanda R. De La Torre et al.   Genome Biology and Evolution

Determinants of nucleosome positioning and their influence on plant gene expression

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

Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites

(2015) María Katherine Mejía-Guerra et al.   PLANT CELL

Dissecting the contributions of GC content and codon usage to gene expression in the model algaChlamydomonas reinhardtii

(2015) Rouhollah Barahimipour et al.   PLANT JOURNAL

Functional Analysis of the Molecular Interactions of TATA Box-Containing Genes and Essential Genes

(2015) Sang-Hun Bae et al.   PLoS One

A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

(2014) Nadia Shakoor et al.   BMC PLANT BIOLOGY

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

(2014) Manju Bansal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Drosophiladuplicate genes evolve new functions on the fly

(2014) Raquel Assis   FLY

Gene length and expression level shape genomic novelties

(2014) Vladislav Grishkevich et al.   GENOME RESEARCH

PLAZA 3.0: an access point for plant comparative genomics

(2014) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

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

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

(2014) Guang Li et al.   PLANT JOURNAL

Sequence, Structural and Expression Divergence of Duplicate Genes in the Bovine Genome

(2014) Xiaoping Liao et al.   PLoS One

Genome-Wide Tissue-Specific Gene Expression, Co-expression and Regulation of Co-expressed Genes in Adult Nematode Ascaris suum

(2014) Bruce A. Rosa et al.   PLoS Neglected Tropical Diseases

Different patterns of gene structure divergence following gene duplication in Arabidopsis

(2013) Yupeng Wang et al.   BMC GENOMICS

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

(2013) S. Lianoglou et al.   GENES & DEVELOPMENT

Gene duplication as a major force in evolution

(2013) SANTOSHKUMAR MAGADUM et al.   JOURNAL OF GENETICS

The structural properties of DNA regulate gene expression

(2013) Sattar Soltani et al.   Molecular BioSystems

Determinants of nucleosome positioning

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

The immediate upstream region of the 5′-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana

(2013) Younghyun Kim et al.   NUCLEIC ACIDS RESEARCH

Identification and validation of promoters and cis-acting regulatory elements

(2013) Carlos M. Hernandez-Garcia et al.   PLANT SCIENCE

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast

(2013) S. Dvir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers

(2013) Leila Taher et al.   GENOME BIOLOGY

DNA STRUCTURAL FEATURES AND ARCHITECTURE OF PROMOTER REGIONS PLAY A ROLE IN GENE RESPONSIVENESS OF S. cerevisiae

(2013) VENKATA RAJESH YELLA et al.   Journal of Bioinformatics and Computational Biology

Genome and gene duplications and gene expression divergence: a view from plants

(2012) Yupeng Wang et al.   Annals of the New York Academy of Sciences

Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators

(2012) D. J. Huebert et al.   MOLECULAR AND CELLULAR BIOLOGY

Gene family evolution in green plants with emphasis on the origination and evolution ofArabidopsis thalianagenes

(2012) Ya-Long Guo   PLANT JOURNAL

Divergence of duplicate genes in exon-intron structure

(2012) G. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CCAAT-box binding transcription factors in plants: Y so many?

(2012) Tom Laloum et al.   TRENDS IN PLANT SCIENCE

Genome-wide functional analysis of human 5' untranslated region introns

(2012) Can Cenik et al.   GENOME BIOLOGY

The Function of Introns

(2012) Michal Chorev et al.   Frontiers in Genetics

A perspective of promoter architecture from the CCAAT box

(2011) Diletta Dolfini et al.   CELL CYCLE

Gene expression patterns are correlated with genomic and genic structure in soybean

(2011) Jenna L. Woody et al.   GENOME

What are the determinants of gene expression levels and breadths in the human genome?

(2011) Jungsun Park et al.   HUMAN MOLECULAR GENETICS

Evolution of 5' Untranslated Region Length and Gene Expression Reprogramming in Yeasts

(2011) Z. Lin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple Sequence-Specific Factors Generate the Nucleosome-Depleted Region on CLN2 Promoter

(2011) Lu Bai et al.   MOLECULAR CELL

Genome-wide atlas of transcription during maize development

(2011) Rajandeep S. Sekhon et al.   PLANT JOURNAL

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

(2011) C. Morey et al.   PLANT PHYSIOLOGY

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

(2011) Yupeng Wang et al.   PLoS One

GC3 biology in corn, rice, sorghum and other grasses

(2010) Tatiana V Tatarinova et al.   BMC GENOMICS

TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation

(2010) Virginie Bernard et al.   BMC GENOMICS

Nucleosome-Depleted Regions in Cell-Cycle-Regulated Promoters Ensure Reliable Gene Expression in Every Cell Cycle

(2010) Lu Bai et al.   DEVELOPMENTAL CELL

Connections between Alternative Transcription and Alternative Splicing in Mammals

(2010) Svetlana A. Shabalina et al.   Genome Biology and Evolution

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome

(2010) Loren Hansen et al.   NUCLEIC ACIDS RESEARCH

Where's Waldo? Visualizing Collinearity Diagnostics

(2009) Michael Friendly et al.   AMERICAN STATISTICIAN

In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure

(2009) Hangxing Yang   Biology Direct

Expression pattern divergence of duplicated genes in rice

(2009) Zhe Li et al.   BMC BIOINFORMATICS

Genome-wide analysis of rice (Oryza sativa L. subsp. japonica) TATA box and Y Patch promoter elements

(2009) P. Civáň et al.   GENOME

A Universal Nonmonotonic Relationship between Gene Compactness and Expression Levels in Multicellular Eukaryotes

(2009) Liran Carmel et al.   Genome Biology and Evolution

Intrinsic variability of gene expression encoded in nucleosome positioning sequences

(2009) Jung Kyoon Choi et al.   NATURE GENETICS

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

A dynamic gene expression atlas covering the entire life cycle of rice

(2009) Lei Wang et al.   PLANT JOURNAL

Mutational Biases and Selective Forces Shaping the Structure of Arabidopsis Genes

(2009) Salvatore Camiolo et al.   PLoS One

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

(2009) H. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple sequence-directed possibilities provide a pool of nucleosome position choices in different states of activity of a gene

(2009) Vinesh Vinayachandran et al.   Epigenetics & Chromatin

Intron and exon length variation in Arabidopsis, rice, nematode, and human

(2008) Sh. A. Atambayeva et al.   MOLECULAR BIOLOGY

Width of Gene Expression Profile Drives Alternative Splicing

(2008) Daniel Wegmann et al.   PLoS One

Generic eukaryotic core promoter prediction using structural features of DNA

(2007) T. Abeel et al.   GENOME RESEARCH