Natural antisense transcripts are significantly involved in regulation of drought stress in maize

Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

(2015) C. Yuan et al.   DNA RESEARCH

The landscape of antisense gene expression in human cancers

(2015) O. Alejandro Balbin et al.   GENOME RESEARCH

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Sense and antisense transcription are associated with distinct chromatin architectures across genes

(2015) Struan C. Murray et al.   NUCLEIC ACIDS RESEARCH

Identification of protein coding regions in RNA transcripts

(2015) Shiyuyun Tang et al.   NUCLEIC ACIDS RESEARCH

Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress

(2015) Lei Lei et al.   PLANT JOURNAL

Overexpression of ARGOS Genes Modifies Plant Sensitivity to Ethylene, Leading to Improved Drought Tolerance in Both Arabidopsis and Maize

(2015) Jinrui Shi et al.   PLANT PHYSIOLOGY

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

(2014) Jie Xu et al.   BMC PLANT BIOLOGY

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

(2014) H. Wang et al.   GENOME RESEARCH

Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs

(2014) X Zhang et al.   HEREDITY

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Genome-wide identification of housekeeping genes in maize

(2014) Feng Lin et al.   PLANT MOLECULAR BIOLOGY

Identification of Maize Long Non-Coding RNAs Responsive to Drought Stress

(2014) Wei Zhang et al.   PLoS One

Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation

(2014) P. Jermann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Wide Association Studies Using a New Nonparametric Model Reveal the Genetic Architecture of 17 Agronomic Traits in an Enlarged Maize Association Panel

(2014) Ning Yang et al.   PLoS Genetics

Genome-Wide Analysis of leafbladeless1-Regulated and Phased Small RNAs Underscores the Importance of the TAS3 ta-siRNA Pathway to Maize Development

(2014) Marcela C. Dotto et al.   PLoS Genetics

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Biological functions of natural antisense transcripts

(2013) Andreas Werner   BMC BIOLOGY

Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

(2013) Xiang Yu et al.   BMC PLANT BIOLOGY

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

(2013) Shannon M. Lauberth et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

(2013) S. Li et al.   GENOME RESEARCH

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

Identification and annotation of small RNA genes using ShortStack

(2013) Saima Shahid et al.   METHODS

Mechanisms of Small RNA Generation from Cis-NATs in Response to Environmental and Developmental Cues

(2013) Xiaoming Zhang et al.   Molecular Plant

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness

(2013) M. Jabnoune et al.   PLANT CELL

Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

(2013) I. Makarevitch et al.   PLANT CELL

Epigenetic mechanisms of plant stress responses and adaptation

(2013) Pranav Pankaj Sahu et al.   PLANT CELL REPORTS

Genome-Wide Analysis of ZmDREB Genes and Their Association with Natural Variation in Drought Tolerance at Seedling Stage of Zea mays L

(2013) Shengxue Liu et al.   PLoS Genetics

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

(2012) Tingting Lu et al.   BMC GENOMICS

Chromatin modification and remodelling: a regulatory landscape for the control of Arabidopsis defence responses upon pathogen attack

(2012) Alexandre Berr et al.   CELLULAR MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Cis-acting noncoding RNAs: friends and foes

(2012) Sònia Guil et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Stress-Induced Chromatin Changes: A Critical View on Their Heritability

(2012) A. Pecinka et al.   PLANT AND CELL PHYSIOLOGY

Identification of sense and antisense transcripts regulated by drought in sugarcane

(2012) Carolina Gimiliani Lembke et al.   PLANT MOLECULAR BIOLOGY

Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq

(2012) A. Kakumanu et al.   PLANT PHYSIOLOGY

Flowering time control: another window to the connection between antisense RNA and chromatin

(2012) Robert Ietswaart et al.   TRENDS IN GENETICS

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

(2012) Xiaoming Zhang et al.   GENOME BIOLOGY

Dual RNAs in plants

(2011) Florian Bardou et al.   BIOCHIMIE

Dual-function RNA regulators in bacteria

(2011) Carin K. Vanderpool et al.   BIOCHIMIE

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Large-scale screening for maize drought resistance using multiple selection criteria evaluated under water-stressed and well-watered environments

(2011) Yanli Lu et al.   FIELD CROPS RESEARCH

Miniature Inverted-Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa

(2011) C. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Dynamics of phytohormone and DNA methylation patterns changes during dormancy induction in strawberry (Fragaria × ananassa Duch.)

(2011) Li Zhang et al.   PLANT CELL REPORTS

The panorama of physiological responses and gene expression of whole plant of maize inbred line YQ7-96 at the three-leaf stage under water deficit and re-watering

(2011) Hai-Feng Lu et al.   THEORETICAL AND APPLIED GENETICS

Dynamic Regulation of H3K27 Trimethylation during Arabidopsis Differentiation

(2011) Marcel Lafos et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize

(2010) Y. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

(2010) Moran Yassour et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

(2009) Tristan E Coram et al.   BMC GENOMICS

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

(2009) Szymon Swiezewski et al.   NATURE

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

(2009) X. Wang et al.   PLANT CELL

Targeted 3' Processing of Antisense Transcripts Triggers Arabidopsis FLC Chromatin Silencing

(2009) F. Liu et al.   SCIENCE

Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis

(2009) Qing-Jun Luo et al.   PLoS Genetics

Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis

(2008) Hailing Jin et al.   BMC MOLECULAR BIOLOGY

Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley

(2008) M. A. Held et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Leighton J. Core et al.   SCIENCE

Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus

(2008) Anders M. Lindroth et al.   PLoS Genetics