Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize

Maize Genic Male-Sterility Genes and Their Applications in Hybrid Breeding: Progress and Perspectives

(2019) Xiangyuan Wan et al.   Molecular Plant

ZmMs30 Encoding a Novel GDSL Lipase Is Essential for Male Fertility and Valuable for Hybrid Breeding in Maize

(2019) Xueli An et al.   Molecular Plant

Map-Based Cloning, Phylogenetic, and Microsynteny Analyses of ZmMs20 Gene Regulating Male Fertility in Maize

(2019) Yanbo Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genome-wide analysis of maize GPAT gene family and cytological characterization and breeding application of ZmMs33/ZmGPAT6 gene

(2019) Taotao Zhu et al.   THEORETICAL AND APPLIED GENETICS

Transcriptome analysis reveals new microRNAs-mediated pathway involved in anther development in male sterile wheat

(2018) Longqing Sun et al.   BMC GENOMICS

Long-term evolutionary DNA methylation dynamic of protein-coding genes and its underlying mechanism

(2018) Ziwen Li et al.   GENE

Map-based cloning and characterization of Zea mays male sterility33 (ZmMs33) gene, encoding a glycerol-3-phosphate acyltransferase

(2018) Ke Xie et al.   THEORETICAL AND APPLIED GENETICS

Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing

(2018) Jin Chen et al.   BMC PLANT BIOLOGY

Pseudogenes provide evolutionary evidence for the competitive endogenous RNA hypothesis

(2018) Cian Glenfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments

(2018) Peng Wang et al.   NUCLEIC ACIDS RESEARCH

A potential role of extended simple sequence repeats in competing endogenous RNA crosstalk

(2018) Tomasz M. Witkos et al.   RNA Biology

Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana

(2017) Johan Reimegård et al.   NUCLEIC ACIDS RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Construction of a multicontrol sterility system for a maize male-sterile line and hybrid seed production based on the ZmMs7 gene encoding a PHD-finger transcription factor

(2017) Danfeng Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Lnc-mg is a long non-coding RNA that promotes myogenesis

(2017) Mu Zhu et al.   Nature Communications

Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA mediated miRNA evasion

(2017) Yong-xi Song et al.   Nature Communications

Regulation of rice root development by a retrotransposon acting as a microRNA sponge

(2017) Jungnam Cho et al.   eLife

Uncovering Male Fertility Transition Responsive miRNA in a Wheat Photo-Thermosensitive Genic Male Sterile Line by Deep Sequencing and Degradome Analysis

(2017) Jian-Fang Bai et al.   Frontiers in Plant Science

MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize

(2016) Guo-Ling Nan et al.   DEVELOPMENT

On the Origin of De Novo Genes inArabidopsis thalianaPopulations

(2016) Zi-Wen Li et al.   Genome Biology and Evolution

Endogenous microRNA sponges: evidence and controversy

(2016) Daniel W. Thomson et al.   NATURE REVIEWS GENETICS

PceRBase: a database of plant competing endogenous RNA

(2016) Chunhui Yuan et al.   NUCLEIC ACIDS RESEARCH

A Rice Ca 2+ Binding Protein Is Required for Tapetum Function and Pollen Formation

(2016) Jing Yu et al.   PLANT PHYSIOLOGY

Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs

(2016) Qiupeng Zheng et al.   Nature Communications

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development

(2016) Scott C. Stelpflug et al.   Plant Genome

Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development

(2016) Niraj Khemka et al.   Scientific Reports

Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics

(2015) Yi Zhao et al.   BMC EVOLUTIONARY BIOLOGY

Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize

(2015) Chunyan Fan et al.   BMC GENOMICS

Anther and pollen development: A conserved developmental pathway

(2015) José Fernández Gómez et al.   Journal of Integrative Plant Biology

To Bloom or Not to Bloom: Role of MicroRNAs in Plant Flowering

(2015) Sachin Teotia et al.   Molecular Plant

SomamiR 2.0: a database of cancer somatic mutations altering microRNA–ceRNA interactions

(2015) Anindya Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits

(2015) Huan Wang et al.   PLANT JOURNAL

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

(2015) Jixian Zhai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction

(2014) Prashant K Srivastava et al.   BMC GENOMICS

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay

(2014) Q. Liu et al.   PLANT CELL

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

(2014) Wei Zhang et al.   PLoS One

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

(2014) Ricardo A. Chávez Montes et al.   Nature Communications

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

(2014) Lin Li et al.   GENOME BIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Evolutionary conservation of microRNA regulatory programs in plant flower development

(2013) Yan Luo et al.   DEVELOPMENTAL BIOLOGY

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

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Complementarity to an miRNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green algaChlamydomonas reinhardtii

(2013) Tomohito Yamasaki et al.   PLANT JOURNAL

AUXIN RESPONSE FACTOR17 Is Essential for Pollen Wall Pattern Formation in Arabidopsis

(2013) J. Yang et al.   PLANT PHYSIOLOGY

PsRobot: a web-based plant small RNA meta-analysis toolbox

(2012) Hua-Jun Wu et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

(2012) Susan Boerner et al.   PLoS One

Genetic Regulation of Sporopollenin Synthesis and Pollen Exine Development

(2011) Tohru Ariizumi et al.   Annual Review of Plant Biology

Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase I

(2011) Guo-Ling Nan et al.   BMC PLANT BIOLOGY

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

PERSISTENT TAPETAL CELL1 Encodes a PHD-Finger Protein That Is Required for Tapetal Cell Death and Pollen Development in Rice

(2011) H. Li et al.   PLANT PHYSIOLOGY

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics

(2010) Eric Bonnet et al.   BIOINFORMATICS

Signaling and Transcriptional Control of Reproductive Development in Arabidopsis

(2010) Xiaochun Ge et al.   CURRENT BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno 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

miR156-Targeted and Nontargeted SBP-Box Transcription Factors Act in Concert to Secure Male Fertility inArabidopsis

(2010) Shuping Xing et al.   PLANT CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa)

(2009) Qian-Hao Zhu et al.   BMC PLANT BIOLOGY

miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana

(2009) Jia-Wei Wang et al.   CELL

The Sequential Action of miR156 and miR172 Regulates Developmental Timing in Arabidopsis

(2009) Gang Wu et al.   CELL

miR319a targeting ofTCP4is critical for petal growth and development inArabidopsis

(2009) Anwesha Nag et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Evolution of microRNAs and their targets: Are all microRNAs biologically relevant?

(2008) M AXTELL   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Floral meristem initiation and meristem cell fate are regulated by the maize AP2 genes ids1 and sid1

(2008) G. Chuck et al.   DEVELOPMENT

Tapetum Degeneration Retardation is Critical for Aliphatic Metabolism and Gene Regulation during Rice Pollen Development

(2008) Da-Sheng Zhang et al.   Molecular Plant