Microgenomics: Genome-Scale, Cell-Specific Monitoring of Multiple Gene Regulation Tiers

Designing a transcriptome next-generation sequencing project for a nonmodel plant species1

(2012) Susan R. Strickler et al.   AMERICAN JOURNAL OF BOTANY

Quantitative Imaging with Fluorescent Biosensors

(2012) Sakiko Okumoto et al.   Annual Review of Plant Biology

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

(2012) Joseph P. Calarco et al.   CELL

Small RNAs in development – insights from plants

(2012) Xuemei Chen   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis

(2012) Virginie Jouannet et al.   EMBO JOURNAL

Dehydration stress activates Arabidopsis MPK6 to signal DCP1 phosphorylation

(2012) Jun Xu et al.   EMBO JOURNAL

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

(2012) F. A. Steiner et al.   GENOME RESEARCH

Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30

(2012) Fulgencio Alatorre-Cobos et al.   JOURNAL OF EXPERIMENTAL BOTANY

Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis

(2012) Dimas M. Ribeiro et al.   JOURNAL OF EXPERIMENTAL BOTANY

Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos

(2012) Michael D. Nodine et al.   NATURE

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

Gene-Sharing Networks Reveal Organizing Principles of Transcriptomes inArabidopsisand Other Multicellular Organisms

(2012) Song Li et al.   PLANT CELL

Selective recruitment of mRNAs and miRNAs to polyribosomes in response to rhizobia infection inMedicago truncatula

(2012) Mauricio Alberto Reynoso et al.   PLANT JOURNAL

Glandular trichomes: what comes after expressed sequence tags?

(2012) Alain Tissier   PLANT JOURNAL

RNA interference-mediated gene knockdown within specific cell types

(2012) Changqing Zhang et al.   PLANT MOLECULAR BIOLOGY

A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing

(2012) Marc W. Schmid et al.   PLoS One

454 Transcriptome Sequencing Suggests a Role for Two-Component Signalling in Cellularization and Differentiation of Barley Endosperm Transfer Cells

(2012) Johannes Thiel et al.   PLoS One

A Versatile Method for Cell-Specific Profiling of Translated mRNAs in Drosophila

(2012) Amanda Thomas et al.   PLoS One

The protein expression landscape of the Arabidopsis root

(2012) J. J. Petricka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics

(2012) Maureen Hummel et al.   PROTEOMICS

miRNA-Mediated Gene Silencing by Translational Repression Followed by mRNA Deadenylation and Decay

(2012) S. Djuranovic et al.   SCIENCE

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

A Gene Regulatory Network for Root Epidermis Cell Differentiation in Arabidopsis

(2012) Angela Bruex et al.   PLoS Genetics

Dynamic Light Regulation of Translation Status in Arabidopsis thaliana

(2012) Piyada Juntawong et al.   Frontiers in Plant Science

Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

(2012) Anireddy S. N. Reddy et al.   Frontiers in Plant Science

Epigenetic control of gene regulation in plants

(2011) Massimiliano Lauria et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes

(2011) Changbin Chen et al.   BMC PLANT BIOLOGY

Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis

(2011) Daphné Autran et al.   CELL

Cell Identity Regulators Link Development and Stress Responses in the Arabidopsis Root

(2011) Anjali S. Iyer-Pascuzzi et al.   DEVELOPMENTAL CELL

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing

(2011) Y. Shen et al.   GENOME RESEARCH

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

(2011) N. W. Breakfield et al.   GENOME RESEARCH

A stele-enriched gene regulatory network in the Arabidopsis root

(2011) S. M. Brady et al.   Molecular Systems Biology

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

Cell-Specific Vacuolar Calcium Storage Mediated byCAX1Regulates Apoplastic Calcium Concentration, Gas Exchange, and Plant Productivity inArabidopsis

(2011) Simon J. Conn et al.   PLANT CELL

Tissue- and Cell-Type Specific Transcriptome Profiling of Expanding Tomato Fruit Provides Insights into Metabolic and Regulatory Specialization and Cuticle Formation

(2011) Antonio J. Matas et al.   PLANT CELL

An insertional mutagenesis programme with an enhancer trap for the identification and tagging of genes involved in abiotic stress tolerance in the tomato wild-related species Solanum pennellii

(2011) Alejandro Atarés et al.   PLANT CELL REPORTS

Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions

(2011) Huan Wang et al.   PLANT JOURNAL

RNA targeting to a specific ER sub-domain is required for efficient transport and packaging of α-globulins to the protein storage vacuole in developing rice endosperm

(2011) Haruhiko Washida et al.   PLANT JOURNAL

A novel procedure for the quantitative analysis of metabolites, storage products and transcripts of laser microdissected seed tissues of Brassica napus

(2011) Silke Schiebold et al.   Plant Methods

Modulation of Abscisic Acid Signaling in Vivo by an Engineered Receptor-Insensitive Protein Phosphatase Type 2C Allele

(2011) F. Dupeux et al.   PLANT PHYSIOLOGY

A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq

(2011) Lin Wang et al.   PLoS One

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

(2011) X. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular control and function of endoreplication in development and physiology

(2011) Lieven De Veylder et al.   TRENDS IN PLANT SCIENCE

Silencing signals in plants: a long journey for small RNAs

(2011) Attila Molnar et al.   GENOME BIOLOGY

Regulatory Mechanisms for Specification and Patterning of Plant Vascular Tissues

(2010) Ana Caño-Delgado et al.   Annual Review of Cell and Developmental Biology

Chloroplast RNA Metabolism

(2010) David B. Stern et al.   Annual Review of Plant Biology

Laser microdissection of conifer stem tissues: Isolation and analysis of high quality RNA, terpene synthase enzyme activity and terpenoid metabolites from resin ducts and cambial zone tissue of white spruce (Picea glauca)

(2010) Eric Abbott et al.   BMC PLANT BIOLOGY

Arabidopsis Female Gametophyte Gene Expression Map Reveals Similarities between Plant and Animal Gametes

(2010) Samuel E. Wuest et al.   CURRENT BIOLOGY

Histone variants and modifications in plant gene regulation

(2010) Roger B Deal et al.   CURRENT OPINION IN PLANT BIOLOGY

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

(2010) Roger B. Deal et al.   DEVELOPMENTAL CELL

Metabolic profiling of Arabidopsis thaliana epidermal cells

(2010) Berit Ebert et al.   JOURNAL OF EXPERIMENTAL BOTANY

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

(2010) Yuling Jiao et al.   Molecular Systems Biology

Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action

(2010) Sona Pandey et al.   Molecular Systems Biology

Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth

(2010) R. Sozzani et al.   NATURE

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

(2010) Kerstin Kaufmann et al.   Nature Protocols

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

(2010) Roger B Deal et al.   Nature Protocols

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Identification of genes expressed in maize root cortical cells during lysigenous aerenchyma formation using laser microdissection and microarray analyses

(2010) Imene Rajhi et al.   NEW PHYTOLOGIST

The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency in Arabidopsis Roots

(2010) T. A. Long et al.   PLANT CELL

Global Gene Profiling of Laser-Captured Pollen Mother Cells Indicates Molecular Pathways and Gene Subfamilies Involved in Rice Meiosis

(2010) X. Tang et al.   PLANT PHYSIOLOGY

Improved Salinity Tolerance of Rice Through Cell Type-Specific Expression of AtHKT1;1

(2010) Darren Plett et al.   PLoS One

Macromolecules in phloem exudates—a review

(2010) Craig A. Atkins et al.   PROTOPLASMA

The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames

(2010) B. Roy et al.   RNA

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

(2010) Robert B. Darnell   Wiley Interdisciplinary Reviews-RNA

Sucrose-mediated translational control

(2009) Maureen Hummel et al.   ANNALS OF BOTANY

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Fly Antiviral RNA Silencing and miRNA Biogenesis Claim ARS2

(2009) Olivier Voinnet   Cell Host & Microbe

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling

(2009) B. Tauris et al.   JOURNAL OF EXPERIMENTAL BOTANY

Plant Micrometabolomics: The Analysis of Endogenous Metabolites Present in a Plant Cell or Tissue

(2009) Sofia Moco et al.   JOURNAL OF PROTEOME RESEARCH

Eukaryotic Stress Granules: The Ins and Outs of Translation

(2009) J. Ross Buchan et al.   MOLECULAR CELL

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

(2009) Yuling Jiao et al.   NATURE GENETICS

Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus

(2009) Valentina Fiorilli et al.   NEW PHYTOLOGIST

A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation

(2009) Ivaylo P. Ivanov et al.   NUCLEIC ACIDS RESEARCH

An Auxin Gradient and Maximum in the Arabidopsis Root Apex Shown by High-Resolution Cell-Specific Analysis of IAA Distribution and Synthesis

(2009) S. V. Petersson et al.   PLANT CELL

Matrix-free UV-laser desorption/ionization (LDI) mass spectrometric imaging at the single-cell level: distribution of secondary metabolites of Arabidopsis thaliana and Hypericum species

(2009) Dirk Hölscher et al.   PLANT JOURNAL

Early transcriptomic events in microdissected Arabidopsis nematode-induced giant cells

(2009) Marta Barcala et al.   PLANT JOURNAL

A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode)

(2009) Vincent P. Klink et al.   PLANT MOLECULAR BIOLOGY

Positive Fluorescent Selection Permits Precise, Rapid, and In-Depth Overexpression Analysis in Plant Protoplasts

(2009) B. O.R. Bargmann et al.   PLANT PHYSIOLOGY

Sucrose Control of Translation Mediated by an Upstream Open Reading Frame-Encoded Peptide

(2009) F. Rahmani et al.   PLANT PHYSIOLOGY

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

(2009) R. K. Yadav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

(2009) A. Mustroph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators

(2009) D. Chandran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Role of plant RNA-binding proteins in development, stress response and genome organization

(2009) Zdravko J. Lorković   TRENDS IN PLANT SCIENCE

Getting the message across: cytoplasmic ribonucleoprotein complexes

(2009) J. Bailey-Serres et al.   TRENDS IN PLANT SCIENCE

Stress-Dependent Coordination of Transcriptome and Translatome in Yeast

(2009) Regula E Halbeisen et al.   PLOS BIOLOGY

Microdissection of Shoot Meristem Functional Domains

(2009) Lionel Brooks et al.   PLoS Genetics

Systems Approaches to Identifying Gene Regulatory Networks in Plants

(2008) Terri A. Long et al.   Annual Review of Cell and Developmental Biology

Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types

(2008) Joseph P. Doyle et al.   CELL

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL

Plant cell types: reporting and sampling with new technologies

(2008) Timothy Nelson et al.   CURRENT OPINION IN PLANT BIOLOGY

Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay

(2008) Zoltán Kerényi et al.   EMBO JOURNAL

Microgenomic analysis reveals cell type-specific gene expression patterns between ray and fusiform initials within the cambial meristem ofPopulus

(2008) Nadia Goué et al.   NEW PHYTOLOGIST

Transcriptome-Wide Analysis of Uncapped mRNAs in Arabidopsis Reveals Regulation of mRNA Degradation

(2008) Y. Jiao et al.   PLANT CELL

Plant stress granules and mRNA processing bodies are distinct from heat stress granules

(2008) Christian Weber et al.   PLANT JOURNAL

Identification ofArabidopsis thalianaphloem RNAs provides a search criterion for phloem-based transcripts hidden in complex datasets of microarray experiments

(2008) Rosalia Deeken et al.   PLANT JOURNAL

Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation inArabidopsis thaliana

(2008) Cristina Branco-Price et al.   PLANT JOURNAL

MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis

(2008) Bikram Datt Pant et al.   PLANT JOURNAL

Comparative Transcriptomics of Arabidopsis Sperm Cells

(2008) F. Borges et al.   PLANT PHYSIOLOGY

Global Characterization of Cell-Specific Gene Expression through Fluorescence-Activated Sorting of Nuclei

(2008) C. Zhang et al.   PLANT PHYSIOLOGY

Bacterial RNA Chaperones Confer Abiotic Stress Tolerance in Plants and Improved Grain Yield in Maize under Water-Limited Conditions

(2008) P. Castiglioni et al.   PLANT PHYSIOLOGY

Longer First Introns Are a General Property of Eukaryotic Gene Structure

(2008) Keith R. Bradnam et al.   PLoS One

Cell-specific nitrogen responses mediate developmental plasticity

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

Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress

(2008) J. R. Dinneny et al.   SCIENCE

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY