Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts

A signal cascade originated from epidermis defines apical-basal patterning of Arabidopsis shoot apical meristems

(2020) Han Han et al.   Nature Communications

A gene expression map of shoot domains reveals regulatory mechanisms

(2019) Caihuan Tian et al.   Nature Communications

Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis

(2019) Brian Reichholf et al.   MOLECULAR CELL

MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis

(2019) Alexandra Plotnikova et al.   PLANT CELL

A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

(2019) Steffen Knauer et al.   GENOME RESEARCH

Despacito: the slow evolutionary changes in plant microRNAs

(2018) Patricia Baldrich et al.   CURRENT OPINION IN PLANT BIOLOGY

A virus-targeted plant receptor-like kinase promotes cell-to-cell spread of RNAi

(2018) Tabata Rosas-Diaz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana

(2018) Jia He et al.   PLoS Genetics

Gating of miRNA movement at defined cell-cell interfaces governs their impact as positional signals

(2018) Damianos S. Skopelitis et al.   Nature Communications

NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA

(2018) Michael A. Schon et al.   GENOME RESEARCH

Efficiency and precision of microRNA biogenesis modes in plants

(2018) Belén Moro et al.   NUCLEIC ACIDS RESEARCH

The ‘how’ and ‘where’ of plant microRNAs

(2017) Yu Yu et al.   NEW PHYTOLOGIST

Gramene 2018: unifying comparative genomics and pathway resources for plant research

(2017) Marcela K Tello-Ruiz et al.   NUCLEIC ACIDS RESEARCH

Target RNA Secondary Structure Is a Major Determinant of miR159 Efficacy

(2017) Zihui Zheng et al.   PLANT PHYSIOLOGY

Small RNAs: Big Impact on Plant Development

(2017) Marco D’Ario et al.   TRENDS IN PLANT SCIENCE

The role of small RNAs in vegetative shoot development

(2016) Jim P Fouracre et al.   CURRENT OPINION IN PLANT BIOLOGY

The Sussex signal: insights into leaf dorsiventrality

(2016) Cris Kuhlemeier et al.   DEVELOPMENT

Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana

(2016) Mingli Xu et al.   PLoS Genetics

Novel DICER-LIKE1 siRNAs Bypass the Requirement for DICER-LIKE4 in Maize Development

(2015) Katherine Petsch et al.   PLANT CELL

Gene regulation by translational inhibition is determined by Dicer partnering proteins

(2015) Rodrigo S. Reis et al.   Nature Plants

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Q. Liu et al.   PLANT CELL

Methylation protects microRNAs from an AGO1-associated activity that uridylates 5' RNA fragments generated by AGO1 cleavage

(2014) G. Ren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The functional scope of plant microRNA-mediated silencing

(2014) Junyan Li et al.   TRENDS IN PLANT SCIENCE

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

Determinants beyond Both Complementarity and Cleavage Govern MicroR159 Efficacy in Arabidopsis

(2014) Junyan Li et al.   PLoS Genetics

MicroRNAs Inhibit the Translation of Target mRNAs on the Endoplasmic Reticulum in Arabidopsis

(2013) Shengben Li et al.   CELL

A Protodermal miR394 Signal Defines a Region of Stem Cell Competence in the Arabidopsis Shoot Meristem

(2013) Steffen Knauer et al.   DEVELOPMENTAL CELL

MicroRNA156: A Potential Graft-Transmissible MicroRNA That Modulates Plant Architecture and Tuberization in Solanum tuberosum ssp. andigena

(2013) S. Bhogale et al.   PLANT PHYSIOLOGY

Mendelian and Non-Mendelian Regulation of Gene Expression in Maize

(2013) Lin Li et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

In situ localization of small RNAs in plants by using LNA probes

(2012) Marie Javelle et al.   Nature Protocols

Plant small RNAs as morphogens

(2011) Damianos S Skopelitis et al.   CURRENT OPINION IN CELL BIOLOGY

Non-cell-autonomous microRNA165 acts in a dose-dependent manner to regulate multiple differentiation status in the Arabidopsis root

(2011) S. Miyashima et al.   DEVELOPMENT

Callose Biosynthesis Regulates Symplastic Trafficking during Root Development

(2011) Anne Vatén et al.   DEVELOPMENTAL CELL

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate

(2010) Annelie Carlsbecker et al.   NATURE

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159

(2009) Nicolás G Bologna et al.   EMBO JOURNAL

Pattern formation via small RNA mobility

(2009) D. H. Chitwood et al.   GENES & DEVELOPMENT

Regulation of Small RNA Accumulation in the Maize Shoot Apex

(2009) Fabio T. S. Nogueira et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE

Evolution of plant microRNAs and their targets

(2008) Michael J. Axtell et al.   TRENDS IN PLANT SCIENCE