Arabidopsis RNA Polymerase IV generates 21–22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes

Paternally acting canonical RNA-directed DNA methylation pathway genes sensitize Arabidopsis endosperm to paternal genome dosage

(2019) P.R. V. Satyaki et al.   PLANT CELL

Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation

(2019) Shengbo He et al.   eLife

An “eFP‐Seq Browser” for Visualizing and Exploring RNA‐Seq Data

(2019) Alexander Sullivan et al.   PLANT JOURNAL

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs

(2018) Matthew B Stocks et al.   BIOINFORMATICS

Paternal easiRNAs regulate parental genome dosage in Arabidopsis

(2018) German Martinez et al.   NATURE GENETICS

Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis

(2018) Filipe Borges et al.   NATURE GENETICS

psRNATarget: a plant small RNA target analysis server (2017 release)

(2018) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Sequestration of a Transposon-Derived siRNA by a Target Mimic Imprinted Gene Induces Postzygotic Reproductive Isolation in Arabidopsis

(2018) Guifeng Wang et al.   DEVELOPMENTAL CELL

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Exogenous Transposable Elements Circumvent Identity-Based Silencing, Permitting the Dissection of Expression-Dependent Silencing

(2017) Dalen Fultz et al.   PLANT CELL

A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis

(2016) Ruiqiang Ye et al.   MOLECULAR CELL

A high resolution map of theArabidopsis thalianadevelopmental transcriptome based on RNA-seq profiling

(2016) Anna V. Klepikova et al.   PLANT JOURNAL

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

(2015) Jixian Zhai et al.   CELL

Ancient Origin and Recent Innovations of RNA Polymerase IV and V

(2015) Yi Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

(2015) Qing Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

(2015) Todd Blevins et al.   eLife

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

(2013) Julie A. Law et al.   NATURE

Genome-wide identification of genes regulated intransby transposable element small interfering RNAs

(2013) Andrea D McCue et al.   RNA Biology

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

(2012) Andrea D. McCue et al.   PLoS Genetics

Genome reprogramming and small interfering RNA in the Arabidopsis germline

(2011) Joseph P Calarco et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci

(2010) E. R. Havecker et al.   PLANT CELL

Form, Function, and Regulation of ARGONAUTE Proteins

(2010) Allison Mallory et al.   PLANT CELL

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation

(2008) Lucia Daxinger et al.   EMBO JOURNAL

Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

(2008) K. Nobuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA