Genome-wide redistribution of 24-nt siRNAs in rice gametes

Step-by-step protocols for rice gamete isolation

(2019) Chenxin Li et al.   Plant Reproduction

24-nt reproductive phasiRNAs are broadly present in angiosperms

(2019) Rui Xia et al.   Nature Communications

Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in Arabidopsis

(2019) Ryan C. Kirkbride et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two-Step Maternal-to-Zygotic Transition with Two-Phase Parental Genome Contributions

(2019) Peng Zhao et al.   DEVELOPMENTAL CELL

Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?

(2019) Mary Gehring   NEW PHYTOLOGIST

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

DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm

(2019) M. Yvonne Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions

(2019) Hugo K. Dooner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Redistribution of CHH Methylation and Small Interfering RNAs across the Genome of Tomato ddm1 Mutants

(2018) Shira Corem et al.   PLANT CELL

Loss of RNA-directed DNA Methylation in Maize Chromomethylase and DDM1-type Nucleosome Remodeler Mutants

(2018) Fang-Fang Fu et al.   PLANT CELL

Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa

(2018) Jeffrey W. Grover et al.   PLANT JOURNAL

Reproductive Long Intergenic Noncoding RNAs Exhibit Male Gamete Specificity and Polycomb Repressive Complex 2-Mediated Repression

(2018) Cameron Johnson et al.   PLANT PHYSIOLOGY

DDM1 Represses Noncoding RNA Expression and RNA-Directed DNA Methylation in Heterochromatin

(2018) Feng Tan et al.   PLANT PHYSIOLOGY

Decrease in DNA methylation 1 (DDM1 ) is required for the formation of m CHH islands in maize

(2018) Jin Cheng Long et al.   Journal of Integrative Plant Biology

Clearance of maternal barriers by paternal miR159 to initiate endosperm nuclear division in Arabidopsis

(2018) Youshang Zhao et al.   Nature Communications

Live-cell analysis of DNA methylation during sexual reproduction inArabidopsisreveals context and sex-specific dynamics controlled by noncanonical RdDM

(2017) Mathieu Ingouff et al.   GENES & DEVELOPMENT

Epigenetic processes in flowering plant reproduction

(2017) Guifeng Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis

(2017) James Walker et al.   NATURE GENETICS

A Small RNA Pathway Mediates Allelic Dosage in Endosperm

(2017) Robert M. Erdmann et al.   Cell Reports

DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes

(2017) David B Lyons et al.   eLife

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways

(2016) Qili Fei et al.   JOURNAL OF EXPERIMENTAL BOTANY

Analysis of Chromatin Regulators Reveals Specific Features of Rice DNA Methylation Pathways

(2016) Feng Tan et al.   PLANT PHYSIOLOGY

DNA demethylation is initiated in the central cells ofArabidopsisand rice

(2016) Kyunghyuk Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsismale sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues

(2016) Ping-Hung Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Jixian Zhai et al.   CELL

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

Chromatin remodelling during male gametophyte development

(2015) Michael Borg et al.   PLANT JOURNAL

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

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

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

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

(2014) Ramesh Yelagandula et al.   CELL

ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation

(2014) A. D. McCue et al.   EMBO JOURNAL

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

Non-equivalent contributions of maternal and paternal genomes to early plant embryogenesis

(2014) Gerardo Del Toro-De León et al.   NATURE

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs

(2014) Reina Komiya et al.   PLANT JOURNAL

The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes

(2014) Zsuzsanna Mérai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes

(2013) Yujun Han et al.   BMC GENOMICS

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Artificial microRNAs reveal cell-specific differences in small RNA activity in pollen

(2013) Robert Grant-Downton et al.   CURRENT BIOLOGY

Chromatin reprogramming during the somatic-to-reproductive cell fate transition in plants

(2013) Wenjing She et al.   DEVELOPMENT

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

(2013) Hume Stroud et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptomes of isolatedOryza sativagametes characterized by deep sequencing: evidence for distinct sex-dependent chromatin and epigenetic states before fertilization

(2013) Sarah N. Anderson et al.   PLANT JOURNAL

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Joseph P. Calarco et al.   CELL

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage

(2012) Scott D. Russell et al.   NEW PHYTOLOGIST

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis

(2011) Daphné Autran et al.   CELL

Zygotic Resetting of the HISTONE 3 Variant Repertoire Participates in Epigenetic Reprogramming in Arabidopsis

(2010) Mathieu Ingouff et al.   CURRENT BIOLOGY

Embryo and Endosperm Inherit Distinct Chromatin and Transcriptional States from the Female Gametes in Arabidopsis

(2010) M. Pillot et al.   PLANT CELL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin

(2009) Vera K Schoft et al.   EMBO REPORTS

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH