The comprehensive epigenome map of piRNA clusters

High-Resolution Genome-wide Mapping of the Primary Structure of Chromatin

(2011) Zhenhai Zhang et al.   CELL

piRNA Production Requires Heterochromatin Formation in Drosophila

(2011) Prashanth Rangan et al.   CURRENT BIOLOGY

Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila

(2011) A. L. Zamparini et al.   DEVELOPMENT

MITOPLD Is a Mitochondrial Protein Essential for Nuage Formation and piRNA Biogenesis in the Mouse Germline

(2011) Toshiaki Watanabe et al.   DEVELOPMENTAL CELL

A systematic analysis ofDrosophilaTUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors

(2011) Dominik Handler et al.   EMBO JOURNAL

Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish

(2011) Hsin-Yi Huang et al.   EMBO JOURNAL

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

(2011) R. Yamashita et al.   GENOME RESEARCH

Molecular characterization of heterochromatin proteins 1a and 1b from the silkworm, Bombyx mori

(2011) H. Mitsunobu et al.   INSECT MOLECULAR BIOLOGY

3′ End Formation of PIWI-Interacting RNAs In Vitro

(2011) Shinpei Kawaoka et al.   MOLECULAR CELL

Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3 Ligase and Tudor Domains

(2011) Zhao Zhang et al.   MOLECULAR CELL

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements

(2011) Serena De Fazio et al.   NATURE

Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing

(2011) Michael Reuter et al.   NATURE

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

A role for transcription from a piRNA cluster in de novo piRNA production

(2011) S. Kawaoka et al.   RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila

(2010) Daniel Olivieri et al.   EMBO JOURNAL

Hen1 is required for oocyte development and piRNA stability in zebrafish

(2010) Leonie M Kamminga et al.   EMBO JOURNAL

Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila

(2010) A. D. Haase et al.   GENES & DEVELOPMENT

Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila

(2010) K. Saito et al.   GENES & DEVELOPMENT

MVH in piRNA processing and gene silencing of retrotransposons

(2010) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

(2010) N. C. Riddle et al.   GENOME RESEARCH

The Yb Body, a Major Site for Piwi-associated RNA Biogenesis and a Gateway for Piwi Expression and Transport to the Nucleus in Somatic Cells

(2010) Hongying Qi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

The Epigenetic Trans-Silencing Effect in Drosophila Involves Maternally-Transmitted Small RNAs Whose Production Depends on the piRNA Pathway and HP1

(2010) Anne-Laure Todeschini et al.   PLoS One

Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway

(2010) K. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs

(2010) R. J. A. Frost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

HP1 Recruitment in the Absence of Argonaute Proteins in Drosophila

(2010) Nellie Moshkovich et al.   PLoS Genetics

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Drosophila HP1 Homolog Rhino Is Required for Transposon Silencing and piRNA Production by Dual-Strand Clusters

(2009) Carla Klattenhoff et al.   CELL

Mili Interacts with Tudor Domain-Containing Protein 1 in Regulating Spermatogenesis

(2009) Jianquan Wang et al.   CURRENT BIOLOGY

The TDRD9-MIWI2 Complex Is Essential for piRNA-Mediated Retrotransposon Silencing in the Mouse Male Germline

(2009) Masanobu Shoji et al.   DEVELOPMENTAL CELL

Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members

(2009) V. V. Vagin et al.   GENES & DEVELOPMENT

Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line

(2009) N. C. Lau et al.   GENOME RESEARCH

A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila

(2009) Kuniaki Saito et al.   NATURE

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Loss of the Mili-interacting Tudor domain–containing protein-1 activates transposons and alters the Mili-associated small RNA profile

(2009) Michael Reuter et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes

(2009) S. Kawaoka et al.   RNA

Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice

(2009) Alexei A. Aravin et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Developmentally synchronized expression of two Bombyx mori Piwi subfamily genes, SIWI and BmAGO3 in germ-line cells

(2008) Shinpei Kawaoka et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Mouse Maelstrom, a Component of Nuage, Is Essential for Spermatogenesis and Transposon Repression in Meiosis

(2008) Sarah F.C. Soper et al.   DEVELOPMENTAL CELL

Bombyx small RNAs: Genomic defense system against transposons in the silkworm, Bombyx mori

(2008) Shinpei Kawaoka et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY