Two modes of targeting transposable elements by piRNA pathway in human testis

piRNA biogenesis in the germline: From transcription of piRNA genomic sources to piRNA maturation

(2016) Shigeki Hirakata et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Transposable elements: Self-seekers of the germline, team-players of the soma

(2016) David Haig   BIOESSAYS

Transposable Element Targeting by piRNAs in Laurasiatherians with Distinct Transposable Element Histories

(2016) Michael W. Vandewege et al.   Genome Biology and Evolution

Sequence-dependent but not sequence-specific piRNA adhesion traps mRNAs to the germ plasm

(2016) Anastassios Vourekas et al.   NATURE

Parallel evolution of male germline epigenetic poising and somatic development in animals

(2016) Bluma J Lesch et al.   NATURE GENETICS

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing

(2016) Benjamin Czech et al.   TRENDS IN BIOCHEMICAL SCIENCES

Biogenesis and Function of Transfer RNA-Related Fragments (tRFs)

(2016) Pankaj Kumar et al.   TRENDS IN BIOCHEMICAL SCIENCES

MIWI2 as an Effector of DNA Methylation and Gene Silencing in Embryonic Male Germ Cells

(2016) Kanako Kojima-Kita et al.   Cell Reports

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

(2015) Walfred W.C. Tang et al.   CELL

MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes

(2015) Peng Zhang et al.   CELL RESEARCH

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

(2015) Kirsten-André Senti et al.   GENES & DEVELOPMENT

piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis

(2015) Wee Siong Sho Goh et al.   GENES & DEVELOPMENT

Profiling of the small RNA populations in human testicular germ cell tumors shows global loss of piRNAs

(2015) TB Rounge et al.   Molecular Cancer

Retrotransposition and Crystal Structure of an Alu RNP in the Ribosome-Stalling Conformation

(2015) Valentina Ahl et al.   MOLECULAR CELL

Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms

(2015) Wei Wang et al.   MOLECULAR CELL

piRNA cluster database: a web resource for piRNA producing loci

(2015) David Rosenkranz   NUCLEIC ACIDS RESEARCH

Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs

(2015) Min-Te Chou et al.   NUCLEIC ACIDS RESEARCH

Tupaia small RNAs provide insights into function and evolution of RNAi-based transposon defense in mammals

(2015) David Rosenkranz et al.   RNA

piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis

(2015) F. Mohn et al.   SCIENCE

piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production

(2015) B. W. Han et al.   SCIENCE

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

(2015) U. Sharma et al.   SCIENCE

MIWI2 and MILI Have Differential Effects on piRNA Biogenesis and DNA Methylation

(2015) Sergei A. Manakov et al.   Cell Reports

PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis

(2015) David Homolka et al.   Cell Reports

Comprehensive DNA Methylation Analysis of Retrotransposons in Male Germ Cells

(2015) Ippei Nagamori et al.   Cell Reports

Discovery and Characterization of piRNAs in the Human Fetal Ovary

(2015) Zev Williams et al.   Cell Reports

Piwi Proteins and piRNAs in Mammalian Oocytes and Early Embryos

(2015) Elke F. Roovers et al.   Cell Reports

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals

(2015) Gung-wei Chirn et al.   PLoS Genetics

RNA-based regulation of transposon expression

(2015) Daniel Gebert et al.   Wiley Interdisciplinary Reviews-RNA

piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals

(2015) Daniel Gebert et al.   PLoS One

A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements

(2014) Hongseok Ha et al.   BMC GENOMICS

Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis

(2014) Lan-Tao Gou et al.   CELL RESEARCH

piRNAs

(2014) Bo W. Han et al.   CURRENT BIOLOGY

piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells

(2014) D. Pezic et al.   GENES & DEVELOPMENT

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

(2014) S. Washietl et al.   GENOME RESEARCH

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate

(2014) Takamasa Hirano et al.   RNA

To be or not to be a piRNA: genomic origin and processing of piRNAs

(2014) Adrien Le Thomas et al.   GENOME BIOLOGY

Defining piRNA primary transcripts

(2013) Xin Zhiguo Li et al.   CELL CYCLE

Analysis of piRNA-Mediated Silencing of Active TEs in Drosophila melanogaster Suggests Limits on the Evolution of Host Genome Defense

(2013) Erin S. Kelleher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple Epigenetic Mechanisms and the piRNA Pathway Enforce LINE1 Silencing during Adult Spermatogenesis

(2013) Monica Di Giacomo et al.   MOLECULAR CELL

An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes

(2013) Xin Zhiguo Li et al.   MOLECULAR CELL

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

MicroRNA and piRNA Profiles in Normal Human Testis Detected by Next Generation Sequencing

(2013) Qingling Yang et al.   PLoS One

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta 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

proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

(2012) David Rosenkranz et al.   BMC BIOINFORMATICS

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Retrotransposon-centered analysis of piRNA targeting shows a shift from active to passive retrotransposon transcription in developing mouse testes

(2011) Tobias Mourier   BMC GENOMICS

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

A Broadly Conserved Pathway Generates 3′UTR-Directed Primary piRNAs

(2009) Nicolas Robine et al.   CURRENT BIOLOGY

Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila

(2009) J. Lu et al.   GENOME RESEARCH

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

(2009) Kuniaki Saito et al.   NATURE

Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes

(2008) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

Active Alu retrotransposons in the human genome

(2008) E. A. Bennett et al.   GENOME RESEARCH

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY