Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors

PNLDC1, mouse pre‐piRNA Trimmer, is required for meiotic and post‐meiotic male germ cell development

(2018) Toru Nishimura et al.   EMBO REPORTS

TDRD5 binds piRNA precursors and selectively enhances pachytene piRNA processing in mice

(2018) Deqiang Ding et al.   Nature Communications

A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals

(2018) Ildar Gainetdinov et al.   MOLECULAR CELL

Zucchini-dependent piRNA processing is triggered by recruitment to the cytoplasmic processing machinery

(2017) Alicia K. Rogers et al.   GENES & DEVELOPMENT

A heterochromatin-dependent transcription machinery drives piRNA expression

(2017) Peter Refsing Andersen et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

PNLDC1 is essential for piRNA 3′ end trimming and transposon silencing during spermatogenesis in mice

(2017) Deqiang Ding et al.   Nature Communications

Identification and Characterization of a Class of MALAT1 -like Genomic Loci

(2017) Bin Zhang et al.   Cell Reports

Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries

(2017) Radha Raman Pandey et al.   PLoS Genetics

Domestic chickens activate a piRNA defense against avian leukosis virus

(2017) Yu Huining Sun et al.   eLife

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets

(2016) Eric W. Mills et al.   Cell Reports

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

(2015) Vicent Pelechano et al.   CELL

Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo

(2015) David J. Young et al.   CELL

The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing

(2015) Anastassios Vourekas et al.   GENES & DEVELOPMENT

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

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

(2015) David Homolka et al.   Cell Reports

Somatic Primary piRNA Biogenesis Driven by cis-Acting RNA Elements and trans-Acting Yb

(2015) Hirotsugu Ishizu et al.   Cell Reports

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

(2014) Bo W. Han et al.   BIOINFORMATICS

Dom34 Rescues Ribosomes in 3′ Untranslated Regions

(2014) Nicholas R. Guydosh et al.   CELL

Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice

(2014) J. Castaneda et al.   EMBO JOURNAL

A Mouse Geneticist's Practical Guide to CRISPR Applications

(2014) P. Singh et al.   GENETICS

Cnidarian microRNAs frequently regulate targets by cleavage

(2014) Y. Moran et al.   GENOME RESEARCH

Evidence of efficient stop codon readthrough in four mammalian genes

(2014) Gary Loughran et al.   NUCLEIC ACIDS RESEARCH

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline

(2013) Jonathan P Saxe et al.   EMBO JOURNAL

A perspective on mammalian upstream open reading frame function

(2013) Joanna Somers et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

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

(2013) Xin Zhiguo Li et al.   MOLECULAR CELL

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

RiboTag Analysis of Actively Translated mRNAs in Sertoli and Leydig Cells In Vivo

(2013) Elisenda Sanz et al.   PLoS One

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

(2013) Joshua G Dunn et al.   eLife

UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery

(2012) Fan Zhang et al.   CELL

An essential role for a mammalian SWI/SNF chromatin-remodeling complex during male meiosis

(2012) Y. Kim et al.   DEVELOPMENT

Observation of dually decoded regions of the human genome using ribosome profiling data

(2012) A. M. Michel et al.   GENOME RESEARCH

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

Blockade of Pachytene piRNA Biogenesis Reveals a Novel Requirement for Maintaining Post-Meiotic Germline Genome Integrity

(2012) Ke Zheng et al.   PLoS Genetics

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Argonaute proteins

(2011) Elif Sarinay Cenik et al.   CURRENT BIOLOGY

The ribosome uses two active mechanisms to unwind messenger RNA during translation

(2011) Xiaohui Qu et al.   NATURE

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

The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect

(2009) Travis Thomson et al.   Annual Review of Cell and Developmental Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Biogenesis of small RNAs in animals

(2009) V. Narry Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members

(2008) T. A. Farazi et al.   DEVELOPMENT

Improved northern blot method for enhanced detection of small RNA

(2008) Gurman S Pall et al.   Nature Protocols