Integrator is recruited to promoter‐proximally paused RNA Pol II to generate Caenorhabditis elegans piRNA precursors

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

(2020) Yuki Aoi et al.   MOLECULAR CELL

Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes

(2019) Eva Gómez-Orte et al.   PLoS Genetics

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis

(2019) Toni Beltran et al.   DEVELOPMENTAL CELL

PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability

(2019) Ricardo J. Cordeiro Rodrigues et al.   GENES & DEVELOPMENT

Functional Proteomics Identifies a PICS Complex Required for piRNA Maturation and Chromosome Segregation

(2019) Chenming Zeng et al.   Cell Reports

Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

(2019) Mei Han et al.   BMC GENOMICS

The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes

(2019) Nathan D. Elrod et al.   MOLECULAR CELL

Reversible and long-term immobilization in a hydrogel-microbead matrix for high-resolution imaging of Caenorhabditis elegans and other small organisms

(2018) Li Dong et al.   PLoS One

The USTC co-opts an ancient machinery to drive piRNA transcription in C. elegans

(2018) Chenchun Weng et al.   GENES & DEVELOPMENT

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

(2018) Nevena Cvetesic et al.   GENOME RESEARCH

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima et al.   MOLECULAR CELL

PIWI-interacting RNAs: small RNAs with big functions

(2018) Deniz M. Ozata et al.   NATURE REVIEWS GENETICS

Chromatin accessibility dynamics across C. elegans development and ageing

(2018) Jürgen Jänes et al.   eLife

Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation

(2017) Yuri Pritykin et al.   RNA

Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide

(2016) Takayuki Nojima et al.   Nature Protocols

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

The C. elegans SNAPc Component SNPC-4 Coats piRNA Domains and Is Globally Required for piRNA Abundance

(2014) Dionna M. Kasper et al.   DEVELOPMENTAL CELL

PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif-dependent piRNAs in C. elegans

(2014) E.-M. Weick et al.   GENES & DEVELOPMENT

Integrator Regulates Transcriptional Initiation and Pause Release following Activation

(2014) Alessandro Gardini et al.   MOLECULAR CELL

Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes

(2014) Bernd Stadelmayer et al.   Nature Communications

Pol II Docking and Pausing at Growth and Stress Genes in C. elegans

(2014) Colin S. Maxwell et al.   Cell Reports

The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures

(2013) R. A.- J. Chen et al.   GENOME RESEARCH

The Genetic Makeup of the Drosophila piRNA Pathway

(2013) Dominik Handler et al.   MOLECULAR CELL

A Transcriptome-wide RNAi Screen in the Drosophila Ovary Reveals Factors of the Germline piRNA Pathway

(2013) Benjamin Czech et al.   MOLECULAR CELL

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

A Conserved Upstream Motif Orchestrates Autonomous, Germline-Enriched Expression of Caenorhabditis elegans piRNAs

(2013) Allison C. Billi et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs

(2012) Germano Cecere et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

(2012) M. P. Bagijn et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Integrator Complex Recognizes a New Double Mark on the RNA Polymerase II Carboxyl-terminal Domain

(2010) Sylvain Egloff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evidence that Transcript Cleavage Is Essential for RNA Polymerase II Transcription and Cell Viability

(2010) Stefan Sigurdsson et al.   MOLECULAR CELL

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline

(2008) Partha P. Das et al.   MOLECULAR CELL

PRG-1 and 21U-RNAs Interact to Form the piRNA Complex Required for Fertility in C. elegans

(2008) Pedro J. Batista et al.   MOLECULAR CELL