Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus

(2015) Shi-Bin Hu et al.   GENES & DEVELOPMENT

Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNAH

(2015) Kentaro Ishida et al.   GENES TO CELLS

SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

(2015) Dhaval Varshney et al.   Nature Communications

Infection-Induced Retrotransposon-Derived Noncoding RNAs Enhance Herpesviral Gene Expression via the NF-κB Pathway

(2015) John Karijolich et al.   PLoS Pathogens

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs

(2015) Kenji Ichiyanagi   GENES & GENETIC SYSTEMS

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data

(2014) Anastasia Conti et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of Alu editability

(2014) L. Bazak et al.   NUCLEIC ACIDS RESEARCH

RNA Polymerase III Transcriptomes in Human Embryonic Stem Cells and Induced Pluripotent Stem Cells, and Relationships with Pluripotency Transcription Factors

(2014) Ravi K. Alla et al.   PLoS One

Evolution of Alu Elements toward Enhancers

(2014) Ming Su et al.   Cell Reports

Alu elements shape the primate transcriptome by cis-regulation of RNA editing

(2014) Chammiran Daniel et al.   GENOME BIOLOGY

RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA

(2013) Stacey D Wagner et al.   EMBO JOURNAL

Control of myogenesis by rodent SINE-containing lncRNAs

(2013) J. Wang et al.   GENES & DEVELOPMENT

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

mRNA–mRNA duplexes that autoelicit Staufen1-mediated mRNA decay

(2013) Chenguang Gong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Binding of TFIIIC to SINE Elements Controls the Relocation of Activity-Dependent Neuronal Genes to Transcription Factories

(2013) Luca Crepaldi et al.   PLoS Genetics

DICER1 Loss and Alu RNA Induce Age-Related Macular Degeneration via the NLRP3 Inflammasome and MyD88

(2012) Valeria Tarallo et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

(2012) D. Canella et al.   GENOME RESEARCH

DICER- and AGO3-dependent generation of retinoic acid–induced DR2 Alu RNAs regulates human stem cell proliferation

(2012) QiDong Hu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch

(2011) A. C. Roman et al.   GENOME RESEARCH

Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development

(2011) K. Ichiyanagi et al.   GENOME RESEARCH

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration

(2011) Hiroki Kaneko et al.   NATURE

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes

(2011) Claudia Kutter et al.   NATURE GENETICS

Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells

(2011) Lucie Carrière et al.   NUCLEIC ACIDS RESEARCH

Identification of Widespread Ultra-Edited Human RNAs

(2011) Shai Carmi et al.   PLoS Genetics

Global mRNA Degradation during Lytic Gammaherpesvirus Infection Contributes to Establishment of Viral Latency

(2011) Justin M. Richner et al.   PLoS Pathogens

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

(2010) D. Canella et al.   GENOME RESEARCH

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

(2010) Andrew J Oler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

(2010) Zarmik Moqtaderi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Murine Gamma-Herpesvirus 68 Hijacks MAVS and IKKβ to Initiate Lytic Replication

(2010) Xiaonan Dong et al.   PLoS Pathogens

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Host Shutoff Is a Conserved Phenotype of Gammaherpesvirus Infection and Is Orchestrated Exclusively from the Cytoplasm

(2009) S. Covarrubias et al.   JOURNAL OF VIROLOGY

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

(2009) Ling-Ling Chen et al.   MOLECULAR CELL

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

(2009) P. Yakovchuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes

(2009) Aristotelis Tsirigos et al.   PLoS Computational Biology

Alu element-mediated gene silencing

(2008) Ling-Ling Chen et al.   EMBO JOURNAL

Shugoshin-2 is essential for the completion of meiosis but not for mitotic cell division in mice

(2008) E. Llano et al.   GENES & DEVELOPMENT

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Using Alu Elements as Polyadenylation Sites: A Case of Retroposon Exaptation

(2008) C. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock

(2008) Peter D. Mariner et al.   MOLECULAR CELL

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols

Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo

(2008) A. C. Roman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA