From 'JUNK' to Just Unexplored Noncoding Knowledge: the case of transcribed Alus

Impact of Alu repeats on the evolution of human p53 binding sites

(2011) Feng Cui et al.   Biology Direct

Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes

(2011) Thomas Bettecken et al.   BMC GENOMICS

DNA methylation in repetitive elements and Alzheimer disease

(2011) V. Bollati et al.   BRAIN BEHAVIOR AND IMMUNITY

Cell cycle control of microRNA-mediated translation regulation

(2011) Shobha Vasudevan et al.   CELL CYCLE

MicroRNA responses and stress granule formation modulate the DNA damage response

(2011) Joris Pothof et al.   CELL CYCLE

Biological and clinical relevance of quantitative global methylation of repetitive DNA sequences in chronic lymphocytic leukemia

(2011) Sonia Fabris et al.   Epigenetics

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

(2011) Chenguang Gong et al.   NATURE

Widespread establishment and regulatory impact of Alu exons in human genes

(2011) S. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of human-specific transcript variants induced by DNA insertions in the human genome

(2010) Dong Seon Kim et al.   BIOINFORMATICS

Pseudogenes as an alternative source of natural antisense transcripts

(2010) Enrique M Muro et al.   BMC EVOLUTIONARY BIOLOGY

Effects of Alu elements on global nucleosome positioning in the human genome

(2010) Yoshiaki Tanaka et al.   BMC GENOMICS

Transcribed dark matter: meaning or myth?

(2010) C. P. Ponting et al.   HUMAN MOLECULAR GENETICS

Knockdown of the Dickkopf 3 gene induces apoptosis in a lung adenocarcinoma

(2010) Kim   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

Mechanism of Down-regulation of RNA Polymerase III-transcribed Non-coding RNA Genes in Macrophages byLeishmania

(2010) Tanu Rana et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA

(2010) Kimika Maki et al.   MOLECULAR MICROBIOLOGY

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

(2010) Yuntao S. Mao et al.   NATURE CELL BIOLOGY

Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

RNAs: regulators of bacterial virulence

(2010) Jonas Gripenland et al.   NATURE REVIEWS MICROBIOLOGY

Pol II and its associated epigenetic marks are present at Pol III–transcribed noncoding RNA genes

(2010) Artem Barski 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

Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation

(2010) Florent Hubé et al.   NUCLEIC ACIDS RESEARCH

Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3′ Trailers

(2010) Jian-You Liao et al.   PLoS One

Alu Sequences in Undifferentiated Human Embryonic Stem Cells Display High Levels of A-to-I RNA Editing

(2010) Sivan Osenberg et al.   PLoS One

Close association of RNA polymerase II and many transcription factors with Pol III genes

(2010) Debasish Raha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates

(2010) N. Paz-Yaacov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

X chromosome inactivation sparked by non-coding RNAs

(2010) Martin Leeb et al.   RNA Biology

Dampening DNA binding: A common mechanism of transcriptional repression for both ncRNAs and protein domains

(2010) James A. Goodrich et al.   RNA Biology

Noncanonical transcript forms in yeast and their regulation during environmental stress

(2010) O. K. Yoon et al.   RNA

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1

(2009) R. Garzon et al.   BLOOD

Alu repeats increase local recombination rates

(2009) David J Witherspoon et al.   BMC GENOMICS

Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates

(2009) Adrian F Gombart et al.   BMC GENOMICS

mRNA Localization: Gene Expression in the Spatial Dimension

(2009) Kelsey C. Martin et al.   CELL

SRA and its binding partners: an expanding role for RNA-binding coregulators in nuclear receptor-mediated gene regulation

(2009) Shane M. Colley et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

From bacteria to humans, chromatin to elongation, and activation to repression: The expanding roles of noncoding RNAs in regulating transcription

(2009) James A. Goodrich et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Lineage specific evolutionary events on SFTPB gene: Alu recombination-mediated deletion (ARMD), exonization, and alternative splicing events

(2009) Ja-Rang Lee et al.   GENE

Transposable elements in disease-associated cryptic exons

(2009) Igor Vorechovsky   HUMAN GENETICS

Nuclear Translocated Ehrlichia chaffeensis Ankyrin Protein Interacts with a Specific Adenine-Rich Motif of Host Promoter and Intronic Alu Elements

(2009) B. Zhu et al.   INFECTION AND IMMUNITY

Wrap53, a Natural p53 Antisense Transcript Required for p53 Induction upon DNA Damage

(2009) Salah Mahmoudi et al.   MOLECULAR CELL

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

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

ALU Repeats in Promoters Are Position-Dependent Co-Response Elements (coRE) that Enhance or Repress Transcription by Dimeric and Monomeric Progesterone Receptors

(2009) Britta M. Jacobsen et al.   MOLECULAR ENDOCRINOLOGY

A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms

(2009) Liang Chen   NUCLEIC ACIDS RESEARCH

Evidence for large diversity in the human transcriptome created by Alu RNA editing

(2009) Michal Barak et al.   NUCLEIC ACIDS RESEARCH

An Alu-derived intronic splicing enhancer facilitates intronic processing and modulates aberrant splicing in ATM

(2009) Tibor Pastor et al.   NUCLEIC ACIDS RESEARCH

C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts

(2009) M.-L. Bortolin-Cavaille et al.   NUCLEIC ACIDS RESEARCH

High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum

(2009) Hehuang Xie et al.   NUCLEIC ACIDS RESEARCH

Evidence for Co-Evolution between Human MicroRNAs and Alu-Repeats

(2009) Stefan Lehnert et al.   PLoS One

A Novel Protein Isoform of the Multicopy Human NAIP Gene Derives from Intragenic Alu SINE Promoters

(2009) Mark T. Romanish et al.   PLoS One

The role of transposable elements in the regulation of IFN-λ1 gene expression

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

Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells

(2009) J. Sheik Mohamed et al.   RNA

Microarray analysis of cytoplasmic versus whole cell RNA reveals a considerable number of missed and false positive mRNAs

(2009) H. W. Trask et al.   RNA

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

(2009) Schraga Schwartz et al.   PLoS Computational Biology

MicroRNAs (miRNAs) in Neurodegenerative Diseases

(2008) Peter T. Nelson et al.   BRAIN PATHOLOGY

mRNA nuclear export and human disease

(2008) J. A. Hurt et al.   Disease Models & Mechanisms

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

(2008) P. M. Kim et al.   GENOME RESEARCH

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

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

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

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

p53 mRNA controls p53 activity by managing Mdm2 functions

(2008) Marco M. Candeias et al.   NATURE CELL BIOLOGY

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

(2008) Jiong-Tang Li et al.   NUCLEIC ACIDS RESEARCH

Frequency and fate of microRNA editing in human brain

(2008) Y. Kawahara et al.   NUCLEIC ACIDS RESEARCH

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE

Human cis natural antisense transcripts initiated by transposable elements

(2008) Andrew B. Conley et al.   TRENDS IN GENETICS

Methylation and deamination of CpGs generate p53-binding sites on a genomic scale

(2008) Tomasz Zemojtel et al.   TRENDS IN GENETICS

REST Regulates Distinct Transcriptional Networks in Embryonic and Neural Stem Cells

(2008) Rory Johnson et al.   PLOS BIOLOGY

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

(2008) Lan Lin et al.   PLoS Genetics

Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes

(2008) Ping Wang et al.   GENOME BIOLOGY