Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

Genome-wide functional analysis of human 5' untranslated region introns

(2012) Can Cenik et al.   GENOME BIOLOGY

Functional evidence of post-transcriptional regulation by pseudogenes

(2011) Enrique M. Muro et al.   BIOCHIMIE

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

(2011) Florian A. Karreth et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

MicroRNA-146a Downregulates NF B Activity via Targeting TRAF6 and Functions as a Tumor Suppressor Having Strong Prognostic Implications in NK/T Cell Lymphoma

(2011) J. H. Paik et al.   CLINICAL CANCER RESEARCH

The central role of RNA in human development and cognition

(2011) John S. Mattick   FEBS LETTERS

Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing

(2011) Y. Fu et al.   GENOME RESEARCH

The 3′-untranslated region length and AU-rich RNA location modulate RNA–protein interaction and translational control of β2-adrenergic receptor mRNA

(2011) Kothandharaman Subramaniam et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

Chaperone Hsp27 Modulates AUF1 Proteolysis and AU-Rich Element-Mediated mRNA Degradation

(2011) A. M. Knapinska et al.   MOLECULAR AND CELLULAR BIOLOGY

Hypoxia-inducible factor-1α mRNA: a new target for destabilization by tristetraprolin in endothelial cells

(2011) Sandrine Chamboredon et al.   MOLECULAR BIOLOGY OF THE CELL

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Poly(A)-binding proteins are functionally distinct and have essential roles during vertebrate development

(2011) B. Gorgoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Posttranscriptional activation of gene expression in Xenopus laevis oocytes by microRNA-protein complexes (microRNPs)

(2011) R. D. Mortensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trisomy-21 gene dosage over-expression of miRNAs results in the haploinsufficiency of specific target proteins

(2011) Terry S. Elton et al.   RNA Biology

Pseudogenes: Pseudo-functional or key regulators in health and disease?

(2011) R. C. Pink et al.   RNA

Long noncoding RNAs in cell biology

(2011) Michael B. Clark et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The central role of RNA in the genetic programming of complex organisms

(2010) John S. Mattick   ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

Natural antisense transcripts regulate gene expression in an epigenetic manner

(2010) Wen-Yu Su et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Expression of oestrogen receptor β isoforms is regulated by transcriptional and post-transcriptional mechanisms

(2010) Laura Smith et al.   BIOCHEMICAL JOURNAL

Regulated and quality-control mRNA turnover pathways in eukaryotes: Figure 1

(2010) Boris Reznik et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Upstream open reading frames: Molecular switches in (patho)physiology

(2010) Klaus Wethmar et al.   BIOESSAYS

Major role for mRNA stability in shaping the kinetics of gene induction

(2010) Ran Elkon et al.   BMC GENOMICS

Thy-1 mRNA destabilization by norepinephrine a 3′ UTR cAMP responsive decay element and involves RNA binding proteins

(2010) Melissa D. LaJevic et al.   BRAIN BEHAVIOR AND IMMUNITY

RNA and transcriptional modulation of gene expression

(2010) Peter G. Hawkins et al.   CELL CYCLE

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

(2010) Satu Nahkuri et al.   CELL CYCLE

Polyadenylation: alternative lifestyles of the A-rich (and famous?)

(2010) Alexa M Dickson et al.   EMBO JOURNAL

5'-3'-UTR interactions regulate p53 mRNA translation and provide a target for modulating p53 induction after DNA damage

(2010) J. Chen et al.   GENES & DEVELOPMENT

Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells

(2010) M. Dejosez et al.   GENES & DEVELOPMENT

Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

(2010) Courtney C. Babbitt et al.   Genome Biology and Evolution

Alternative Ways to Think about Cellular Internal Ribosome Entry

(2010) Wendy V. Gilbert   JOURNAL OF BIOLOGICAL CHEMISTRY

Expression of miR-33 from anSREBP2Intron Inhibits Cholesterol Export and Fatty Acid Oxidation

(2010) Isabelle Gerin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Involvement of the 3′-untranslated region of the brain-derived neurotrophic factor gene in activity-dependent mRNA stabilization

(2010) Mamoru Fukuchi et al.   JOURNAL OF NEUROCHEMISTRY

Biological functions of microRNAs: a review

(2010) Yong Huang et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

The structure of the 5′-untranslated region of mammalian poly(A) polymerase-α mRNA suggests a mechanism of translational regulation

(2010) Aikaterini Rapti et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

An Upstream Open Reading Frame and the Context of the Two AUG Codons Affect the Abundance of Mitochondrial and Nuclear RNase H1

(2010) Y. Suzuki et al.   MOLECULAR AND CELLULAR BIOLOGY

The 5′-7-Methylguanosine Cap on Eukaryotic mRNAs Serves Both to Stimulate Canonical Translation Initiation and to Block an Alternative Pathway

(2010) Sarah F. Mitchell et al.   MOLECULAR CELL

Cap- and IRES-independent scanning mechanism of translation initiation as an alternative to the concept of cellular IRESs

(2010) Ivan N. Shatsky et al.   MOLECULES AND CELLS

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

(2010) Laura Poliseno et al.   NATURE

Tomio Tada 1934–2010

(2010) Masaru Taniguchi   NATURE IMMUNOLOGY

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MicroRNAs – targeting and target prediction

(2010) Takaya Saito et al.   New Biotechnology

A G-quadruplex structure within the 5′-UTR of TRF2 mRNA represses translation in human cells

(2010) Dennis Gomez et al.   NUCLEIC ACIDS RESEARCH

5'-UTR G-quadruplex structures acting as translational repressors

(2010) J.-D. Beaudoin et al.   NUCLEIC ACIDS RESEARCH

Expression of distinct RNAs from 3′ untranslated regions

(2010) Tim R. Mercer et al.   NUCLEIC ACIDS RESEARCH

Systematic Analysis of Cis-Elements in Unstable mRNAs Demonstrates that CUGBP1 Is a Key Regulator of mRNA Decay in Muscle Cells

(2010) Jerome E. Lee et al.   PLoS One

Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution

(2010) Pawandeep Dhami et al.   PLoS One

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

RNA regulation of epigenetic processes

(2009) John S. Mattick et al.   BIOESSAYS

Role of 5′- and 3′-untranslated regions of mRNAs in human diseases

(2009) Sangeeta Chatterjee et al.   BIOLOGY OF THE CELL

Evolution of alternative and constitutive regions of mammalian 5'UTRs

(2009) Alissa M Resch et al.   BMC GENOMICS

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Epigenetics: heterochromatin meets RNAi

(2009) Ingela Djupedal et al.   CELL RESEARCH

Riboactivators: Transcription activation by noncoding RNA

(2009) Aseem Z. Ansari   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

MicroRNA control of muscle development and disease

(2009) Andrew H Williams et al.   CURRENT OPINION IN CELL BIOLOGY

Toward a structural understanding of IRES RNA function

(2009) Megan E Filbin et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PKCη confers protection against apoptosis by inhibiting the pro-apoptotic JNK activity in MCF-7 cells

(2009) Noa Rotem-Dai et al.   EXPERIMENTAL CELL RESEARCH

A potent enhancer element in the 5′-UTR intron is crucial for transcriptional regulation of the human ubiquitin C gene

(2009) Marzia Bianchi et al.   GENE

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites

(2009) I. Lee et al.   GENOME RESEARCH

Eukaryotic snoRNAs: A paradigm for gene expression flexibility

(2009) Giorgio Dieci et al.   GENOMICS

Additional layers of gene regulatory complexity from recently discovered microRNA mechanisms

(2009) Clark D. Jeffries et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Poly(A) Tail Length Is Controlled by the Nuclear Poly(A)-binding Protein Regulating the Interaction between Poly(A) Polymerase and the Cleavage and Polyadenylation Specificity Factor

(2009) Uwe Kühn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Small but influential: the role of microRNAs on gene regulatory network and 3′UTR evolution

(2009) Rui Zhang et al.   Journal of Genetics and Genomics

Non-coding RNAs: regulators of disease

(2009) Ryan J Taft et al.   JOURNAL OF PATHOLOGY

Translational Control of Protein Kinase C  by Two Upstream Open Reading Frames

(2009) H. Raveh-Amit et al.   MOLECULAR AND CELLULAR BIOLOGY

Efficient cap-dependent translation of mammalian mRNAs with long and highly structured 5′-untranslated regions in vitro and in vivo

(2009) S. E. Dmitriev et al.   MOLECULAR BIOLOGY

Evolutionary Origin and Functions of Retrogene Introns

(2009) M. Fablet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Loss-of-function mutations of an inhibitory upstream ORF in the human hairless transcript cause Marie Unna hereditary hypotrichosis

(2009) Yaran Wen et al.   NATURE GENETICS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs

(2009) Shuo Gu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Alternative polyadenylation variants of the RNA binding protein, HuR: abundance, role of AU-rich elements and auto-Regulation

(2009) Wijdan Al-Ahmadi et al.   NUCLEIC ACIDS RESEARCH

RNA-Directed Transcriptional Gene Silencing and Activation in Human Cells

(2009) Kevin V. Morris   OLIGONUCLEOTIDES

Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types

(2009) Zhe Ji et al.   PLoS One

Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

(2009) Z. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factors mediate long-range enhancer-promoter interactions

(2009) I. K. Nolis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

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

Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus

(2009) C. J. Ott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of post-transcriptional RNA processing and plasmid vector sequences on transient transgene expression in zebrafish

(2009) Sumantra Chatterjee et al.   TRANSGENIC RESEARCH

To localize or not to localize: mRNA fate is in 3′UTR ends

(2009) Catia Andreassi et al.   TRENDS IN CELL BIOLOGY

A global view of genomic information – moving beyond the gene and the master regulator

(2009) John S. Mattick et al.   TRENDS IN GENETICS

Regulation of Translational Efficiency by Disparate5′-UTRs of PPARγSplice Variants

(2009) Shawn McClelland et al.   PPAR Research

A Single SNP in an Evolutionary Conserved Region within Intron 86 of the HERC2 Gene Determines Human Blue-Brown Eye Color

(2008) Richard A. Sturm et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Post-transcriptional regulation of gene expression by alternative 5′-untranslated regions in carcinogenesis

(2008) Laura Smith   BIOCHEMICAL SOCIETY TRANSACTIONS

Nucleolin Stabilizes Bcl-XL Messenger RNA in Response to UVA Irradiation

(2008) J. Zhang et al.   CANCER RESEARCH

miR-192 Regulates Dihydrofolate Reductase and Cellular Proliferation through the p53-microRNA Circuit

(2008) B. Song et al.   CLINICAL CANCER RESEARCH

The RNA polymerase II core promoter — the gateway to transcription

(2008) Tamar Juven-Gershon et al.   CURRENT OPINION IN CELL BIOLOGY

Alternative promoter use in eye development: the complex role and regulation of the transcription factor MITF

(2008) K. Bharti et al.   DEVELOPMENT

Long intronic noncoding RNA transcription: Expression noise or expression choice?

(2008) Rodrigo Louro et al.   GENOMICS

RNAs as extracellular signaling molecules

(2008) Marcel E Dinger et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Conserved GU-Rich Elements Mediate mRNA Decay by Binding to CUG-Binding Protein 1

(2008) Irina A. Vlasova et al.   MOLECULAR CELL

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Human uniqueness: genome interactions with environment, behaviour and culture

(2008) Ajit Varki et al.   NATURE REVIEWS GENETICS

Endogenous small interfering RNAs in animals

(2008) Katsutomo Okamura et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic β-actin gene

(2008) Tanay Ghosh et al.   NUCLEIC ACIDS RESEARCH

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes

(2008) Johanna Eddy et al.   NUCLEIC ACIDS RESEARCH

Longer First Introns Are a General Property of Eukaryotic Gene Structure

(2008) Keith R. Bradnam et al.   PLoS One

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Rapidly regulated genes are intron poor

(2008) Daniel C. Jeffares et al.   TRENDS IN GENETICS

The functional consequences of alternative promoter use in mammalian genomes

(2008) Ramana V. Davuluri et al.   TRENDS IN GENETICS

RNA editing, DNA recoding and the evolution of human cognition

(2008) John S. Mattick et al.   TRENDS IN NEUROSCIENCES

Structure and function of HCV IRES domains

(2008) Peter J. Lukavsky   VIRUS RESEARCH

Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region

(2008) Andrea B Eberle et al.   PLOS BIOLOGY

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

(2007) E. Torarinsson et al.   GENOME RESEARCH