Identification and consequences of miRNA–target interactions — beyond repression of gene expression

Identifying mRNA sequence elements for target recognition by human Argonaute proteins

(2014) J. Li et al.   GENOME RESEARCH

Widespread context dependency of microRNA-mediated regulation

(2014) F. Erhard et al.   GENOME RESEARCH

Global Analyses of the Effect of Different Cellular Contexts on MicroRNA Targeting

(2014) Jin-Wu Nam et al.   MOLECULAR CELL

Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance

(2014) Rémy Denzler et al.   MOLECULAR CELL

MicroRNAs as a Selective Channel of Communication between Competing RNAs: a Steady-State Theory

(2013) Matteo Figliuzzi et al.   BIOPHYSICAL JOURNAL

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Online resources for miRNA analysis

(2013) Ioannis S. Vlachos et al.   CLINICAL BIOCHEMISTRY

Endogenous miRNA Sponge lincRNA-RoR Regulates Oct4, Nanog, and Sox2 in Human Embryonic Stem Cell Self-Renewal

(2013) Yue Wang et al.   DEVELOPMENTAL CELL

The rough endoplasmatic reticulum is a central nucleation site of siRNA-mediated RNA silencing

(2013) Lukas Stalder et al.   EMBO JOURNAL

Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation

(2013) J. Hausser et al.   GENOME RESEARCH

Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP

(2013) James P. Broughton et al.   METHODS

The Imprinted H19 LncRNA Antagonizes Let-7 MicroRNAs

(2013) Amanda N. Kallen et al.   MOLECULAR CELL

Timescales and bottlenecks in miRNA-dependent gene regulation

(2013) J. Hausser et al.   Molecular Systems Biology

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

MicroRNA target site identification by integrating sequence and binding information

(2013) William H Majoros et al.   NATURE METHODS

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets

(2013) Mohsen Khorshid et al.   NATURE METHODS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Modelling Competing Endogenous RNA Networks

(2013) Carla Bosia et al.   PLoS One

Genome-wide identification of translationally inhibited and degraded miR-155 targets using RNA-interacting protein-IP

(2013) Jan Meier et al.   RNA Biology

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

(2013) J. Mohammed et al.   RNA

Translational Repression and eIF4A2 Activity Are Critical for MicroRNA-Mediated Gene Regulation

(2013) H. A. Meijer et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

PARma: identification of microRNA target sites in AGO-PAR-CLIP data

(2013) Florian Erhard et al.   GENOME BIOLOGY

Functional microRNA targets in protein coding sequences

(2012) Martin Reczko et al.   BIOINFORMATICS

Roles for MicroRNAs in Conferring Robustness to Biological Processes

(2012) Margaret S. Ebert et al.   CELL

Argonaute Divides Its RNA Guide into Domains with Distinct Functions and RNA-Binding Properties

(2012) Liang Meng Wee et al.   CELL

Kinetic analysis reveals successive steps leading to miRNA-mediated silencing in mammalian cells

(2012) Julien Béthune et al.   EMBO REPORTS

Quantitative functions of Argonaute proteins in mammalian development

(2012) D. Wang et al.   GENES & DEVELOPMENT

Transcriptome-wide miR-155 Binding Map Reveals Widespread Noncanonical MicroRNA Targeting

(2012) Gabriel B. Loeb et al.   MOLECULAR CELL

Maintenance of muscle stem-cell quiescence by microRNA-489

(2012) Tom H. Cheung et al.   NATURE

An alternative mode of microRNA target recognition

(2012) Sung Wook Chi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

miRNA-Mediated Gene Silencing by Translational Repression Followed by mRNA Deadenylation and Decay

(2012) S. Djuranovic et al.   SCIENCE

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

A Resource for the Conditional Ablation of microRNAs in the Mouse

(2012) Chong Yon Park et al.   Cell Reports

Degradation of Cellular miR-27 by a Novel, Highly Abundant Viral Transcript Is Important for Efficient Virus Replication In Vivo

(2012) Lisa Marcinowski et al.   PLoS Pathogens

Select microRNAs are essential for early development in the sea urchin

(2011) Jia L. Song et al.   DEVELOPMENTAL BIOLOGY

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

MicroRNAs can generate thresholds in target gene expression

(2011) Shankar Mukherji et al.   NATURE GENETICS

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

Gene silencing by microRNAs: contributions of translational repression and mRNA decay

(2011) Eric Huntzinger et al.   NATURE REVIEWS GENETICS

Experimental strategies for microRNA target identification

(2011) D. W. Thomson et al.   NUCLEIC ACIDS RESEARCH

The Impact of miRNA Target Sites in Coding Sequences and in 3′UTRs

(2011) Zhuo Fang et al.   PLoS One

The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering

(2011) Matteo Osella et al.   PLoS Computational Biology

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Signatures of RNA binding proteins globally coupled to effective microRNA target sites

(2010) A. Jacobsen et al.   GENOME RESEARCH

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

mRNA turnover rate limits siRNA and microRNA efficacy

(2010) Erik Larsson et al.   Molecular Systems Biology

Target mRNA abundance dilutes microRNA and siRNA activity

(2010) Aaron Arvey et al.   Molecular Systems Biology

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

A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility

(2010) Martijn Kedde et al.   NATURE CELL BIOLOGY

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

(2010) Dimitrios G Zisoulis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Down-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA

(2010) D. Cazalla et al.   SCIENCE

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

Lost in translation: an assessment and perspective for computational microRNA target identification

(2009) Panagiotis Alexiou et al.   BIOINFORMATICS

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

HuR recruits let-7/RISC to repress c-Myc expression

(2009) H. H. Kim et al.   GENES & DEVELOPMENT

Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets

(2009) J. Hausser et al.   GENOME RESEARCH

Genome-wide survey of microRNA–transcription factor feed-forward regulatory circuits in human

(2009) Angela Re et al.   Molecular BioSystems

Enhancement of the Seed-Target Recognition Step in RNA Silencing by a PIWI/MID Domain Protein

(2009) James S. Parker et al.   MOLECULAR CELL

miR-24 Inhibits Cell Proliferation by Targeting E2F2, MYC, and Other Cell-Cycle Genes via Binding to “Seedless” 3′UTR MicroRNA Recognition Elements

(2009) Ashish Lal et al.   MOLECULAR CELL

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

(2009) Yanli Wang et al.   NATURE

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

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

Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer

(2009) Young-Kook Kim et al.   NUCLEIC ACIDS RESEARCH

miR-375 maintains normal pancreatic  - and  -cell mass

(2009) M. N. Poy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dicer Ablation Affects Antibody Diversity and Cell Survival in the B Lymphocyte Lineage

(2008) Sergei B. Koralov et al.   CELL

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Most mammalian mRNAs are conserved targets of microRNAs

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

Molecular Titration and Ultrasensitivity in Regulatory Networks

(2008) Nicolas E. Buchler et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Structure of the guide-strand-containing argonaute silencing complex

(2008) Yanli Wang et al.   NATURE

A skin microRNA promotes differentiation by repressing ‘stemness’

(2008) Rui Yi et al.   NATURE

MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation

(2008) Yvonne Tay et al.   NATURE

The impact of target site accessibility on the design of effective siRNAs

(2008) Hakim Tafer et al.   NATURE BIOTECHNOLOGY

MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells

(2008) Lasse Sinkkonen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases

(2008) Roberta Benetti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells

(2008) Thomas Ohrt et al.   NUCLEIC ACIDS RESEARCH

miR-17-92 cluster accelerates adipocyte differentiation by negatively regulating tumor-suppressor Rb2/p130

(2008) Q. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure

(2008) J.-F. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA