MicroRNA binding sites in the coding region of mRNAs: Extending the repertoire of post-transcriptional gene regulation

Poly(A)-tail profiling reveals an embryonic switch in translational control

(2014) Alexander O. Subtelny et al.   NATURE

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

(2013) J. Hausser et al.   GENOME RESEARCH

Tumor suppressor miR-375 regulates MYC expression via repression of CIP2A coding sequence through multiple miRNA–mRNA interactions

(2013) Hyun Min Jung et al.   MOLECULAR BIOLOGY OF THE CELL

Highly Complementary Target RNAs Promote Release of Guide RNAs from Human Argonaute2

(2013) Nabanita De et al.   MOLECULAR CELL

Timescales and bottlenecks in miRNA-dependent gene regulation

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

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3′ UTRs

(2013) David Zünd et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Searching the coding region for microRNA targets

(2013) R. M. Marin et al.   RNA

Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression

(2013) A. Brummer et al.   RNA

Functional microRNA targets in protein coding sequences

(2012) Martin Reczko et al.   BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

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

(2012) Julien Béthune et al.   EMBO REPORTS

RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans

(2012) M. Jovanovic et al.   GENOME RESEARCH

A conserved PUF–Ago–eEF1A complex attenuates translation elongation

(2012) Kyle Friend et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

(2012) F. Li et al.   PLANT CELL

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

Genome-Wide Analysis of GLD-1–Mediated mRNA Regulation Suggests a Role in mRNA Storage

(2012) Claudia Scheckel et al.   PLoS Genetics

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

(2011) Jennifer C. Darnell et al.   CELL

Highly Efficient miRNA-Mediated Reprogramming of Mouse and Human Somatic Cells to Pluripotency

(2011) Frederick Anokye-Danso et al.   Cell Stem Cell

Select microRNAs are essential for early development in the sea urchin

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

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs

(2011) M. Schnall-Levin et al.   GENOME RESEARCH

MicroRNAs Dysregulation in Human Malignant Pleural Mesothelioma

(2011) Veronica Balatti et al.   Journal of Thoracic Oncology

In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites

(2011) Anna-Carina Jungkamp et al.   MOLECULAR CELL

MicroRNAs 103 and 107 regulate insulin sensitivity

(2011) Mirko Trajkovski et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

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

(2011) Eric Huntzinger et al.   NATURE REVIEWS GENETICS

Specific sequence determinants of miR-15/107 microRNA gene group targets

(2011) Peter T. Nelson et al.   NUCLEIC ACIDS RESEARCH

MicroRNAs Differentially Expressed in Postnatal Aortic Development Downregulate Elastin via 3′ UTR and Coding-Sequence Binding Sites

(2011) Claus Eric Ott et al.   PLoS One

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

(2011) Zhuo Fang et al.   PLoS One

Proteome Half-Life Dynamics in Living Human Cells

(2011) E. Eden et al.   SCIENCE

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

(2011) Matteo Osella et al.   PLoS Computational Biology

TargetSpy: a supervised machine learning approach for microRNA target prediction

(2010) Martin Sturm et al.   BMC BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

Translational control in the C. elegans hermaphrodite germ line

(2010) Hilary Racher et al.   GENOME

mRNA turnover rate limits siRNA and microRNA efficacy

(2010) Erik Larsson et al.   Molecular Systems Biology

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

MicroRNA-181a modulates gene expression of zinc finger family members by directly targeting their coding regions

(2010) Shenglin Huang et al.   NUCLEIC ACIDS RESEARCH

miR-24 Regulates Apoptosis by Targeting the Open Reading Frame (ORF) Region of FAF1 in Cancer Cells

(2010) Wenming Qin et al.   PLoS One

Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs

(2010) M. Schnall-Levin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2009) Christine Mayr et al.   CELL

Characterization of B- and T-lineage acute lymphoblastic leukemia by integrated analysis of MicroRNA and mRNA expression profiles

(2009) Valerio Fulci et al.   GENES CHROMOSOMES & CANCER

Mammalian Staufen 1 is recruited to stress granules and impairs their assembly

(2009) M. G. Thomas et al.   JOURNAL OF CELL SCIENCE

Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation

(2009) A R R Forrest et al.   LEUKEMIA

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

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

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

(2009) Caroline C. Friedel et al.   NUCLEIC ACIDS RESEARCH

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

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

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

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

(2008) Yvonne Tay et al.   NATURE

miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes

(2008) Q. Liu et al.   NUCLEIC ACIDS RESEARCH

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

A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence

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

miR-148 targets human DNMT3b protein coding region

(2008) A. M. Duursma et al.   RNA

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

(2008) R. Sandberg et al.   SCIENCE