Competition between target sites of regulators shapes post-transcriptional gene regulation

The Transcription Factor Titration Effect Dictates Level of Gene Expression

(2014) Robert C. Brewster et al.   CELL

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism

(2014) M. Stoeckius et al.   EMBO JOURNAL

Cnidarian microRNAs frequently regulate targets by cleavage

(2014) Y. Moran et al.   GENOME RESEARCH

A Feedforward Regulatory Loop between HuR and the Long Noncoding RNA linc-MD1 Controls Early Phases of Myogenesis

(2014) Ivano Legnini et al.   MOLECULAR CELL

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions

(2014) Stefanie Grosswendt et al.   MOLECULAR CELL

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

(2014) Rémy Denzler et al.   MOLECULAR CELL

Competitive Endogenous RNAs Cannot Alter MicroRNA Function In Vivo

(2014) Jennifer A. Broderick et al.   MOLECULAR CELL

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

Nanophotonic trapping for precise manipulation of biomolecular arrays

(2014) Mohammad Soltani et al.   Nature Nanotechnology

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Differential protein occupancy profiling of the mRNA transcriptome

(2014) Markus Schueler et al.   GENOME BIOLOGY

RNA Protein Interaction in Neurons

(2013) Robert B. Darnell   Annual Review of Neuroscience

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

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Regulation of maternal Wnt mRNA translation in C. elegans embryos

(2013) M. Oldenbroek et al.   DEVELOPMENT

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

(2013) S. Lianoglou et al.   GENES & DEVELOPMENT

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

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

Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments

(2013) U. Ala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation

(2013) Robin Graf et al.   RNA Biology

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

(2013) M. Hafner et al.   RNA

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

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

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

(2012) Alfredo Castello et al.   CELL

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

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries

(2012) Gavriel Mullokandov et al.   NATURE METHODS

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

The Local Transcriptome in the Synaptic Neuropil Revealed by Deep Sequencing and High-Resolution Imaging

(2012) Iván J. Cajigas et al.   NEURON

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs

(2012) Julien Roux et al.   NUCLEIC ACIDS RESEARCH

A Molecular Link between miRISCs and Deadenylases Provides New Insight into the Mechanism of Gene Silencing by MicroRNAs

(2012) J. E. Braun et al.   Cold Spring Harbor Perspectives in Biology

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

(2011) Pavel Sumazin et al.   CELL

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

miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA

(2011) Thomas B Hansen et al.   EMBO JOURNAL

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

(2011) S. Islam et al.   GENOME RESEARCH

microRNAs and the Operon Paper

(2011) Nikolaus Rajewsky   JOURNAL OF MOLECULAR BIOLOGY

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

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

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

miRNA repression involves GW182-mediated recruitment of CCR4–NOT through conserved W-containing motifs

(2011) Marina Chekulaeva et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

doRiNA: a database of RNA interactions in post-transcriptional regulation

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-wide analysis of protein–RNA interactions using high-throughput sequencing

(2011) Miha Milek et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

RNA Granules in Germ Cells

(2011) E. Voronina et al.   Cold Spring Harbor Perspectives in Biology

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

(2011) Matteo Osella et al.   PLoS Computational Biology

Identification of RNA-protein interaction networks using PAR-CLIP

(2011) Manuel Ascano et al.   Wiley Interdisciplinary Reviews-RNA

SnapShot: Key Numbers in Biology

(2010) Uri Moran et al.   CELL

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

(2010) Markus Hafner et al.   CELL

Emerging Roles for Natural MicroRNA Sponges

(2010) Margaret S. Ebert et al.   CURRENT BIOLOGY

A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1

(2010) Jane E Wright et al.   EMBO JOURNAL

Target mRNA abundance dilutes microRNA and siRNA activity

(2010) Aaron Arvey et al.   Molecular Systems Biology

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

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MicroRNA sponges: Progress and possibilities

(2010) M. S. Ebert et al.   RNA

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

(2010) D. Cazalla et al.   SCIENCE

Target RNA-Directed Trimming and Tailing of Small Silencing RNAs

(2010) S. L. Ameres et al.   SCIENCE

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

(2010) Robert B. Darnell   Wiley Interdisciplinary Reviews-RNA

mRNA Localization: Gene Expression in the Spatial Dimension

(2009) Kelsey C. Martin et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Redefining MicroRNA Targets

(2009) Hervé Seitz   CURRENT BIOLOGY

Gene expression during the oocyte-to-embryo transition in mammals

(2009) Alexei V. Evsikov et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

Erratum: Corrigendum: Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

(2009) Aly A Khan et al.   NATURE BIOTECHNOLOGY

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs

(2009) E. Lanet et al.   PLANT CELL

Neuron-type specific regulation of a 3'UTR through redundant and combinatorially acting cis-regulatory elements

(2009) D. Didiano et al.   RNA

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

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

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes

(2008) S. Hellwig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY