Architecture and dynamics of overlapped RNA regulatory networks

Recurrent rewiring and emergence of RNA regulatory networks

(2017) Daniel Wilinski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins

(2016) Aoife C. McMahon et al.   CELL

The PUF binding landscape in metazoan germ cells

(2016) Aman Prasad et al.   RNA

The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion

(2015) Guramrit Singh et al.   Annual Review of Biochemistry

Conditional regulation of Puf1p, Puf4p, and Puf5p activity alters YHB1 mRNA stability for a rapid response to toxic nitric oxide stress in yeast

(2015) Joseph Russo et al.   MOLECULAR BIOLOGY OF THE CELL

Protein-RNA networks revealed through covalent RNA marks

(2015) Christopher P Lapointe et al.   NATURE METHODS

Target selection by natural and redesigned PUF proteins

(2015) Douglas F. Porter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA regulatory networks diversified through curvature of the PUF protein scaffold

(2015) Daniel Wilinski et al.   Nature Communications

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

(2015) Gregory J. Hogan et al.   PLOS BIOLOGY

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

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

(2014) Marvin Jens et al.   NATURE REVIEWS GENETICS

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

(2013) Shatakshi Pandit et al.   MOLECULAR CELL

Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels

(2013) Mai Sun et al.   MOLECULAR CELL

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

(2013) Hong Han et al.   NATURE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

How cells get the message: dynamic assembly and function of mRNA–protein complexes

(2013) Michaela Müller-McNicoll et al.   NATURE REVIEWS GENETICS

Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins

(2012) Eric T. Wang et al.   CELL

Pumilio 1 Suppresses Multiple Activators of p53 to Safeguard Spermatogenesis

(2012) Dong Chen et al.   CURRENT BIOLOGY

A Eukaryotic Translation Initiation Factor 4E-Binding Protein Promotes mRNA Decapping and Is Required for PUF Repression

(2012) N. H. Blewett et al.   MOLECULAR AND CELLULAR BIOLOGY

FMRP targets distinct mRNA sequence elements to regulate protein expression

(2012) Manuel Ascano et al.   NATURE

Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site

(2012) C. T. Valley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity

(2012) Zachary T. Campbell et al.   Cell Reports

FungiDB: an integrated functional genomics database for fungi

(2011) J. E. Stajich et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Markus Hafner et al.   CELL

PUF3 Acceleration of Deadenylation in Vivo Can Operate Independently of CCR4 Activity, Possibly Involving Effects on the PAB1–mRNP Structure

(2010) Darren Lee et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator

(2010) Aaron M. Kershner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PUF proteins: repression, activation and mRNA localization

(2010) Tara Quenault et al.   TRENDS IN CELL BIOLOGY

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs

(2009) D. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs

(2008) Fumihito Miura et al.   BMC GENOMICS

Ribonomic Analysis of Human Pum1 Reveals cis-trans Conservation across Species despite Evolution of Diverse mRNA Target Sets

(2008) A. R. Morris et al.   MOLECULAR AND CELLULAR BIOLOGY

Multifunctional deadenylase complexes diversify mRNA control

(2008) Aaron C. Goldstrohm et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p

(2008) Matthew T Miller et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System

(2008) Alessia Galgano et al.   PLoS One

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