Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

m 6 A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

(2017) Shengdong Ke et al.   GENES & DEVELOPMENT

Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition

(2017) Vladimir Despic et al.   GENOME RESEARCH

A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation

(2017) Michal Rabani et al.   MOLECULAR CELL

m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition

(2017) Boxuan Simen Zhao et al.   NATURE

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43

(2017) Gregor Rot et al.   Cell Reports

High-throughput discovery of post-transcriptional cis-regulatory elements

(2016) Erin M. Wissink et al.   BMC GENOMICS

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition

(2016) Ariel A Bazzini et al.   EMBO JOURNAL

The mRNA-bound proteome of the early fly embryo

(2016) Hans-Hermann Wessels et al.   GENOME RESEARCH

Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish

(2016) Yuichiro Mishima et al.   MOLECULAR CELL

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

RESA identifies mRNA-regulatory sequences at high resolution

(2016) Valeria Yartseva et al.   NATURE METHODS

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

RNA-binding proteins ZFP36L1 and ZFP36L2 promote cell quiescence

(2016) A. Galloway et al.   SCIENCE

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

(2016) Yalin Liao et al.   Cell Reports

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

(2016) Claudia Scheckel et al.   eLife

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt

(2015) Jernej Murn et al.   GENES & DEVELOPMENT

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

(2015) Miguel A Moreno-Mateos et al.   NATURE METHODS

Systematic analysis of theHmga23′ UTR identifies many independent regulatory sequences and a novel interaction between distal sites

(2015) Katla Kristjánsdóttir et al.   RNA

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

(2015) Heidi Theil Hansen et al.   GENOME BIOLOGY

Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression

(2015) Jorge Boucas et al.   PLoS One

Zygotic Genome Activation During the Maternal-to-Zygotic Transition

(2014) Miler T. Lee et al.   Annual Review of Cell and Developmental Biology

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem 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

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3′ processing

(2014) Serena L. Chan et al.   GENES & DEVELOPMENT

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

(2014) Alexander O. Subtelny et al.   NATURE

Massively parallel functional annotation of 3′ untranslated regions

(2014) Wenxue Zhao et al.   NATURE BIOTECHNOLOGY

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing–RNA affinity profiling

(2014) Jacob M Tome et al.   NATURE METHODS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Systematic Identification of Regulatory Elements in Conserved 3′ UTRs of Human Transcripts

(2014) Panos Oikonomou et al.   Cell Reports

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Reply to: "On the robustness of germ cell migration and microRNA-mediated regulation of chemokine signaling"

(2013) Alison A Staton et al.   NATURE GENETICS

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

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

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Alfredo Castello et al.   CELL

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

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

Dectin-1 is an extracellular pathogen sensor for the induction and processing of IL-1β via a noncanonical caspase-8 inflammasome

(2012) Sonja I Gringhuis et al.   NATURE IMMUNOLOGY

Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs

(2012) Xin Lai et al.   NUCLEIC ACIDS RESEARCH

HuR protein attenuates miRNA-mediated repression by promoting miRISC dissociation from the target RNA

(2012) Pradipta Kundu et al.   NUCLEIC ACIDS RESEARCH

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

(2012) A. A. Bazzini et al.   SCIENCE

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

(2012) Minna-Liisa Änkö et al.   GENOME BIOLOGY

Transcript clearance during the maternal-to-zygotic transition

(2011) Claudia B Walser et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

A Systematic Analysis of the 3′UTR of HNF4A mRNA Reveals an Interplay of Regulatory Elements Including miRNA Target Sites

(2011) Andrea Wirsing et al.   PLoS One

Phonon-tunnelling dissipation in mechanical resonators

(2011) Garrett D. Cole et al.   Nature Communications

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

(2010) Markus Hafner et al.   CELL

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

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

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

A Novel Role for MAPKAPK2 in Morphogenesis during Zebrafish Development

(2009) Beth A. Holloway et al.   PLoS Genetics

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways

(2008) M. P. van der Brug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution in situ hybridization to whole-mount zebrafish embryos

(2007) Christine Thisse et al.   Nature Protocols