Structural and functional basis of mammalian microRNA biogenesis by Dicer

Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB

(2022) Karina Jouravleva et al.   MOLECULAR CELL

A Glimpse of “Dicer Biology” Through the Structural and Functional Perspective

(2021) Sneha Paturi et al.   Frontiers in Molecular Biosciences

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

MirGeneDB 2.1: toward a complete sampling of all major animal phyla

(2021) Bastian Fromm et al.   NUCLEIC ACIDS RESEARCH

Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

(2021) Qian Wang et al.   SCIENCE

Chronic Dicer1 deficiency promotes atrophic and neovascular outer retinal pathologies in mice

(2020) Charles B. Wright et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

microRNA strand selection: Unwinding the rules

(2020) Jeffrey C. Medley et al.   Wiley Interdisciplinary Reviews-RNA

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components

(2019) Federico Marini et al.   BMC BIOINFORMATICS

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

(2019) Tristan Bepler et al.   NATURE METHODS

Restricted and non-essential redundancy of RNAi and piRNA pathways in mouse oocytes

(2019) Eliska Taborska et al.   PLoS Genetics

Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate

(2018) Zhongmin Liu et al.   CELL

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

Functional Redundancy of DICER Cofactors TARBP2 and PRKRA During Murine Embryogenesis Does Not Involve miRNA Biogenesis

(2018) Sri Ramulu N. Pullagura et al.   GENETICS

Functional Redundancy of DICER Cofactors TARBP2 and PRKRA During Murine Embryogenesis Does Not Involve miRNA Biogenesis

(2018) Sri Ramulu N. Pullagura et al.   GENETICS

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Increased Affinity for RNA Targets Evolved Early in Animal and Plant Dicer Lineages through Different Structural Mechanisms

(2017) Haiyan Jia et al.   MOLECULAR BIOLOGY AND EVOLUTION

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

Dicer uses distinct modules for recognizing dsRNA termini

(2017) Niladri K. Sinha et al.   SCIENCE

Gctf: Real-time CTF determination and correction

(2016) Kai Zhang   JOURNAL OF STRUCTURAL BIOLOGY

Dicer-TRBP Complex Formation Ensures Accurate Mammalian MicroRNA Biogenesis

(2015) Ross C. Wilson et al.   MOLECULAR CELL

Production of functional small interfering RNAs by an amino-terminal deletion mutant of human Dicer

(2015) Edward M. Kennedy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes

(2015) Paula Stein et al.   PLoS Genetics

A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer

(2014) Yuan Tian et al.   MOLECULAR CELL

Oligoasthenoteratozoospermia and Infertility in Mice Deficient for miR-34b/c and miR-449 Loci

(2014) Stefano Comazzetto et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

A Retrotransposon-Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes

(2013) Matyas Flemr et al.   CELL

ADAR1 Forms a Complex with Dicer to Promote MicroRNA Processing and RNA-Induced Gene Silencing

(2013) Hiromitsu Ota et al.   CELL

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Substrate-specific structural rearrangements of human Dicer

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

Multiple sensors ensure guide strand selection in human RNAi pathways

(2013) C. L. Noland et al.   RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Discovery of hundreds of mirtrons in mouse and human small RNA data

(2012) E. Ladewig et al.   GENOME RESEARCH

Birth and expression evolution of mammalian microRNA genes

(2012) J. Meunier et al.   GENOME RESEARCH

Cancer-associated somaticDICER1hotspot mutations cause defective miRNA processing and reverse-strand expression bias to predominantly mature 3p strands through loss of 5p strand cleavage

(2012) MS Anglesio et al.   JOURNAL OF PATHOLOGY

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

The molecular architecture of human Dicer

(2012) Pick-Wei Lau et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

The Many Faces of RNAi

(2011) René F. Ketting   DEVELOPMENTAL CELL

microRNA complements in deuterostomes: origin and evolution of microRNAs

(2011) Florent Campo-Paysaa et al.   EVOLUTION & DEVELOPMENT

Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease

(2011) Elif Sarinay Cenik et al.   MOLECULAR CELL

Dicer's Helicase Domain Discriminates dsRNA Termini to Promote an Altered Reaction Mode

(2011) Noah C. Welker et al.   MOLECULAR CELL

siRNA Repositioning for Guide Strand Selection by Human Dicer Complexes

(2011) Cameron L. Noland et al.   MOLECULAR CELL

Recognition of the pre-miRNA structure by Drosophila Dicer-1

(2011) Akihisa Tsutsumi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells

(2011) Jana Nejepinska et al.   NUCLEIC ACIDS RESEARCH

Structure of a Yeast RNase III dsRBD Complex with a Noncanonical RNA Substrate Provides New Insights into Binding Specificity of dsRBDs

(2011) Zhonghua Wang et al.   STRUCTURE

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove

(2010) Richard Stefl et al.   CELL

MicroRNA Activity Is Suppressed in Mouse Oocytes

(2010) Jun Ma et al.   CURRENT BIOLOGY

MicroRNA Function Is Globally Suppressed in Mouse Oocytes and Early Embryos

(2010) Nayoung Suh et al.   CURRENT BIOLOGY

SF1 and SF2 helicases: family matters

(2010) Margaret E Fairman-Williams et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

(2010) H. R. Chiang et al.   GENES & DEVELOPMENT

Analysis of microRNA knockouts in mice

(2010) C. Y. Park et al.   HUMAN MOLECULAR GENETICS

Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss

(2009) Ángeles Mencía et al.   NATURE GENETICS

Structure of the Human Dicer-TRBP Complex by Electron Microscopy

(2009) Pick-Wei Lau et al.   STRUCTURE

Autoinhibition of Human Dicer by Its Internal Helicase Domain

(2008) Enbo Ma et al.   JOURNAL OF MOLECULAR BIOLOGY

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE