The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1.

PubWeight™: 1.66‹?› | Rank: Top 3%

🔗 View Article (PMC 3236499)

Published in Curr Biol on November 03, 2011

Authors

Bo W Han1, Jui-Hung Hung, Zhiping Weng, Phillip D Zamore, Stefan L Ameres

Author Affiliations

1: Howard Hughes Medical Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

Articles citing this

Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol (2013) 3.80

The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila. Nature (2012) 2.94

Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell (2012) 1.57

MicroRNA biogenesis: regulating the regulators. Crit Rev Biochem Mol Biol (2012) 1.41

MicroRNAs and neurodegeneration: role and impact. Trends Cell Biol (2012) 1.38

Regulation of small RNA stability: methylation and beyond. Cell Res (2012) 1.33

Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs. Cell Rep (2013) 1.28

Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA (2011) 1.20

Uridylation of miRNAs by hen1 suppressor1 in Arabidopsis. Curr Biol (2012) 1.19

Degradation of host microRNAs by poxvirus poly(A) polymerase reveals terminal RNA methylation as a protective antiviral mechanism. Cell Host Microbe (2012) 1.15

Complexity of murine cardiomyocyte miRNA biogenesis, sequence variant expression and function. PLoS One (2012) 1.15

Insect microRNAs: biogenesis, expression profiling and biological functions. Insect Biochem Mol Biol (2012) 1.15

Lower and upper stem-single-stranded RNA junctions together determine the Drosha cleavage site. Proc Natl Acad Sci U S A (2013) 1.12

Specific miRNA stabilization by Gld2-catalyzed monoadenylation. Cell Rep (2012) 1.08

One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing. Trends Biochem Sci (2016) 1.08

A highly expressed miR-101 isomiR is a functional silencing small RNA. BMC Genomics (2013) 1.05

YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res (2012) 1.04

Functional small RNAs are generated from select miRNA hairpin loops in flies and mammals. Genes Dev (2013) 1.01

Argonaute identity defines the length of mature mammalian microRNAs. Nucleic Acids Res (2012) 1.00

Zcchc11 uridylates mature miRNAs to enhance neonatal IGF-1 expression, growth, and survival. PLoS Genet (2012) 0.99

PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proc Natl Acad Sci U S A (2014) 0.99

Wolbachia infection modifies the profile, shuttling and structure of microRNAs in a mosquito cell line. PLoS One (2014) 0.99

Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes. PLoS One (2013) 0.99

A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis. Mol Cell (2014) 0.98

Transcriptome analysis of microRNAs in developing cerebral cortex of rat. BMC Genomics (2012) 0.96

MUT-16 promotes formation of perinuclear mutator foci required for RNA silencing in the C. elegans germline. Genes Dev (2012) 0.96

Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation. J Nucleic Acids (2012) 0.94

Identification and Functional Analysis of the Pre-piRNA 3' Trimmer in Silkworms. Cell (2016) 0.90

Impact of age-associated increase in 2'-O-methylation of miRNAs on aging and neurodegeneration in Drosophila. Genes Dev (2014) 0.88

The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans. Cell (2016) 0.87

The exonuclease Nibbler regulates age-associated traits and modulates piRNA length in Drosophila. Aging Cell (2015) 0.87

Target repression induced by endogenous microRNAs: large differences, small effects. PLoS One (2014) 0.87

Principles of miRNA-target regulation in metazoan models. Int J Mol Sci (2013) 0.86

Reconstitution of an Argonaute-dependent small RNA biogenesis pathway reveals a handover mechanism involving the RNA exosome and the exonuclease QIP. Mol Cell (2012) 0.86

Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Mol Cell (2015) 0.86

Distinctive profile of IsomiR expression and novel microRNAs in rat heart left ventricle. PLoS One (2013) 0.85

Sequence features of Drosha and Dicer cleavage sites affect the complexity of isomiRs. Int J Mol Sci (2015) 0.84

The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in Drosophila wing imaginal discs. RNA Biol (2015) 0.83

The 5'-3' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs. RNA Biol (2013) 0.82

Argonaute-dependent small RNAs derived from single-stranded, non-structured precursors. Front Genet (2014) 0.81

Loading and pre-loading processes generate a distinct siRNA population in Tetrahymena. Biochem Biophys Res Commun (2013) 0.80

Transcriptome analysis and systemic RNAi response in the African sweetpotato weevil (Cylas puncticollis, Coleoptera, Brentidae). PLoS One (2015) 0.80

Small RNAs meet their targets: when methylation defends miRNAs from uridylation. RNA Biol (2014) 0.80

Genetic and mechanistic diversity of piRNA 3'-end formation. Nature (2016) 0.80

The highly expressed 5'isomiR of hsa-miR-140-3p contributes to the tumor-suppressive effects of miR-140 by reducing breast cancer proliferation and migration. BMC Genomics (2016) 0.79

Intertwined pathways for Argonaute-mediated microRNA biogenesis in Drosophila. Nucleic Acids Res (2013) 0.79

Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3' ends in Drosophila. Development (2015) 0.79

Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences. Nucleic Acids Res (2015) 0.79

The possible impact of persistent virus infection on the function of the RNAi machinery in insects: a hypothesis. Front Physiol (2013) 0.77

Dengue virus infection alters post-transcriptional modification of microRNAs in the mosquito vector Aedes aegypti. Sci Rep (2015) 0.77

Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila. EMBO J (2016) 0.77

Role of the Trypanosoma brucei HEN1 family methyltransferase in small interfering RNA modification. Eukaryot Cell (2013) 0.76

Regulation of miRNA processing and miRNA mediated gene repression in cancer. Microrna (2014) 0.75

The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site. Cell Rep (2016) 0.75

Post-transcriptional control of miRNA abundance in Arabidopsis. Plant Signal Behav (2012) 0.75

Asian Citrus Psyllid RNAi Pathway - RNAi evidence. Sci Rep (2016) 0.75

Co-chaperone Hsp70/Hsp90-organizing protein (Hop) is required for transposon silencing and Piwi-interacting RNA (piRNA) biogenesis. J Biol Chem (2017) 0.75

Drosophila exoribonuclease nibbler is a tumor suppressor, acts within the RNA(i) machinery and is not enriched in the nuage during early oogenesis. Hereditas (2017) 0.75

Evolution of miRNA tailing by 3' terminal uridylyl transferases in Metazoa. Genome Biol Evol (2017) 0.75

Articles cited by this

MicroRNAs: target recognition and regulatory functions. Cell (2009) 92.17

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell (1993) 64.62

MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell (2007) 38.42

The nuclear RNase III Drosha initiates microRNA processing. Nature (2003) 35.49

Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell (1993) 33.79

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet (2008) 32.08

A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science (2001) 31.33

Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell (2001) 25.86

Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev (2001) 21.82

Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol (2009) 19.99

MicroRNA maturation: stepwise processing and subcellular localization. EMBO J (2002) 19.47

A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature (2007) 18.38

microRNA functions. Annu Rev Cell Dev Biol (2007) 15.74

Argonaute2, a link between genetic and biochemical analyses of RNAi. Science (2001) 15.32

Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12

Small silencing RNAs: an expanding universe. Nat Rev Genet (2009) 13.88

Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell (2004) 13.51

A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science (2001) 11.86

Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev (2004) 9.32

Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell (1999) 9.01

Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis. Curr Biol (2005) 5.99

A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature (2004) 5.57

miRNA profiling of naïve, effector and memory CD8 T cells. PLoS One (2007) 5.43

The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr Biol (2007) 5.35

The many pathways of RNA degradation. Cell (2009) 5.31

Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell (2007) 5.26

Pimet, the Drosophila homolog of HEN1, mediates 2'-O-methylation of Piwi- interacting RNAs at their 3' ends. Genes Dev (2007) 4.68

Sorting of Drosophila small silencing RNAs. Cell (2007) 4.67

Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet (2010) 4.27

A conserved 3'----5' exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell (1989) 4.15

Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature (2003) 4.09

Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA* strands in flies. Curr Biol (2008) 4.07

Genetic requirements for inheritance of RNAi in C. elegans. Science (2000) 4.04

Target RNA-directed trimming and tailing of small silencing RNAs. Science (2010) 3.98

Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res (2001) 3.88

A parsimonious model for gene regulation by miRNAs. Science (2011) 3.79

Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2. Nature (2010) 3.77

A genetic link between co-suppression and RNA interference in C. elegans. Nature (2000) 3.67

Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science (2008) 3.46

Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell (2009) 3.43

Hierarchical rules for Argonaute loading in Drosophila. Mol Cell (2009) 3.20

Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA (2009) 3.19

Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA (2005) 3.11

Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol Cell (2009) 3.02

A novel repeat-associated small interfering RNA-mediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the Drosophila ovary. J Virol (2006) 2.87

Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells. Curr Biol (2011) 2.53

Differential regulation of microRNA stability. RNA (2010) 2.24

In vitro analysis of RNA interference in Drosophila melanogaster. Methods (2003) 2.20

Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat Struct Mol Biol (2009) 2.01

Target-mediated protection of endogenous microRNAs in C. elegans. Dev Cell (2011) 1.74

Purification and characterization of Escherichia coli RNase T. J Biol Chem (1985) 1.68

Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli. Biochemistry (1999) 1.31

Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA (2010) 1.19

A 5'-uridine amplifies miRNA/miRNA* asymmetry in Drosophila by promoting RNA-induced silencing complex formation. Silence (2011) 1.08

Escherichia coli RNase D. Purification and structural characterization of a putative processing nuclease. J Biol Chem (1981) 1.01

Articles by these authors

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41

A microRNA in a multiple-turnover RNAi enzyme complex. Science (2002) 23.36

Asymmetry in the assembly of the RNAi enzyme complex. Cell (2003) 22.18

A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65

High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93

Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29

Small silencing RNAs: an expanding universe. Nat Rev Genet (2009) 13.88

A distinct small RNA pathway silences selfish genetic elements in the germline. Science (2006) 11.63

A biochemical framework for RNA silencing in plants. Genes Dev (2003) 9.95

Perspective: machines for RNAi. Genes Dev (2005) 9.37

Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell (2005) 9.35

Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science (2008) 8.62

microPrimer: the biogenesis and function of microRNA. Development (2005) 8.19

Sequence-specific inhibition of small RNA function. PLoS Biol (2004) 7.98

A protein sensor for siRNA asymmetry. Science (2004) 7.77

ZDOCK: an initial-stage protein-docking algorithm. Proteins (2003) 7.52

Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol (2004) 7.26

Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol (2005) 7.23

Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol Cell (2002) 6.43

Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res (2004) 6.31

MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. EMBO J (2004) 6.27

Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93

RNAi: nature abhors a double-strand. Curr Opin Genet Dev (2002) 5.74

The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67

The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr Biol (2007) 5.35

Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A (2006) 5.27

Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell (2007) 5.26

Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell (2010) 5.22

Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99

The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet (2008) 4.91

Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89

RISC assembly defects in the Drosophila RNAi mutant armitage. Cell (2004) 4.88

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80

Sorting of Drosophila small silencing RNAs. Cell (2007) 4.67

Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell (2009) 4.39

Modular recognition of RNA by a human pumilio-homology domain. Cell (2002) 4.17

Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep (2006) 4.15

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA* strands in flies. Curr Biol (2008) 4.07

Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res (2003) 3.99

Target RNA-directed trimming and tailing of small silencing RNAs. Science (2010) 3.98

Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol (2013) 3.80

The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr Biol (2004) 3.68

Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35

Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genet (2006) 3.23

Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA (2009) 3.19

Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell (2011) 3.19

The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell (2009) 3.13

Protein-Protein Docking Benchmark 2.0: an update. Proteins (2005) 3.13

Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins (2002) 2.95

A protein-protein docking benchmark. Proteins (2003) 2.90

MicroRNA biogenesis: drosha can't cut it without a partner. Curr Biol (2005) 2.85

ZRANK: reranking protein docking predictions with an optimized energy function. Proteins (2007) 2.79

Protein-protein docking benchmark version 4.0. Proteins (2010) 2.78

Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res (2009) 2.71

Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A (2005) 2.69

Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66

Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res (2010) 2.56

Protein-protein docking benchmark version 3.0. Proteins (2008) 2.54

Integrating statistical pair potentials into protein complex prediction. Proteins (2007) 2.53

The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol (2008) 2.51

Why do miRNAs live in the miRNP? Genes Dev (2002) 2.41

Transcription factor binding and modified histones in human bidirectional promoters. Genome Res (2007) 2.40

Finding functional sequence elements by multiple local alignment. Nucleic Acids Res (2004) 2.37

Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PLoS One (2011) 2.33

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res (2012) 2.32

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res (2002) 2.30

dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res (2006) 2.28

FAST: a novel protein structure alignment algorithm. Proteins (2005) 2.27

RDOCK: refinement of rigid-body protein docking predictions. Proteins (2003) 2.24

An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell (2013) 2.23

Unexpected role of interferon-γ in regulating neuronal connectivity and social behaviour. Nature (2016) 2.21

In vitro analysis of RNA interference in Drosophila melanogaster. Methods (2003) 2.20

Five siRNAs targeting three SNPs may provide therapy for three-quarters of Huntington's disease patients. Curr Biol (2009) 2.19

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol (2010) 2.15

CisML: an XML-based format for sequence motif detection software. Bioinformatics (2004) 2.13

Functional analysis of transcription factor binding sites in human promoters. Genome Biol (2012) 2.12

Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell (2012) 2.07

Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc Natl Acad Sci U S A (2010) 2.06

A novel shape complementarity scoring function for protein-protein docking. Proteins (2003) 2.03

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res (2007) 2.03

Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. Nat Methods (2008) 2.02

The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell (2012) 1.88

Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis. Aging Cell (2003) 1.88

The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins (2007) 1.85

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res (2004) 1.84