Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Global identification of miRNAs and targets in Populus euphratica under salt stress

(2013) Bosheng Li et al.   PLANT MOLECULAR BIOLOGY

Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing

(2012) Md Shamimuzzaman et al.   BMC GENOMICS

A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa

(2012) Ting-Ting Liu et al.   Molecular Plant

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

(2012) Alexander Sherstnev et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing

(2012) Leighton Folkes et al.   NUCLEIC ACIDS RESEARCH

Cloning and Characterization of Maize miRNAs Involved in Responses to Nitrogen Deficiency

(2012) Meng Zhao et al.   PLoS One

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

(2012) Y. Harigaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts

(2011) Petya Zhelyazkova et al.   NUCLEIC ACIDS RESEARCH

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

(2011) Cameron P. Bracken et al.   NUCLEIC ACIDS RESEARCH

SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants

(2011) Yun Zheng et al.   NUCLEIC ACIDS RESEARCH

Short non-coding RNA fragments accumulating in chloroplasts: footprints of RNA binding proteins?

(2011) Hannes Ruwe et al.   NUCLEIC ACIDS RESEARCH

Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Smad Proteins Bind a Conserved RNA Sequence to Promote MicroRNA Maturation by Drosha

(2010) Brandi N. Davis et al.   MOLECULAR CELL

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

Transcriptome-wide identification of microRNA targets in rice

(2010) Yong-Fang Li et al.   PLANT JOURNAL

Site-specific binding of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts

(2009) Jeannette Pfalz et al.   EMBO JOURNAL

Molecular characterization of Arabidopsis thaliana PUF proteins - binding specificity and target candidates

(2009) Carlos W. Francischini et al.   FEBS Journal

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis

(2009) Ho-Ming Chen et al.   NUCLEIC ACIDS RESEARCH

Rice MicroRNA Effector Complexes and Targets

(2009) L. Wu et al.   PLANT CELL

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

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