Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome.
The exosome complex plays a central and essential role in RNA metabolism. However, comprehensive studies of exosome substrates and functional analyses of its subunits are lacking. Here, we demonstrate that as opposed to yeast and metazoans the plant exosome core possesses an unanticipated functional plasticity and present a genome-wide atlas of Arabidopsis exosome targets. Additionally, our study provides evidence for widespread polyadenylation- and exosome-mediated RNA quality control in plants, reveals unexpected aspects of stable structural RNA metabolism, and uncovers numerous novel exosome substrates. These include a select subset of mRNAs, miRNA processing intermediates, and hundreds of noncoding RNAs, the vast majority of which have not been previously described and belong to a layer of the transcriptome that can only be visualized upon inhibition of exosome activity. These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes.
Chekanova
Julia A
JA
School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
Gregory
Brian D
BD
Reverdatto
Sergei V
SV
Chen
Huaming
H
Kumar
Ravi
R
Hooker
Tanya
T
Yazaki
Junshi
J
Li
Pinghua
P
Skiba
Nikolai
N
Peng
Qian
Q
Alonso
Jose
J
Brukhin
Vladimir
V
Grossniklaus
Ueli
U
Ecker
Joseph R
JR
Belostotsky
Dmitry A
DA
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D002874:Chromosome Mapping / Q000379:methods; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism*; D063326:Exosome Multienzyme Ribonuclease Complex; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D005838:Genotype; D035683:MicroRNAs / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D009687:Nuclear Proteins / Q000378:metabolism; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D010449:Peptide Mapping; D010641:Phenotype; D030821:Plants, Genetically Modified / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D034622:RNA Interference; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism; D053719:Tandem Mass Spectrometry
D029681:Arabidopsis Proteins; D035683:MicroRNAs; D009687:Nuclear Proteins; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D022661:RNA, Untranslated; D012313:RNA; D005095:Exoribonucleases; D063326:Exosome Multienzyme Ribonuclease Complex; C485933:RRP41 protein, Arabidopsis