title: Certain adenylated non-coding RNAs, including 5' leader sequences of primary microRNA transcripts, accumulate in mouse cells following depletion of the RNA helicase MTR4.
abstract: RNA surveillance plays an important role in posttranscriptional regulation. Seminal work in this field has largely focused on yeast as a model system, whereas exploration of RNA surveillance in mammals is only recently begun. The increased transcriptional complexity of mammalian systems provides a wider array of targets for RNA surveillance, and, while many questions remain unanswered, emerging data suggest the nuclear RNA surveillance machinery exhibits increased complexity as well. We have used a small interfering RNA in mouse N2A cells to target the homolog of a yeast protein that functions in RNA surveillance (Mtr4p). We used high-throughput sequencing of polyadenylated RNAs (PA-seq) to quantify the effects of the mMtr4 knockdown (KD) on RNA surveillance. We demonstrate that overall abundance of polyadenylated protein coding mRNAs is not affected, but several targets of RNA surveillance predicted from work in yeast accumulate as adenylated RNAs in the mMtr4KD. microRNAs are an added layer of transcriptional complexity not found in yeast. After Drosha cleavage separates the pre-miRNA from the microRNA's primary transcript, the byproducts of that transcript are generally thought to be degraded. We have identified the 5' leading segments of pri-miRNAs as novel targets of mMtr4 dependent RNA surveillance.
authors.affiliation: Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America.
authors.forename: Jane E
authors.initials: JE
authors.lastname: Dorweiler
authors.affiliation: DNA Sequencing and Genomics Core, Genetics and Development Biology Center, National Institutes of Health, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America.
authors.forename: Ting
authors.initials: T
authors.lastname: Ni
authors.affiliation: DNA Sequencing and Genomics Core, Genetics and Development Biology Center, National Institutes of Health, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America.
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Munroe
authors.affiliation: Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America.
authors.forename: James T
authors.initials: JT
authors.lastname: Anderson
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D002460:Cell Line; D055785:Gene Knockdown Techniques; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism*; D011061:Poly A / Q000378:metabolism; D020365:RNA Helicases; D020871:RNA Stability; D034741:RNA, Small Interfering / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism*; D043244:Ribonuclease III / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D020121:5' Untranslated Regions; D035683:MicroRNAs; D009687:Nuclear Proteins; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins; D011061:Poly A; C513400:Drosha protein, mouse; D043244:Ribonuclease III; D020365:RNA Helicases; C569190:SKIV2L2 protein, mouse