title: Profiling of T helper cell-derived small RNAs reveals unique antisense transcripts and differential association of miRNAs with argonaute proteins 1 and 2.
abstract: RNA interference mediated through antisense transcripts is a fundamentally important mechanism regulating gene expression that remains incompletely understood. Here, we have used next-generation sequencing to determine from mouse CD4+ T cells the functional implications of antisense transcripts binding to argonaute (AGO) proteins that mediate RNA interference and post-transcriptional gene silencing. This effort identified 90 new microRNAs (miRNAs) and six endogenous hairpin RNA-derived small interfering RNAs (siRNAs) mapping to distinct introns. Unexpectedly, 69 miRNAs were expressed as non-canonical isomiRs as the dominant AGO-binding transcript, with extensive 3' terminal nucleotide modifications. Furthermore, differential expression analysis between AGO1- and AGO2-bound miRNAs suggested preferential binding of isomiRs ending with 3' adenine residues to AGO1 and 3' uridine residues to AGO2. Analysis of the putative targets of all miRNAs suggested a striking preference for regulating transcription and transcription factors with additional evidence of a functional division of labor between AGO proteins in this regard. We further provide evidence that multiple mitochondrial genomic loci serve as the source of endogenous cis-natural antisense transcripts. These findings imply diversity in AGO protein function based on differential miRNA binding and indicate that RNA interference-based gene regulation is more complex than previously recognized.
authors.affiliation: Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Sumanth
authors.initials: S
authors.lastname: Polikepahad
authors.forename: David B
authors.initials: DB
authors.lastname: Corry
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000378:metabolism*; D039642:Eukaryotic Initiation Factors / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D012313:RNA / Q000235:genetics; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism*; D000077278:RNA, Mitochondrial; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics; D006377:T-Lymphocytes, Helper-Inducer / Q000378:metabolism*
chemical_list: C549050:Ago1 protein, mouse; C526735:Ago2 protein, mouse; D060565:Argonaute Proteins; D039642:Eukaryotic Initiation Factors; D035683:MicroRNAs; D012322:RNA Precursors; D016372:RNA, Antisense; D000077278:RNA, Mitochondrial; D034741:RNA, Small Interfering; D012313:RNA