title: Computer-assisted annotation of murine Sertoli cell small RNA transcriptome.
abstract: Mammalian genomes encode a large number of small noncoding RNAs (sncRNAs) that play regulatory roles during development and adulthood by affecting gene expression. Several sncRNA species, including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs), and small nucleolar RNAs (snoRNAs), are abundantly expressed in the testis and required for normal testicular development and spermatogenesis. To evaluate global changes in sncRNA expression, the next-generation sequencing (NGS)-based sncRNA transcriptomic analysis has become routine, because it allows rapid determination of the small RNA transcriptome of a particular testicular cell type. However, annotation of small RNA NGS reads can be challenging due to the volume of reads obtained, which is usually in the millions. Therefore, we developed a computer-assisted sncRNA annotation protocol that could identify not only known sncRNAs but also previously uncharacterized ones. Using this protocol, we annotated NGS reads of a Sertoli cell sncRNA library, and we report to our knowledge the first comprehensive annotation of the sncRNA transcriptome of immature murine Sertoli cells. Moreover, the computer-assisted sncRNA annotation pipeline that we report is applicable for annotating NGS reads derived from other cell types and/or sequencing platforms.
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV 89557, USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Ortogero
authors.forename: Grant W
authors.initials: GW
authors.lastname: Hennig
authors.forename: Chad
authors.initials: C
authors.lastname: Langille
authors.forename: Seungil
authors.initials: S
authors.lastname: Ro
authors.forename: John R
authors.initials: JR
authors.lastname: McCarrey
authors.forename: Wei
authors.initials: W
authors.lastname: Yan
mesh_terms: D000818:Animals; D005786:Gene Expression Regulation / Q000502:physiology*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods; D012708:Sertoli Cells / Q000378:metabolism*; D012984:Software; D059467:Transcriptome
chemical_list: D058727:RNA, Small Untranslated; D012313:RNA