title: Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification.
abstract: Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6) is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I) cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available.
authors.affiliation: Institute for Translational Oncology and Immunology, Mainz, Germany. castle@uni-mainz.de
authors.forename: John C
authors.initials: JC
authors.lastname: Castle
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Armour
authors.forename: Martin
authors.initials: M
authors.lastname: Löwer
authors.forename: David
authors.initials: D
authors.lastname: Haynor
authors.forename: Matthew
authors.initials: M
authors.lastname: Biery
authors.forename: Heather
authors.initials: H
authors.lastname: Bouzek
authors.forename: Ronghua
authors.initials: R
authors.lastname: Chen
authors.forename: Stuart
authors.initials: S
authors.lastname: Jackson
authors.forename: Jason M
authors.initials: JM
authors.lastname: Johnson
authors.forename: Carol A
authors.initials: CA
authors.lastname: Rohl
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Raymond
mesh_terms: D020869:Gene Expression Profiling; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D007031:Hypothalamus / Q000378:metabolism; D016133:Polymerase Chain Reaction; D020537:RNA, Small Nucleolar / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D013154:Spleen / Q000378:metabolism
chemical_list: D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated