title: RNA maps reveal new RNA classes and a possible function for pervasive transcription.
abstract: Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a novel role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome.
authors.affiliation: Affymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USA.
authors.forename: Philipp
authors.initials: P
authors.lastname: Kapranov
authors.forename: Jill
authors.initials: J
authors.lastname: Cheng
authors.forename: Sujit
authors.initials: S
authors.lastname: Dike
authors.forename: David A
authors.initials: DA
authors.lastname: Nix
authors.forename: Radharani
authors.initials: R
authors.lastname: Duttagupta
authors.forename: Aarron T
authors.initials: AT
authors.lastname: Willingham
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Jana
authors.initials: J
authors.lastname: Hertel
authors.forename: Jörg
authors.initials: J
authors.lastname: Hackermüller
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: Ian
authors.initials: I
authors.lastname: Bell
authors.forename: Evelyn
authors.initials: E
authors.lastname: Cheung
authors.forename: Jorg
authors.initials: J
authors.lastname: Drenkow
authors.forename: Erica
authors.initials: E
authors.lastname: Dumais
authors.forename: Sandeep
authors.initials: S
authors.lastname: Patel
authors.forename: Gregg
authors.initials: G
authors.lastname: Helt
authors.forename: Madhavan
authors.initials: M
authors.lastname: Ganesh
authors.forename: Srinka
authors.initials: S
authors.lastname: Ghosh
authors.forename: Antonio
authors.initials: A
authors.lastname: Piccolboni
authors.forename: Victor
authors.initials: V
authors.lastname: Sementchenko
authors.forename: Hari
authors.initials: H
authors.lastname: Tammana
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000378:metabolism; D003600:Cytosol / Q000378:metabolism; D005091:Exons; D015870:Gene Expression; D016678:Genome; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D026801:Synteny; D013728:Terminator Regions, Genetic; D014158:Transcription, Genetic
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger; D012313:RNA