RNA maps reveal new RNA classes and a possible function for pervasive transcription.
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.
Kapranov
Philipp
P
Affymetrix Laboratory, Affymetrix, Inc., 3420 Central Expressway, Santa Clara, CA, 95051, USA.
Cheng
Jill
J
Dike
Sujit
S
Nix
David A
DA
Duttagupta
Radharani
R
Willingham
Aarron T
AT
Stadler
Peter F
PF
Hertel
Jana
J
Hackermüller
Jörg
J
Hofacker
Ivo L
IL
Bell
Ian
I
Cheung
Evelyn
E
Drenkow
Jorg
J
Dumais
Erica
E
Patel
Sandeep
S
Helt
Gregg
G
Ganesh
Madhavan
M
Ghosh
Srinka
S
Piccolboni
Antonio
A
Sementchenko
Victor
V
Tammana
Hari
H
Gingeras
Thomas R
TR
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
D012322:RNA Precursors; D012333:RNA, Messenger; D012313:RNA