Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.
Sites of transcription of polyadenylated and nonpolyadenylated RNAs for 10 human chromosomes were mapped at 5-base pair resolution in eight cell lines. Unannotated, nonpolyadenylated transcripts comprise the major proportion of the transcriptional output of the human genome. Of all transcribed sequences, 19.4, 43.7, and 36.9% were observed to be polyadenylated, nonpolyadenylated, and bimorphic, respectively. Half of all transcribed sequences are found only in the nucleus and for the most part are unannotated. Overall, the transcribed portions of the human genome are predominantly composed of interlaced networks of both poly A+ and poly A- annotated transcripts and unannotated transcripts of unknown function. This organization has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene.
Cheng
Jill
J
Affymetrix Inc., Santa Clara, CA 95051, USA.
Kapranov
Philipp
P
Drenkow
Jorg
J
Dike
Sujit
S
Brubaker
Shane
S
Patel
Sandeep
S
Long
Jeffrey
J
Stern
David
D
Tammana
Hari
H
Helt
Gregg
G
Sementchenko
Victor
V
Piccolboni
Antonio
A
Bekiranov
Stefan
S
Bailey
Dione K
DK
Ganesh
Madhavan
M
Ghosh
Srinka
S
Bell
Ian
I
Gerhard
Daniela S
DS
Gingeras
Thomas R
TR
D002460:Cell Line; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000378:metabolism; D002877:Chromosomes, Human / Q000235:genetics*; D002882:Chromosomes, Human, Pair 13 / Q000235:genetics; D002883:Chromosomes, Human, Pair 14 / Q000235:genetics; D002888:Chromosomes, Human, Pair 19 / Q000235:genetics; D002890:Chromosomes, Human, Pair 20 / Q000235:genetics; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D002896:Chromosomes, Human, Pair 6 / Q000235:genetics; D002897:Chromosomes, Human, Pair 7 / Q000235:genetics; D041321:Chromosomes, Human, X / Q000235:genetics; D041322:Chromosomes, Human, Y / Q000235:genetics; D019295:Computational Biology; D003600:Cytosol / Q000378:metabolism; D018076:DNA, Complementary; D021901:DNA, Intergenic; D005091:Exons; D005260:Female; D015894:Genome, Human; D006801:Humans; D007438:Introns; D008297:Male; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis; D020161:Physical Chromosome Mapping; D012326:RNA Splicing; D012333:RNA, Messenger / Q000032:analysis*; D014158:Transcription, Genetic
D018076:DNA, Complementary; D021901:DNA, Intergenic; D012333:RNA, Messenger