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Originally published in Science Express on 24 March 2005
Science 20 May 2005:
Vol. 308. no. 5725, pp. 1149 - 1154
DOI: 10.1126/science.1108625
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Research Articles

Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution

Jill Cheng,1* Philipp Kapranov,1* Jorg Drenkow,1 Sujit Dike,1 Shane Brubaker,1 Sandeep Patel,1 Jeffrey Long,1 David Stern,1 Hari Tammana,1 Gregg Helt,1 Victor Sementchenko,1 Antonio Piccolboni,1 Stefan Bekiranov,1 Dione K. Bailey,1 Madhavan Ganesh,1 Srinka Ghosh,1 Ian Bell,1 Daniela S. Gerhard,2 Thomas R. Gingeras1{dagger}

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.

1 Affymetrix Inc., Santa Clara, CA 95051, USA.
2 Office of Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: tom_gingeras{at}affymetrix.com

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