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Published Online March 24, 2005
Science DOI: 10.1126/science.1108625

Research Articles

Submitted on December 13, 2004
Accepted on March 15, 2005

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. Gingeras 1*

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

* To whom correspondence should be addressed.
Thomas R. Gingeras , E-mail: tom_gingeras{at}affymetrix.com

Sites of transcription of polyadenylated and nonpolyadenylated RNAs for 10 human chromosomes were mapped at 5-bp resolution in eight cell lines. Unannotated, nonpolyadenylated transcripts comprise the major proportion of the transcriptional output of the human genome. 19.4%, 43.7%, and 36.9% of all transcribed sequences 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 predominately composed of interlaced networks of both poly A+ and 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.


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